Tomorrow evening Casey Luskin will participate in a live debate on The NonSequitur Show with Rutgers University evolutionary biologist Dr. Daniel Stern Cardinale. The subject of the debate is whether our genome is largely non-functional “junk” DNA. In view of this discussion (which you can see streamed here), scheduled for 5:30 pm Pacific time, we thought it would be appropriate to post a list of papers that pertain to supposed junk DNA. Below is a far from exhaustive (but nonetheless exhausting) list of papers documenting function for various classes of non-coding DNA — including transposable elements, endogenous retroviruses, pseudogenes, and more — all of which were called “junk DNA” in the past. 

The list contains over 800 papers which are divided into the following categories according to the type of genetic element for which they focus on finding function: 1) SINEs, 2) LINEs, 3) introns, 4) repetitive DNA (generally), 5) satellite DNA, 6) transposons, 7) pseudogenes, 8) ERVs / retrotransposons, 9) lncRNAs, 10) microRNAs, 11) large-scale genomic transcription, 12) transposable element and 3D genome hierarchy, and 13) other / general function for junk DNA. We realize that within each category the papers are not in any particular order — we’ll leave that organizational task for another day. But given that we only took about a day and a half to put this list together, we think it’s an impressive showing. 

It must be re-emphasized that this list is nowhere close to comprehensive. Indeed, we could have multiplied the list many times over. Nonetheless, we hope that it gives the reader a sense of how vast the literature is that has accumulated in recent years that has served to significantly undermine the paradigm that much of our genome (and those of other organisms) is nonfunctional debris that has accumulated over evolutionary history.

1. Sines

• Ku J, Lee K, Ku D, Kim S, Lee J, Bang H, Kim N, Do H, Lee H, Lim C, Han J, Lee YS, Kim Y. Alternative polyadenylation determines the functional landscape of inverted Alu repeats. Mol Cell. 2024 Mar 21;84(6):1062-1077.e9.
• Hall LL, Creamer KM, Byron M, Lawrence JB. Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs. bioRxiv [Preprint]. 2024 Jan 9:2024.01.09.574742.
• Liang L, Cao C, Ji L, Cai Z, Wang D, Ye R, Chen J, Yu X, Zhou J, Bai Z, Wang R, Yang X, Zhu P, Xue Y. Complementary Alu sequences mediate enhancer-promoter selectivity. Nature. 2023 Jul;619(7971):868-875.
• Zaytsev K, Fedorov A, Korotkov E. Classification of Promoter Sequences from Human Genome. Int J Mol Sci. 2023 Aug 8;24(16):12561.
• Li Z, Xu H, Li J, Xu X, Wang J, Wu D, Zhang J, Liu J, Xue Z, Zhan G, Tan BCP, Chen D, Chan YS, Ng HH, Liu W, Hsu CH, Zhang D, Shen Y, Liang H. Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network. Nat Commun. 2023 Jun 20;14(1):3646.
• Wickramage I, VanWye J, Max K, Lockhart JH, Hortu I, Mong EF, Canfield J, Lamabadu Warnakulasuriya Patabendige HM, Guzeloglu-Kayisli O, Inoue K, Ogura A, Lockwood CJ, Akat KM, Tuschl T, Kayisli UA, Totary-Jain H. SINE RNA of the imprinted miRNA clusters mediates constitutive type III interferon expression and antiviral protection in hemochorial placentas. Cell Host Microbe. 2023 Jul 12;31(7):1185-1199.e10.
• Millrine D, Cardus Figueras A, Uceda Fernandez J, Andrews R, Szomolay B, Cossins BC, Rice CM, Li J, Tyrrell VJ, McLeod L, Holmans P, O’Donnell VB, Taylor PR, Turner SJ, Jenkins BJ, Jones GW, Topley N, Williams NM, Jones SA. Th1 Cells Alter the Inflammatory Signature of IL-6 by Channeling STAT Transcription Factors to Alu-like Retroelements. J Immunol. 2023 Jul 15;211(2):274-286.
• Li S, Shen X. Long interspersed nuclear element 1 and B1/Alu repeats blueprint genome compartmentalization. Curr Opin Genet Dev. 2023 Jun;80:102049.
• Osipovich AB, Dudek KD, Trinh LT, Kim LH, Shrestha S, Cartailler JP, Magnuson MA. ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes. PLoS Genet. 2023 May 8;19(5):e1010729.
• Nadler MJS, Chang W, Ozkaynak E, Huo Y, Nong Y, Boillot M, Johnson M, Moreno A, Matthew P Anderson. Hominoid SVA-lncRNA AK057321 targets human-specific SVA retrotransposons in SCN8A and CDK5RAP2 to initiate neuronal maturation. Commun Biol. 2023 Mar 30;6(1):347.
• Singhal K, Dhamija S, Mukerji M. Exonized Alu repeats in the 3’UTR of a CYP20A1_Alu-LT transcript act as a miRNA sponge. BMC Res Notes. 2023 Mar 9;16(1):32.
• Sun T, Rosenberg BR, Chung H, Rice CM. Identification of ADAR1 p150 and p110 Associated Edit Sites. Methods Mol Biol. 2023;2651:285-294.
• Ji N, Wu CG, Wang XD, Song ZX, Wu PY, Liu X, Feng X, Zhang XM, Wang XF, Lv ZJ. Anti-aging Effects of Alu Antisense RNA on Human Fibroblast Senescence Through the MEK-ERK Pathway Mediated by KIF15. Curr Med Sci. 2023 Feb;43(1):35-47.
• Gassler J, Kobayashi W, Gáspár I, Ruangroengkulrith S, Mohanan A, Gómez Hernández L, Kravchenko P, Kümmecke M, Lalic A, Rifel N, Ashburn RJ, Zaczek M, Vallot A, Cuenca Rico L, Ladstätter S, Tachibana K. Zygotic genome activation by the totipotency pioneer factor Nr5a2. Science. 2022 Dec 23;378(6626):1305-1315.
• Wang J, Weatheritt R, Voineagu I. Alu-minating the Mechanisms Underlying Primate Cortex Evolution. Biol Psychiatry. 2022 Nov 15;92(10):760-771.
• Wang L, Dong C, Lu C, Li S, Fu L, Cong B. A study of strong nucleosomes in the human genome. iScience. 2022 Jun 13;25(7):104593.
• Bezzecchi E, Pagani G, Forte B, Percio S, Zaffaroni N, Dolfini D, Gandellini P. MIR205HG/LEADR Long Noncoding RNA Binds to Primed Proximal Regulatory Regions in Prostate Basal Cells Through a Triplex- and Alu-Mediated Mechanism. Front Cell Dev Biol. 2022 Jun 17;10:909097.
• D’Souza MH, Mrozowich T, Badmalia MD, Geeraert M, Frederickson A, Henrickson A, Demeler B, Wolfinger MT, Patel TR. Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Res. 2022 Jun 10;50(10):5881-5898.
• Costallat M, Batsché E, Rachez C, Muchardt C. The ‘Alu-ome’ shapes the epigenetic environment of regulatory elements controlling cellular defense. Nucleic Acids Res. 2022 May 20;50(9):5095-5110.
• de Llobet Cucalon L, Di Vona C, Morselli M, Vezzoli M, Montanini B, Teichmann M, de la Luna S, Ferrari R. An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping. Int J Mol Sci. 2022 Feb 18;23(4):2260.
• Aune TM, Tossberg JT, Heinrich RM, Porter KP, Crooke PS 3rd. Alu RNA Structural Features Modulate Immune Cell Activation and A-to-I Editing of Alu RNAs Is Diminished in Human Inflammatory Bowel Disease. Front Immunol. 2022 Jan 20;13:818023.
• Navarro E, Mallén A, Hueso M. Dynamic Variations of 3’UTR Length Reprogram the mRNA Regulatory Landscape. Biomedicines. 2021 Oct 28;9(11):1560.
• Payer LM, Steranka JP, Kryatova MS, Grillo G, Lupien M, Rocha PP, Burns KH. Alu insertion variants alter gene transcript levels. Genome Res. 2021 Dec;31(12):2236-2248.
• Li M, Larsen PA. Primate-specific retrotransposons and the evolution of circadian networks in the human brain. Neurosci Biobehav Rev. 2021 Dec;131:988-1004
• Florea L, Payer L, Antonescu C, Yang G, Burns K. Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data. Front Mol Biosci. 2021 Sep 10;8:727537.
• Wang J, Ness S, Brown R, Yu H, Oyebamiji O, Jiang L, Sheng Q, Samuels DC, Zhao YY, Tang J, Guo Y. EditPredict: Prediction of RNA editable sites with convolutional neural network. Genomics. 2021 Nov;113(6):3864-3871.
• Bai X, Li F, Zhang Z. A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements. J Genet Genomics. 2021 Nov 20;48(11):1007-1019.
• Herbert A. To “Z” or not to “Z”: Z-RNA, self-recognition, and the MDA5 helicase. PLoS Genet. 2021 May 13;17(5):e1009513.
• Yan R, Gu C, You D, Huang Z, Qian J, Yang Q, Cheng X, Zhang L, Wang H, Wang P, Guo F. Decoding dynamic epigenetic landscapes in human oocytes using single-cell multi-omics sequencing. Cell Stem Cell. 2021 Sep 2;28(9):1641-1656.e7.
• Roberts BS, Partridge EC, Moyers BA, Agarwal V, Newberry KM, Martin BK, Shendure J, Myers RM, Cooper GM. Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands. Genome Res. 2021 May;31(5):866-876.
• Zhang XO, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annu Rev Genomics Hum Genet. 2021 Aug 31;22:199-218.
• Telonis AG, Rigoutsos I. The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content. BMC Biol. 2021 Mar 25;19(1):60.
• Saldi T, Riemondy K, Erickson B, Bentley DL. Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing. Mol Cell. 2021 Apr 15;81(8):1789-1801.e5.
• Cho HM, Choe SH, Kim YH, Park HR, Lee HE, Lee JR, Park SJ, Huh JW. Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation. Sci Rep. 2021 Feb 11;11(1):3665.
• Lu JY, Chang L, Li T, Wang T, Yin Y, Zhan G, Han X, Zhang K, Tao Y, Percharde M, Wang L, Peng Q, Yan P, Zhang H, Bi X, Shao W, Hong Y, Wu Z, Ma R, Wang P, Li W, Zhang J, Chang Z, Hou Y, Zhu B, Ramalho-Santos M, Li P, Xie W, Na J, Sun Y, Shen X. Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome. Cell Res. 2021 Jun;31(6):613-630.
• Stagsted LVW, O’Leary ET, Ebbesen KK, Hansen TB. The RNA-binding protein SFPQ preserves long-intron splicing and regulates circRNA biogenesis in mammals. Elife. 2021 Jan 21;10:e63088.
• Bhattacharya A, Jha V, Singhal K, Fatima M, Singh D, Chaturvedi G, Dholakia D, Kutum R, Pandey R, Bakken TE, Seth P, Pillai B, Mukerji M. Multiple Alu Exonization in 3’UTR of a Primate-Specific Isoform of CYP20A1 Creates a Potential miRNA Sponge. Genome Biol Evol. 2021 Jan 7;13(1):evaa233.
• Hall A, Moore AK, Hernandez DG, Billingsley KJ, Bubb VJ, Quinn JP, Nabec North American Brain Expression Consortium. A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus. Int J Mol Sci. 2020 Nov 11;21(22):8486.
• Pérez-Molina R, Arzate-Mejía RG, Ayala-Ortega E, Guerrero G, Meier K, Suaste-Olmos F, Recillas-Targa F. An Intronic Alu Element Attenuates the Transcription of a Long Non-coding RNA in Human Cell Lines. Front Genet. 2020 Aug 31;11:928.
• Shiromoto Y, Sakurai M, Qu H, Kossenkov AV, Nishikura K. Processing of Alu small RNAs by DICER/ADAR1 complexes and their RNAi targets. RNA. 2020 Dec;26(12):1801-1814.
• Zheng D, Cho H, Wang W, Rambout X, Tian B, Maquat LE. 3’READS + RIP defines differential Staufen1 binding to alternative 3’UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association. RNA. 2020 Nov;26(11):1621-1636.
• Herbert A. ALU non-B-DNA conformations, flipons, binary codes and evolution. R Soc Open Sci. 2020 Jun 3;7(6):200222.
• Schaffer AA, Levanon EY. ALU A-to-I RNA Editing: Millions of Sites and Many Open Questions. Methods Mol Biol. 2021;2181:149-162.
• Heraud-Farlow JE, Walkley CR. What do editors do? Understanding the physiological functions of A-to-I RNA editing by adenosine deaminase acting on RNAs. Open Biol. 2020 Jul;10(7):200085.
• Lo Giudice C, Silvestris DA, Roth SH, Eisenberg E, Pesole G, Gallo A, Picardi E. Quantifying RNA Editing in Deep Transcriptome Datasets. Front Genet. 2020 Mar 6;11:194. doi: 10.3389/fgene.2020.00194.
• González-Rico FJ, Vicente-García C, Fernández A, Muñoz-Santos D, Montoliu L, Morales-Hernández A, Merino JM, Román AC, Fernández-Salguero PM. Alu retrotransposons modulate Nanog expression through dynamic changes in regional chromatin conformation via aryl hydrocarbon receptor. Epigenetics Chromatin. 2020 Mar 14;13(1):15.
• Maquat LE. Short interspersed nuclear element (SINE)-mediated post-transcriptional effects on human and mouse gene expression: SINE-UP for active duty. Philos Trans R Soc Lond B Biol Sci. 2020 Mar 30;375(1795):20190344.
• Li L, Zhang S, Li LM. Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae. Mol Biol Evol. 2020 Jun 1;37(6):1679-1693.
• Zhang P, Zhang XO, Jiang T, Cai L, Huang X, Liu Q, Li D, Lu A, Liu Y, Xue W, Zhang P, Weng Z. Comprehensive identification of alternative back-splicing in human tissue transcriptomes. Nucleic Acids Res. 2020 Feb 28;48(4):1779-1789.
• Hernandez AJ, Zovoilis A, Cifuentes-Rojas C, Han L, Bujisic B, Lee JT. B2 and ALU retrotransposons are self-cleaving ribozymes whose activity is enhanced by EZH2. Proc Natl Acad Sci U S A. 2020 Jan 7;117(1):415-425.
• Pagliarini V, Jolly A, Bielli P, Di Rosa V, De la Grange P, Sette C. Sam68 binds Alu-rich introns in SMN and promotes pre-mRNA circularization. Nucleic Acids Res. 2020 Jan 24;48(2):633-645.
• Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A, Oliete JQ, Jochem L, Cutts E, Dieci G, Vannini A, Teichmann M, de la Luna S, Beato M. TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. Mol Cell. 2020 Feb 6;77(3):475-487.e11.
• Morera AA, Ahmed NS, Schwartz JC. TDP-43 regulates transcription at protein-coding genes and Alu retrotransposons. Biochim Biophys Acta Gene Regul Mech. 2019 Oct;1862(10):194434.
• Roth SH, Levanon EY, Eisenberg E. Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity. Nat Methods. 2019 Nov;16(11):1131-1138.
• Shrestha S, Sewell JA, Santoso CS, Forchielli E, Carrasco Pro S, Martinez M, Fuxman Bass JI. Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays. Genome Res. 2019 Sep;29(9):1533-1544.
• Zhang XO, Gingeras TR, Weng Z. Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Genome Res. 2019 Sep;29(9):1402-1414.
• Cantarella S, Carnevali D, Morselli M, Conti A, Pellegrini M, Montanini B, Dieci G. Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts. Int J Mol Sci. 2019 Jul 5;20(13):3315.
• Jang S, Shin H, Lee Y. Functional analysis of RNA motifs essential for BC200 RNA-mediated translational regulation. BMB Rep. 2020 Feb;53(2):94-99.
• Madissoon E, Damdimopoulos A, Katayama S, Krjutškov K, Einarsdottir E, Mamia K, De Groef B, Hovatta O, Kere J, Damdimopoulou P. Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development. Sci Rep. 2019 Jun 10;9(1):8411.
• Roychowdhury T, Abyzov A. Chromatin organization modulates the origin of heritable structural variations in human genome. Nucleic Acids Res. 2019 Apr 8;47(6):2766-2777.
• Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X. Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol. 2019 Jan 14;2:19.
• Hwang YE, Baek YM, Baek A, Kim DE. Oxidative stress causes Alu RNA accumulation via PIWIL4 sequestration into stress granules. BMB Rep. 2019 Mar;52(3):196-201.
• Nikopoulou C, Panagopoulos G, Sianidis G, Psarra E, Ford E, Thanos D. The Transcription Factor ThPOK Orchestrates Stochastic Interchromosomal Interactions Required for IFNB1 Virus-Inducible Gene Expression. Mol Cell. 2018 Jul 19;71(2):352-361.e5.
• Weltner J, Balboa D, Katayama S, Bespalov M, Krjutškov K, Jouhilahti EM, Trokovic R, Kere J, Otonkoski T. Human pluripotent reprogramming with CRISPR activators. Nat Commun. 2018 Jul 6;9(1):2643.
• Rozenberg JM, Taylor JM, Mack CP. RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF. Nucleic Acids Res. 2018 Sep 19;46(16):8232-8244.
• Mafra FFP, Gattai PP, Macedo MM, Mori MA, Araujo RC. The angiotensin-I-converting enzyme insertion/deletion in polymorphic element codes for an AluYa5 RNA that downregulates gene expression. Pharmacogenomics J. 2018 Jul;18(4):517-527.
• Shevchenko G, Morris KV. All I’s on the RADAR: role of ADAR in gene regulation. FEBS Lett. 2018 Sep;592(17):2860-2873.
• Zeng L, Pederson SM, Cao D, Qu Z, Hu Z, Adelson DL, Wei C. Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that Alu Elements Have the Largest Overall Regulatory Impact. J Comput Biol. 2018 Jun;25(6):551-562.
• Nakama M, Otsuka H, Ago Y, Sasai H, Abdelkreem E, Aoyama Y, Fukao T. Intronic antisense Alu elements have a negative splicing effect on the inclusion of adjacent downstream exons. Gene. 2018 Jul 20;664:84-89.
• Howard JM, Lin H, Wallace AJ, Kim G, Draper JM, Haeussler M, Katzman S, Toloue M, Liu Y, Sanford JR. HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo. Genome Res. 2018 May;28(5):689-698.
• Brunet FG, Audit B, Drillon G, Argoul F, Volff JN, Arneodo A. Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates. Biophys J. 2018 May 22;114(10):2308-2316.
• Chen K, Wang Y, Sun J. A statistical analysis on transcriptome sequences: The enrichment of Alu-element is associated with subcellular location. Biochem Biophys Res Commun. 2018 May 15;499(3):397-402.
• Lavi E, Carmel L. Alu exaptation enriches the human transcriptome by introducing new gene ends. RNA Biol. 2018;15(6):715-725.
• Lubelsky Y, Ulitsky I. Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells. Nature. 2018 Mar 1;555(7694):107-111.
• Chung H, Calis JJA, Wu X, Sun T, Yu Y, Sarbanes SL, Dao Thi VL, Shilvock AR, Hoffmann HH, Rosenberg BR, Rice CM. Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown. Cell. 2018 Feb 8;172(4):811-824.e14.
• Tristán-Flores FE, Guzmán P, Ortega-Kermedy MS, Cruz-Torres G, de la Rocha C, Silva-Martínez GA, Rodríguez-Ríos D, Alvarado-Caudillo Y, Barbosa-Sabanero G, Sayols S, Lund G, Zaina S. Liver X Receptor-Binding DNA Motif Associated With Atherosclerosis-Specific DNA Methylation Profiles of AluElements and Neighboring CpG Islands. J Am Heart Assoc. 2018 Jan 31;7(3):e007686.
• Chuang TJ, Chen YJ, Chen CY, Mai TL, Wang YD, Yeh CS, Yang MY, Hsiao YT, Chang TH, Kuo TC, Cho HH, Shen CN, Kuo HC, Lu MY, Chen YH, Hsieh SC, Chiang TW. Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells. Nucleic Acids Res. 2018 Apr 20;46(7):3671-3691.
• Burenina OY, Oretskaya TS, Kubareva EA. Non-Coding RNAs As Transcriptional Regulators In Eukaryotes. Acta Naturae. 2017 Oct-Dec;9(4):13-25.
• Lucas BA, Lavi E, Shiue L, Cho H, Katzman S, Miyoshi K, Siomi MC, Carmel L, Ares M Jr, Maquat LE. Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay. Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):968-973. [Includes rat Identifier (ID) elements]
• Xiang JF, Yang Q, Liu CX, Wu M, Chen LL, Yang L. N⁶-Methyladenosines Modulate A-to-I RNA Editing. Mol Cell. 2018 Jan 4;69(1):126-135.e6.
• Vrljicak P, Lucas ES, Lansdowne L, Lucciola R, Muter J, Dyer NP, Brosens JJ, Ott S. Analysis of chromatin accessibility in decidualizing human endometrial stromal cells. FASEB J. 2018 May;32(5):2467-2477.
• Ottesen EW, Seo J, Singh NN, Singh RN. A Multilayered Control of the Human Survival Motor NeuronGene Expression by Alu Elements. Front Microbiol. 2017 Nov 15;8:2252.
• Chen H, Chen L, Wu Y, Shen H, Yang G, Deng C. The Exonization and Functionalization of an Alu-J Element in the Protein Coding Region of Glycoprotein Hormone Alpha Gene Represent a Novel Mechanism to the Evolution of Hemochorial Placentation in Primates. Mol Biol Evol. 2017 Dec 1;34(12):3216-3231.
• Elbarbary RA, Maquat LE. Distinct mechanisms obviate the potentially toxic effects of inverted-repeat Alu elements on cellular RNA metabolism. Nat Struct Mol Biol. 2017 Jun 6;24(6):496-498.
• Qin Z, Zhang X. The identification of switch-like alternative splicing exons among multiple samples with RNA-Seq data. PLoS One. 2017 May 25;12(5):e0178320.
• Yang CC, Chen YT, Chang YF, Liu H, Kuo YP, Shih CT, Liao WC, Chen HW, Tsai WS, Tan BC. ADAR1-mediated 3′ UTR editing and expression control of antiapoptosis genes fine-tunes cellular apoptosis response. Cell Death Dis. 2017 May 25;8(5):e2833.
• Krufczik M, Sievers A, Hausmann A, Lee JH, Hildenbrand G, Schaufler W, Hausmann M. Combining Low Temperature Fluorescence DNA-Hybridization, Immunostaining, and Super-Resolution Localization Microscopy for Nano-Structure Analysis of ALU Elements and Their Influence on Chromatin Structure. Int J Mol Sci. 2017 May 7;18(5):1005.
• Sakurai M, Shiromoto Y, Ota H, Song C, Kossenkov AV, Wickramasinghe J, Showe LC, Skordalakes E, Tang HY, Speicher DW, Nishikura K. ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay. Nat Struct Mol Biol. 2017 Jun;24(6):534-543.
• Collings CK, Anderson JN. Links between DNA methylation and nucleosome occupancy in the human genome. Epigenetics Chromatin. 2017 Apr 11;10:18.
• Ma Z, Kong X, Liu S, Yin S, Zhao Y, Liu C, Lv Z, Wang X. Combined sense-antisense Alu elements activate the EGFP reporter gene when stable transfection. Mol Genet Genomics. 2017 Aug;292(4):833-846.
• Goldberg L, Abutbul-Amitai M, Paret G, Nevo-Caspi Y. Alternative Splicing of STAT3 Is Affected by RNA Editing. DNA Cell Biol. 2017 May;36(5):367-376.
• Babenko VN, Chadaeva IV, Orlov YL. Genomic landscape of CpG rich elements in human. BMC Evol Biol. 2017 Feb 7;17(Suppl 1):19.
• Ge SX. Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development. BMC Genomics. 2017 Feb 23;18(1):200.
• Chen LL, Yang L. ALUternative Regulation for Gene Expression. Trends Cell Biol. 2017 Jul;27(7):480-490.
• Torres M, Becquet D, Blanchard MP, Guillen S, Boyer B, Moreno M, Franc JL, François-Bellan AM. Paraspeckles as rhythmic nuclear mRNA anchorages responsible for circadian gene expression. Nucleus. 2017 May 4;8(3):249-254.
• Ketele A, Kiss T, Jády BE. Human intron-encoded AluACA RNAs and telomerase RNA share a common element promoting RNA accumulation. RNA Biol. 2016 Dec;13(12):1274-1285.
• Chillón I, Pyle AM. Inverted repeat Alu elements in the human lincRNA-p21 adopt a conserved secondary structure that regulates RNA function. Nucleic Acids Res. 2016 Nov 2;44(19):9462-9471.
• Yu S, Lemos B. A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome. Genome Biol Evol. 2016 Dec 31;8(11):3545-3558.
• Hu S, Wang X, Shan G. Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing. Nat Struct Mol Biol. 2016 Nov;23(11):1011-1019.
• Tajaddod M, Tanzer A, Licht K, Wolfinger MT, Badelt S, Huber F, Pusch O, Schopoff S, Janisiw M, Hofacker I, Jantsch MF. Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity. Genome Biol. 2016 Oct 25;17(1):220.
• Schein A, Zucchelli S, Kauppinen S, Gustincich S, Carninci P. Identification of antisense long noncoding RNAs that function as SINEUPs in human cells. Sci Rep. 2016 Sep 20;6:33605.
• Bouttier M, Laperriere D, Memari B, Mangiapane J, Fiore A, Mitchell E, Verway M, Behr MA, Sladek R, Barreiro LB, Mader S, White JH. Alu repeats as transcriptional regulatory platforms in macrophage responses to M. tuberculosis infection. Nucleic Acids Res. 2016 Dec 15;44(22):10571-10587.
• Rajendiran S, Gibbs LD, Van Treuren T, Klinkebiel DL, Vishwanatha JK. MIEN1 is tightly regulated by SINE Alu methylation in its promoter. Oncotarget. 2016 Oct 4;7(40):65307-65319.
• Pandey R, Bhattacharya A, Bhardwaj V, Jha V, Mandal AK, Mukerji M. Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection. Sci Rep. 2016 Sep 2;6:32348.
• Guo W, Zhang MQ, Wu H. Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Sci Rep. 2016 Aug 30;6:32207.
• Wang X, Ma Z, Kong X, Lv Z. Effects of RNAs on chromatin accessibility and gene expression suggest RNA-mediated activation. Int J Biochem Cell Biol. 2016 Oct;79:24-32.
• Torres M, Becquet D, Blanchard MP, Guillen S, Boyer B, Moreno M, Franc JL, François-Bellan AM. Circadian RNA expression elicited by 3′-UTR IRAlu-paraspeckle associated elements. Elife. 2016 Jul 21;5:e14837.
• Caudron-Herger M, Pankert T, Rippe K. Regulation of nucleolus assembly by non-coding RNA polymerase II transcripts. Nucleus. 2016 May 3;7(3):308-18.
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2. Lines

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• Upton KR, Gerhardt DJ, Jesuadian JS, Richardson SR, Sánchez-Luque FJ, Bodea GO, Ewing AD, Salvador-Palomeque C, van der Knaap MS, Brennan PM, Vanderver A, Faulkner GJ. Ubiquitous L1 mosaicism in hippocampal neurons. Cell. 2015 Apr 9;161(2):228-39.
• Richardson SR, Morell S, Faulkner GJ. L1 retrotransposons and somatic mosaicism in the brain. Annu Rev Genet. 2014;48:1-27.
• Hall LL, Carone DM, Gomez AV, Kolpa HJ, Byron M, Mehta N, Fackelmayer FO, Lawrence JB. Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes. Cell. 2014 Feb 27;156(5):907-19.
• Wanichnopparat W, Suwanwongse K, Pin-On P, Aporntewan C, Mutirangura A. Genes associated with the cis-regulatory functions of intragenic LINE-1 elements. BMC Genomics. 2013 Mar 27;14:205.
• Fadloun A, Le Gras S, Jost B, Ziegler-Birling C, Takahashi H, Gorab E, Carninci P, Torres-Padilla ME. Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nat Struct Mol Biol. 2013 Mar;20(3):332-8.
• Calabrese JM, Sun W, Song L, Mugford JW, Williams L, Yee D, Starmer J, Mieczkowski P, Crawford GE, Magnuson T. Site-specific silencing of regulatory elements as a mechanism of X inactivation. Cell. 2012 Nov 21;151(5):951-63.
• Onoguchi M, Zeng C, Matsumaru A, Hamada M. Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements. NAR Genom Bioinform. 2021 Jul 2;3(3):lqab055.
• Percharde M, Lin CJ, Yin Y, Guan J, Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X, Ramalho-Santos M. A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity. Cell. 2018 Jul 12;174(2):391-405.e19.
• Honson DD, Macfarlan TS. A lncRNA-like Role for LINE1s in Development. Dev Cell. 2018 Jul 16;46(2):132-134.
• Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, Lehmann HS, Parker JJ, Atabay KD, Gilmore EC, Poduri A, Park PJ, Walsh CA. Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell. 2012 Oct 26;151(3):483-96.
• Singh DK, Rath PC. Long interspersed nuclear elements (LINEs) show tissue-specific, mosaic genome and methylation-unrestricted, widespread expression of noncoding RNAs in somatic tissues of the rat. RNA Biol. 2012 Nov;9(11):1380-96.
• Thomas CA, Paquola AC, Muotri AR. LINE-1 retrotransposition in the nervous system. Annu Rev Cell Dev Biol. 2012;28:555-73.
• Ikeno M, Suzuki N, Kamiya M, Takahashi Y, Kudoh J, Okazaki T. LINE1 family member is negative regulator of HLA-G expression. Nucleic Acids Res. 2012 Nov;40(21):10742-52.
• Thomas CA, Muotri AR. LINE-1: creators of neuronal diversity. Front Biosci (Elite Ed). 2012 Jan 1;4(5):1663-8.
• Kines KJ, Belancio VP. Expressing genes do not forget their LINEs: transposable elements and gene expression. Front Biosci (Landmark Ed). 2012 Jan 1;17(4):1329-44.
• Muotri AR, Marchetto MC, Coufal NG, Oefner R, Yeo G, Nakashima K, Gage FH. L1 retrotransposition in neurons is modulated by MeCP2. Nature. 2010 Nov 18;468(7322):443-6.
• Chow JC, Ciaudo C, Fazzari MJ, Mise N, Servant N, Glass JL, Attreed M, Avner P, Wutz A, Barillot E, Greally JM, Voinnet O, Heard E. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell. 2010 Jun 11;141(6):956-69.
• Singer T, McConnell MJ, Marchetto MC, Coufal NG, Gage FH. LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes? Trends Neurosci. 2010 Aug;33(8):345-54. 
• Harris CR, Dewan A, Zupnick A, Normart R, Gabriel A, Prives C, Levine AJ, Hoh J. p53 responsive elements in human retrotransposons. Oncogene. 2009 Nov 5;28(44):3857-65.
• Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Morell M, O’Shea KS, Moran JV, Gage FH. L1 retrotransposition in human neural progenitor cells. Nature. 2009 Aug 27;460(7259):1127-31.
• Kano H, Godoy I, Courtney C, Vetter MR, Gerton GL, Ostertag EM, Kazazian HH Jr. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev. 2009 Jun 1;23(11):1303-12.
• Chueh AC, Northrop EL, Brettingham-Moore KH, Choo KH, Wong LH. LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin. PLoS Genet. 2009 Jan;5(1):e1000354.
• Kambere MB, Lane RP. Exceptional LINE density at V1R loci: the Lyon repeat hypothesis revisited on autosomes. J Mol Evol. 2009 Feb;68(2):145-59.
• Zemojtel T, Penzkofer T, Schultz J, Dandekar T, Badge R, Vingron M. Exonization of active mouse L1s: a driver of transcriptome evolution? BMC Genomics. 2007 Oct 26;8:392.
• Vogel MJ, Guelen L, de Wit E, Peric-Hupkes D, Lodén M, Talhout W, Feenstra M, Abbas B, Classen AK, van Steensel B. Human heterochromatin proteins form large domains containing KRAB-ZNF genes. Genome Res. 2006 Dec;16(12):1493-504.
• Beraldi R, Pittoggi C, Sciamanna I, Mattei E, Spadafora C. Expression of LINE-1 retroposons is essential for murine preimplantation development. Mol Reprod Dev. 2006 Mar;73(3):279-87.
• Muotri AR, Chu VT, Marchetto MC, Deng W, Moran JV, Gage FH. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature. 2005 Jun 16;435(7044):903-10.
• Smalheiser NR, Torvik VI. Mammalian microRNAs derived from genomic repeats. Trends Genet. 2005 Jun;21(6):322-6.
• Purbowasito W, Suda C, Yokomine T, Zubair M, Sado T, Tsutsui K, Sasaki H. Large-scale identification and mapping of nuclear matrix-attachment regions in the distal imprinted domain of mouse chromosome 7. DNA Res. 2004 Dec 31;11(6):391-407. 
• Hiratani I, Leskovar A, Gilbert DM. Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16861-6.
• Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schübeler D, Gilbert DM. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 Oct 7;6(10):e245.
• Heskett MB, Smith LG, Spellman P, Thayer MJ. Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6. RNA. 2020 Jun;26(6):724-738.
• Allen E, Horvath S, Tong F, Kraft P, Spiteri E, Riggs AD, Marahrens Y. High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes. Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9940-5.
• Han JS, Szak ST, Boeke JD. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature. 2004 May 20;429(6989):268-74.
• T. A. Morrish et al., “DNA repair mediated by endonuclease-independent LINE-1 retrotransposition,” Nature Genetics, Vol. 31(2):159-165 (June, 2002).
• Ansaloni F, Gustincich S, Sanges R. In silico characterisation of minor wave genes and LINE-1s transcriptional dynamics at murine zygotic genome activation. Front Cell Dev Biol. 2023 Jun 14;11:1124266.
• Pal D, Patel M, Boulet F, Sundarraj J, Grant OA, Branco MR, Basu S, Santos SDM, Zabet NR, Scaffidi P, Pradeepa MM. H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function. Nat Struct Mol Biol. 2023 Jul;30(7):935-947.
• Jeffrey A. Bailey, Laura Carrel, Aravinda Chakravarti & Evan E. Eichler, “Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis,” Proceedings of the National Academy of Sciences USA 97 (2000): 6634–6639.
• Y. Amy Tang, Derek Huntley, Giovanni Montana, Andrea Cerase, Tatyana B. Nesterova & Neil Brockdorff, “Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organization,” Epigenetics & Chromatin 3 (2010): 10.
• Jennifer C. Chow, Constance Ciaudo, Melissa J. Fazzari. Nathan Mise, Nicolas Servant, Jacob L. Glass, Matthew Attreed, Philip Avner, Anton Wutz, Emmanuel Barillot, John M. Greally, Olivier Voinnet & Edith Heard, “LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation,” Cell 141 (2010): 956–969.
• Tammy A. Morrish, Nicolas Gilbert, Jeremy S. Myers, Bethaney J. Vincent, Thomas D. Stamato, Guillermo E. Taccioli, Mark A. Batzer & John V. Moran, “DNA repair mediated by endonucleaseindependent LINE-1 retrotransposition,” Nature Genetics 31 (2002): 159–165.
• José L. Garcia-Perez, Aurélien J. Doucet, Alain Bucheton, John V. Moran & Nicolas Gilbert, “Distinct mechanisms for transmediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase,” Genome Research 17 (2007): 602–611.
• Elizabeth A. Shepard, Pritpal Chandan, Milena Stevanovic-Walker, Mina Edwards & Ian R. Phillips, “Alternative promoters and repetitive DNA elements define the species-dependent tissuespecific expression of the FMO1 genes of human and mouse,” Biochemical Journal 406 (2007): 491–499.
• Corrado Spadafora, “A reverse transcriptase-dependent mechanism plays central roles in fundamental biological processes,” Systems Biology in Reproductive Medicine 54 (2008): 11–21.
• Anderly C. Chueh, Emma L. Northrop, Kate H. Brettingham-Moore, K. H. Andy Choo & Lee H. Wong, “LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin,” PLoS Genetics 5:1 (2009): e1000354.
• Anthony W. I. Lo, Jeffrey M. Craig, Richard Saffery, Paul Kalitsis, Danielle V. Irvine, Elizabeth Earle, Dianna J. Magliano & K. H. Andy Choo, “A 330 kb CENP-A binding domain and altered replication timing at a human neocentromere,” EMBO Journal 20 (2001): 2087–2096.
• Anderly C. Chueh, Lee H. Wong, Nicholas Wong & K.H. Andy Choo, “Variable and hierarchical size distribution of L1- retroelement-enriched CENP-A clusters within a functional human neocentromere,” Human Molecular Genetics 14 (2005): 85– 93.
• Anderly C. Chueh, Emma L. Northrop, Kate H. Brettingham-Moore, K. H. Andy Choo & Lee H. Wong, “LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin,” PLoS Genetics 5:1 (2009): e1000354.
• Speek M. (2001) Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Molecular and Cellular Biology 21: 1973–85.
• Marasca F. et al. (2022) LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion. Nature Genetics 50: 180–93.
• Petri R, Brattås PL, Sharma Y, Jönsson ME, Pircs K, Bengzon J, Jakobsson J. LINE-2 transposable elements are a source of functional human microRNAs and target sites. PLoS Genet. 2019 Mar 13;15(3):e1008036.
• Nelson JO, Slicko A, Raz AA, Yamashita YM. Insulin signaling regulates R2 retrotransposon expression to orchestrate transgenerational rDNA copy number maintenance. bioRxiv [Preprint]. 2024 Feb 29:2024.02.28.582629.
• Nelson JO, Slicko A, Yamashita YM. The retrotransposon R2 maintains Drosophila ribosomal DNA repeats. Proc Natl Acad Sci U S A. 2023 Jun 6;120(23):e2221613120.
• Azpiazu N, Morata G. Chromatin remodelling and retrotransposons activities during regeneration in Drosophila. Dev Biol. 2022 Feb;482:7-16.
• Ellison CE, Kagda MS, Cao W. Telomeric TART elements target the piRNA machinery in Drosophila. PLoS Biol. 2020 Dec 21;18(12):e3000689.
• Pathak RU, Srinivasan A, Mishra RK. Genome-wide mapping of matrix attachment regions in Drosophila melanogaster. BMC Genomics. 2014 Nov 25;15(1):1022.
• Santinello B, Sun R, Amjad A, Hoyt SJ, Ouyang L, Courret C, Drennan R, Leo L, Larracuente AM, Core LM, O’Neill RJ, Mellone BG. A centromere-derived retroelement RNA localizes in cis and is a core element of the transcriptional landscape of Drosophila centromeres. bioRxiv [Preprint]. 2024 Jan 16:2024.01.14.574223.

3. Introns

• Rotem Sorek & Gil Ast, “Intronic Sequences Flanking Alternatively Spliced Exons Are Conserved between Human and Mouse,” Genome Research 13 (2003): 1631–1637. 
• Simon Minovitsky, Sherry L. Gee, Shiruyeh Schokrpur, Inna Dubchak & John G. Conboy, “The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons,” Nucleic Acids Research 33 (2005): 714–724.
• Charles W. Sugnet, Karpagam Srinivasan, Tyson A. Clark, Georgeann O’Brien, Melissa S. Cline, Hui Wang, Alan Williams, David Kulp, John E. Blume, David Haussler & Manuel Ares Jr., “Unusual Intron Conservation near Tissue-regulated Exons Found by Splicing Microarrays,” PLoS Computational Biology 2:1 (2006): e4.
• Andrea N. Ladd and Thomas A. Cooper, “Finding signals that regulate alternative splicing in the post-genomic era,” Genome Biology 3:11 (2002): reviews0008.
• Jingyi Hui, Lee-Hsueh Hung, Monika Heiner, Silke Schreiner, Norma Neumüller, Gregor Reither, Stefan A Haas & Albrecht Bindereif, “Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing,” EMBO Journal 24 (2005): 1988–1998.
• Helder I. Nakaya, Paulo P. Amaral, Rodrigo Louro, André Lopes, Angela A. Fachel, Yuri B. Moreira, Tarik A. El-Jundi, Aline M. da Silva, Eduardo M. Reis & Sergio Verjovski-Almeida, “Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription,” Genome Biology 8:3 (2007): R43.
• Michelle L. Hastings, Catherine M. Wilson & Stephen H. Munroe, “A purine-rich intronic element enhances alternative splicing of thyroid hormone receptor mRNA,” RNA 7 (2001): 859–874.
• Shingo Nakahata & Sachiyo Kawamoto, “Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissuespecific splicing activities,” Nucleic Acids Research 33 (2005): 2078–2089.
• Eric J. Wagner, Andrew P. Baraniak, October M. Sessions, David Mauger, Eric Moskowitz & Mariano A. GarciaBlanco, “Characterization of the Intronic Splicing Silencers Flanking FGFR2 Exon IIIb,” Journal of Biological Chemistry 280 (2005): 14017–14027.
• Roberto Marcucci, Francisco E. Baralle & Maurizio Romano, “Complex splicing control of the human Thrombopoietin gene by intronic G runs,” Nucleic Acids Research 35 (2007): 132–142.
• Zefeng Wang & Christopher B. Burge, “Splicing regulation: from a parts list of regulatory elements to an integrated splicing code,” RNA 14 (2008): 802–813.
• John W. S. Brown, David F. Marshall & Manuel Echeverria, “Intronic noncoding RNAs and splicing,” Trends in Plant Science 13 (2008): 335–342.
• Ji Wen, Akira Chiba & Xiaodong Cai, “Computational identification of tissue-specific alternative splicing elements in mouse genes from RNA-Seq,” Nucleic Acids Research (August 4, 2010).
• Shengdong Ke & Lawrence A. Chasin, “Intronic motif pairs cooperate across exons to promote pre-mRNA splicing,” Genome Biology 11 (2010): R84.
• Yoseph Barash, John A. Calarco, Weijun Gao, Qun Pan, Xinchen Wang, Ofer Shai, Benjamin J. Blencowe & Brendan J. Frey “Deciphering the splicing code,” Nature 465 (2010): 53–59.
• Amir Ali Abbasi, Zissis Paparidis, Sajid Malik, Debbie K. Goode, Heather Callaway, Greg Elgar & Karl-Heinz Grzeschik, “Human GLI3 Intragenic Conserved Non-Coding Sequences Are Tissue-Specific Enhancers,” PLoS One 2:4 (2007): e366.
• Rodrigo Louro, Tarik El-Jundi, Helder I. Nakaya, Eduardo M. Reis & Sergio Verjovski-Almeida, “Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci,” Genomics 92 (2008): 18–25.
• Marc P. Hoeppner, Simon White, Daniel C. Jeffares & Anthony M. Poole, “Evolutionarily Stable Association of Intronic snoRNAs and microRNAs with Their Host Genes,” Genome Biology and Evolution 2009 (2009): 420–428.
• Antony Rodriguez, Sam Griffiths-Jones, Jennifer L. Ashurst & Allan Bradley, “Identification of Mammalian MicroRNA Host Genes and Transcription Units,” Genome Research 14 (2004): 1902–1910.
• Scott Baskerville & David P. Bartel, “Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes,” RNA 11 (2005): 241–247.
• Young-Kook Kim & V. Narry Kim, “Processing of intronic microRNAs,” EMBO Journal 26 (2007): 775–783.
• S. Hani Najafi-Shoushtari, Fjoralba Kristo, Yingxia Li, Toshi Shioda, David E. Cohen, Robert E. Gerszten & Anders M. Näär, “MicroRNA-33 and the SREBP Host Genes Cooperate to Control Cholesterol Homeostasis,” Science 328 (2010): 1566–1569.
• Alex Mas Monteys, Ryan M. Spengler, Ji Wan, Luis Tecedor, Kimberly A. Lennox, Yi Xing & Beverly L. Davidson, “Structure and activity of putative intronic miRNA promoters,” RNA 16 (2010): 495–505.
• Shawn P. Grogan, Tsaiwei Olee, Koji Hiraoka & Martin K. Lotz, “Repression of Chondrogenesis through Binding of Notch Signaling Proteins HES-1 and HEY-1 to N-box Domains in the COL2A1 Enhancer Site,” Arthritis & Rheumatism 58 (2008): 2754–2763.
• Christopher J. Ott, Neil P. Blackledge, Jenny L. Kerschner, Shih-Hsing Leir, Gregory E. Crawford, Calvin U. Cotton &Ann Harris, “Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus,” Proceedings of the National Academy of Sciences USA 106 (2009): 19934–19939.
• Hani Alotaibi, Elif Yaman, Domenico Salvatore, Valeria Di Dato, Pelin Telkoparan, Roberto Di Lauro & Uygar H. Tazebay, “Intronic elements in the Na+/Isymporter gene (NIS) interact with retinoic acid receptors and mediate initiation of transcription,” Nucleic Acids Research 38 (2010): 3172–3185.
• Tanmoy Mondal, Markus Rasmussen, Gaurav Kumar Pandey, Anders Isaksson & Chandrasekhar Kanduri, “Characterization of the RNA content of chromatin,” Genome Research 20 (2010): 899–907.
• W. F. Chen, K. H. Low, C. Lim & I. Edery, “Thermosensitive splicing of a clock gene and seasonal adaptation,” Cold Spring Harbor Symposia on Quantitative Biology 72 (2007): 599–606.
• Dan Xia, Xinxin Huang& Hong Zhang, “The temporally regulated transcription factor sel-7 controls developmental timing in C. elegans,” Developmental Biology 332 (2009): 246–257.
• David Gubb, “Intron-Delay and the Precision of Expression of Homeotic Gene Products in Drosophila,” Developmental Genetics 7 (1986): 119–131.
• Carl S. Thummel, “Mechanisms of Transcriptional Timing in Drosophila,” Science 255 (1992): 39–40.
• Ian A. Swinburne & Pamela A. Silver, “Intron Delays and Transcriptional Timing During Development,” Developmental Cell 14 (2008): 324–330.
• Matlik K., Redik K. and Speek M. (2006) L1 antisense promoter drives tissue-specific transcription of human genes. Journal of Biomedicine and Biotechnology 2006: 71753.
• Nigumann P., Redik K., Matlik K. and Speek M. (2002) Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics 79: 628–34.

4. Repetitive DNA Generally 

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• Biscotti MA, Olmo E, Heslop-Harrison JS. Repetitive DNA in eukaryotic genomes. Chromosome Res. 2015 Sep;23(3):415-20. doi: 10.1007/s10577-015-9499-z. PMID: 26514350.
• Biscotti MA, Canapa A, Forconi M, Olmo E, Barucca M. Transcription of tandemly repetitive DNA: functional roles. Chromosome Res. 2015 Sep;23(3):463-77. doi: 10.1007/s10577-015-9494-4. PMID: 26403245.
• Natale F, Scholl A, Rapp A, Yu W, Rausch C, Cardoso MC. DNA replication and repair kinetics of Alu, LINE-1 and satellite III genomic repetitive elements. Epigenetics Chromatin. 2018 Oct 23;11(1):61.
• Cho HM, Park SJ, Choe SH, Lee JR, Kim SU, Jin YB, Kim JS, Lee SR, Kim YH, Huh JW. Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene. BMC Evol Biol. 2019 Oct 30;19(1):196.
• Pehrsson EC, Choudhary MNK, Sundaram V, Wang T. The epigenomic landscape of transposable elements across normal human development and anatomy. Nat Commun. 2019 Dec 10;10(1):5640.
• Lu JY, Shao W, Chang L, Yin Y, Li T, Zhang H, Hong Y, Percharde M, Guo L, Wu Z, Liu L, Liu W, Yan P, Ramalho-Santos M, Sun Y, Shen X. Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation. Cell Rep. 2020 Mar 10;30(10):3296-3311.e5.
• R. Sternberg, “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic–Epigenetic System,” Annals of the NY Academy of Science, Vol. 981:154–188 (2002).
• J. A. Shapiro, and R. Sternberg, “Why repetitive DNA is essential to genome function,” Biol. Rev., Vol. 80:227–250 (2005).
• S. A. Lavrov & M. V. Kibanov, “Noncoding RNAs and Chromatin Structure,” Biochemistry (Moscow) 72 (2007): 1422–1438.
• Antonio Rodríguez-Campos & Fernando Azorín, “RNA Is an Integral Component of Chromatin that Contributes to Its Structural Organization,” PLoS One 2:11 (2007): e1182.
• Barbora Malecová & Kevin V Morris, “Transcriptional gene silencing through epigenetic changes mediated by non-coding RNAs,” Current Opinion in Molecular Therapeutics 12 (2010): 214–222.
• Sam Janssen, Olivier Cuvier, Martin Müller & Ulrich K Laemmli, “Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster,” Molecular Cell 6 (2000): 1013–1024.
• Steven Henikoff & Danielle Vermaak, “Bugs on drugs go GAGAA,” Cell 103 (2000): 695–698.
• Mary-Lou Pardue & P. Gregory DeBaryshe, “Drosophila telomeres: two transposable elements with important roles in chromosomes,” Genetica 107 (1999): 189–196.
• Mary-Lou Pardue & P. Gregory DeBaryshe, “Drosophila telomere transposons: genetically active elements in heterochromatin,” Genetica 109 (2000): 45-52.
• M.-L. Pardue, S. Rashkova, E. Casacuberta, P. G. DeBaryshe, J. A. George & K. L. Traverse, “Two retrotransposons maintain telomeres in Drosophila,” Chromosome Research 13 (2005): 443–453.
• Ram Parikshan Kumar, Ramamoorthy Senthilkumar, Vipin Singh & Rakesh K. Mishra, “Repeat performance: how do genome packaging and regulation depend on simple sequence repeats?” BioEssays 32 (2010): 165–174.
• Satoru Ide, Takaaki Miyazaki, Hisaji Maki & Takehiko Kobayashi, “Abundance of ribosomal RNA gene copies maintains genome integrity,” Science 327 (2010): 693–696.
• Kuniaki Saito, Kazumichi M. Nishida, Tomoko Mori, Yoshinori Kawamura, Keita Miyoshi, Tomoko Nagami, Haruhiko Siomi & Mikiko C. Siomi, “Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome,” Genes & Development 20 (2006): 2214–2222.
• Yoshinori Kawamura, Kuniaki Saito, Taishin Kin, Yukiteru Ono, Kiyoshi Asai, Takafumi Sunohara, Tomoko N. Okada, Mikiko C. Siomi & Haruhiko Siomi, “Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells,” Nature 453 (2008): 793–797.
• Megha Ghildiyal, Hervé Seitz, Michael D. Horwich, Chengjian Li, Tingting Du, Soohyun Lee, Jia Xu, Ellen L.W. Kittler, Maria L. Zapp, Zhiping Weng & Phillip D. Zamore, “Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells,” Science 320 (2008): 1077–1081.
• Haifan Lin, “piRNAs in the germ line,” Science 316 (2007): 397.
• Travis Thomson & Haifan Lin, “The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect,” Annual Review of Cell and Developmental Biology 25 (2009): 355–376
• Christel Rouget, Catherine Papin, Anthony Boureux, Anne-Cécile Meunier, Bénédicte Franco, Nicolas Robine, Eric C. Lai, Alain Pelisson & Martine Simonelig, “Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo,” Nature 467 (2010): 1128–1132.
• James A. Shapiro & Richard von Sternberg, “Why repetitive DNA is essential to genome function,” Biological Reviews 80 (2005): 227–250.  
• Silva J.C., Shabalina S.A., Harris D.G., Spouge J.L. and Kondrashovi A.S. (2003) Conserved fragments of transposable elements in intergenic regions: Evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes. Genetics Research 82: 1–18.
• Brosius J. (1999) RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238: 115–34.
• Britten R. (2006) Transposable elements have contributed to thousands of human proteins. Proceedings of the National Academy of Sciences USA 103: 1798–803.
• Cordaux R., Udit S., Batzer M.A. and Feschotte C. (2006) Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proceedings of the National Academy of Sciences USA 103: 8101–6.
• Gerdes P., Richardson S.R., Mager D.L. and Faulkner G.J. (2016) Transposable elements in the mammalian embryo: Pioneers surviving through stealth and service. Genome Biology 17: 100.
• van de Lagemaat L.N., Landry J.-R., Mager D.L. and Medstrand P. (2003) Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends in Genetics 19: 530–6.
• Bourque G. et al. (2008) Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Research 18: 1752–62.
• Hermant C. and Torres-Padilla M.-E. (2021) TFs for TEs: The transcription factor repertoire of mammalian transposable elements. Genes & Development 35: 22–39.
• Trizzino M. et al. (2017) Transposable elements are the primary source of novelty in primate gene regulation. Genome Research 27: 1623–33.
• Gehring M., Bubb K.L. and Henikoff S. (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447–51.
• McCue A.D., Nuthikattu S., Reeder S.H. and Slotkin R.K. (2012) Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLOS Genetics 8: e1002474.
• Brind’Amour J. et al. (2018) LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. Nature Communications 9: 3331.
• Kelley D.R., Hendrickson D.G., Tenen D. and Rinn J.L. (2014) Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. Genome Biology 15: 537.
• Landry J.R., Medstrand P. and Mager D.L. (2001) Repetitive elements in the 5′ untranslated region of a human zinc-finger gene modulate transcription and translation efficiency. Genomics 76: 110–6.
• Moore R.S. et al. (2021) The role of the Cer1 transposon in horizontal transfer of transgenerational memory. Cell 184: 4697–712.
• Hsu PS, Yu SH, Tsai YT, Chang JY, Tsai LK, Ye CH, Song NY, Yau LC, Lin SP. More than causing (epi)genomic instability: emerging physiological implications of transposable element modulation. J Biomed Sci. 2021 Aug 7;28(1):58.
• McCarthy RL, Kaeding KE, Keller SH, Zhong Y, Xu L, Hsieh A, Hou Y, Donahue G, Becker JS, Alberto O, Lim B, Zaret KS. Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements. Nat Cell Biol. 2021 Aug;23(8):905-914.
• McCarthy RL, Kaeding KE, Keller SH, Zhong Y, Xu L, Hsieh A, Hou Y, Donahue G, Becker JS, Alberto O, Lim B, Zaret KS. Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements. Nat Cell Biol. 2021 Aug;23(8):905-914. doi: 10.1038/s41556-021-00725-7.
• Ng SK, Hu T, Long X, Chan CH, Tsang SY, Xue H. Feature co-localization landscape of the human genome. Sci Rep. 2016 Feb 8;6:20650.
• Wilusz JE. Repetitive elements regulate circular RNA biogenesis. Mob Genet Elements. 2015 May 21;5(3):1-7.
• Kelley DR, Hendrickson DG, Tenen D, Rinn JL. Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. Genome Biol. 2014 Dec 3;15(12):537.
• Bythwood TN, Xu W, Li W, Rao W, Li Q, Xue X, Richards J, Ma L, Song Q. The mirror RNA expression pattern in human tissues. Precis Med. 2015;1:e1036. [Also lncRNAs]
• Ichiyanagi K. Regulating Pol III transcription to change Pol II transcriptome. Cell Cycle. 2014;13(23):3625-6.
• Okae H, Chiba H, Hiura H, Hamada H, Sato A, Utsunomiya T, Kikuchi H, Yoshida H, Tanaka A, Suyama M, Arima T. Genome-wide analysis of DNA methylation dynamics during early human development. PLoS Genet. 2014 Dec 11;10(12):e1004868.
• Lexa M, Steflova P, Martinek T, Vorlickova M, Vyskot B, Kejnovsky E. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics. 2014 Nov 27;15(1):1032.
• Dios F, Barturen G, Lebrón R, Rueda A, Hackenberg M, Oliver JL. DNA clustering and genome complexity. Comput Biol Chem. 2014 Dec;53 Pt A:71-8.
• Huda A, Bushel PR. Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription. Transcr Open Access. 2013 Jun 19;1(1):1000101.
• Spengler RM, Oakley CK, Davidson BL. Functional microRNAs and target sites are created by lineage-specific transposition. Hum Mol Genet. 2014 Apr 1;23(7):1783-93.
• Cotton AM, Chen CY, Lam LL, Wasserman WW, Kobor MS, Brown CJ. Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains. Hum Mol Genet. 2014 Mar 1;23(5):1211-23.
• Du ZQ, Yang CX, Rothschild MF, Ross JW. Novel microRNA families expanded in the human genome. BMC Genomics. 2013 Feb 12;14:98.
• Kim YJ, Lee J, Han K. Transposable Elements: No More ‘Junk DNA’. Genomics Inform. 2012 Dec;10(4):226-33.
• Conley AB, Jordan IK. Cell type-specific termination of transcription by transposable element sequences. Mob DNA. 2012 Sep 30;3(1):15.
• Ashida H, Asai K, Hamada M. Shape-based alignment of genomic landscapes in multi-scale resolution. Nucleic Acids Res. 2012 Aug;40(14):6435-48.
• Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, De Sapio F, Brennan PM, Rizzu P, Smith S, Fell M, Talbot RT, Gustincich S, Freeman TC, Mattick JS, Hume DA, Heutink P, Carninci P, Jeddeloh JA, Faulkner GJ. Somatic retrotransposition alters the genetic landscape of the human brain. Nature. 2011 Oct 30;479(7374):534-7.
• Kim DS, Hahn Y. Human-specific antisense transcripts induced by the insertion of transposable element. Int J Mol Med. 2010 Jul;26(1):151-7.
• McVean G. What drives recombination hotspots to repeat DNA in humans? Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1213-8.
• Jacques, Pierre-Étienne, Justin Jeyakani, Guillaume Bourque. 2013. The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements. PLoS Genetics 9(5): e1003504. https://doi.org/10.1371/journal.pgen.1003504.
• Goodier JL, Mandal PK, Zhang L, Kazazian HH Jr. Discrete subcellular partitioning of human retrotransposon RNAs despite a common mechanism of genome insertion. Hum Mol Genet. 2010 May 1;19(9):1712-25.
• Thomson SJ, Goh FG, Banks H, Krausgruber T, Kotenko SV, Foxwell BM, Udalova IA. The role of transposable elements in the regulation of IFN-lambda1 gene expression. Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11564-9.
• Lee JY, Ji Z, Tian B. Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes. Nucleic Acids Res. 2008 Oct;36(17):5581-90.
• Huh JW, Kim DS, Ha HS, Lee JR, Kim YJ, Ahn K, Lee SR, Chang KT, Kim HS. Cooperative exonization of MaLR and AluJo elements contributed an alternative promoter and novel splice variants of RNF19. Gene. 2008 Nov 15;424(1-2):63-70.
• Polavarapu N, Mariño-Ramírez L, Landsman D, McDonald JF, Jordan IK. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics. 2008 May 17;9:226.
• Sharif J, Koseki H, Parrish NF. Bridging multiple dimensions: roles of transposable elements in higher-order genome regulation. Curr Opin Genet Dev. 2023 Jun;80:102035.
• Yandım C, Karakülah G. Expression dynamics of repetitive DNA in early human embryonic development. BMC Genomics. 2019 May 31;20(1):439.
• Trizzino M, Kapusta A, Brown CD. Transposable elements generate regulatory novelty in a tissue-specific fashion. BMC Genomics. 2018 Jun 18;19(1):468.
• Alhaddad H, Zhang C, Rannala B, Lyons LA. A Glance at Recombination Hotspots in the Domestic Cat. PLoS One. 2016 Feb 9;11(2):e0148710.
• Bernardi G. Chromosome Architecture and Genome Organization. PLoS One. 2015 Nov 30;10(11):e0143739.
• Kejnovsky E, Lexa M. Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators. Mob Genet Elements. 2014 Jan 1;4(1):e28084.
• Creamer KM, Kolpa HJ, Lawrence JB. Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction. Mol Cell. 2021 Sep 2;81(17):3509-3525.e5.
• Hall LL, Lawrence JB. RNA as a fundamental component of interphase chromosomes: could repeats prove key? Curr Opin Genet Dev. 2016 Apr;37:137-147.
• Rangasamy D. Distinctive patterns of epigenetic marks are associated with promoter regions of mouse LINE-1 and LTR retrotransposons. Mob DNA. 2013 Dec 2;4(1):27.
• Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature. 2012 Mar 28;484(7394):339-44.
• Pathak RU, Phanindhar K, Mishra RK. Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes. Front Mol Biosci. 2024 Feb 22;10:1326933.
• Bernardi G. The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”. Life (Basel). 2021 Apr 13;11(4):342.
• Bernardi G. The Genomic Code: A Pervasive Encoding/Molding of Chromatin Structures and a Solution of the “Non-Coding DNA” Mystery. Bioessays. 2019 Dec;41(12):e1900106.
• Bernardi G. The formation of chromatin domains involves a primary step based on the 3-D structure of DNA. Sci Rep. 2018 Dec 13;8(1):17821.
• Bernaola-Galván P, Carpena P, Gómez-Martín C, Oliver JL. Compositional Structure of the Genome: A Review. Biology (Basel). 2023 Jun 13;12(6):849.
• Johansson PA, Brattås PL, Douse CH, Hsieh P, Adami A, Pontis J, Grassi D, Garza R, Sozzi E, Cataldo R, Jönsson ME, Atacho DAM, Pircs K, Eren F, Sharma Y, Johansson J, Fiorenzano A, Parmar M, Fex M, Trono D, Eichler EE, Jakobsson J. A cis-acting structural variation at the ZNF558 locus controls a gene regulatory network in human brain development. Cell Stem Cell. 2022 Jan 6;29(1):52-69.e8.

5. Satellite DNA

• Stitz, Maria et al. 2021. Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biology and Evolution 13 (10): evab204. https://doi.org/10.1093/gbe/evab204.
• Fernandes LP, Enriquez-Gasca R, Gould PA, Holt JH, Conde L, Ecco G, Herrero J, Gifford R, Trono D, Kassiotis G, Rowe HM. A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819. Sci Adv. 2022 Oct 28;8(43):eabp8085.
• F. Rudert, S. Bronner, J. M. Garnier & P. Dollé, “Transcripts from opposite strands of gamma satellite DNA are differentially expressed during mouse development,” Mammalian Genome 6 (1995): 76–83.
• Brenda J. Reinhart & David P. Bartel, “Small RNAs Correspond to Centromere Heterochromatic Repeats,” Science 297 (2002): 1831.
• Bruce P. May, Zachary B. Lippman, Yuda Fang, David L. Spector & Robert A. Martienssen, “Differential Regulation of Strand-Specific Transcripts from Arabidopsis Centromeric Satellite Repeats,” PLoS Genetics 1:6 (2005): e79.
• Junjie Lu & David M. Gilbert, “Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin,” Journal of Cell Biology 179 (2007): 411–412.
• Rachel J. O’Neill & Dawn M. Carone, “The role of ncRNA in centromeres: a lesson from marsupials,” Progress in Molecular and Subcellular Biology 48 (2009): 77–101.
• Thomas A. Volpe, Catherine Kidner, Ira M. Hall, Grace Teng, Shiv I. S. Grewal & Robert A. Martienssen, “Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi,” Science 297 (2002): 1833–1837.
• Christopher N. Topp, Cathy X. Zhong & R. Kelly Dawe, “Centromere-encoded RNAs are integral components of the maize kinetochore,” Proceedings of the National Academy of Sciences USA 101 (2004): 15986–15991.
• Haniaa Bouzinba-Segard, Adeline Guais & Claire Francastel, “Accumulation of small murine minor satellite transcripts leads to impaired centromeric architecture and function,” Proceedings of the National Academy of Sciences USA 103 (2006): 8709–8714.
• Federica Ferri, Haniaa Bouzinba-Segard, Guillaume Velasco, Florent Hubé & Claire Francastel, “Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase,” Nucleic Acids Research 37 (2009): 5071–5080.
• Lee H. Wong, Kate H. BrettinghamMoore, Lyn Chan, Julie M. Quach, Melissa A. Anderson, Emma L. Northrop, Ross Hannan, Richard Saffery, Margaret L. Shaw, Evan Williams & K. H. Andy Choo, “Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere,” Genome Research 17 (2007): 1146–1160. 
• Shiv I. S. Grewal & Sarah C. R. Elgin, “Transcription and RNA interference in the formation of heterochromatin,” Nature 447 (2007): 399–406.
• Tom Volpe, Vera Schramke, Georgina L. Hamilton, Sharon A. White, Grace Teng, Robert A. Martienssen & Robin C. Allshire, “RNA interference is required for normal centromere function in fission yeast,” Chromosome Research 11 (2003): 137–146.
• André Verdel, Songtao Jia, Scott Gerber, Tomoyasu Sugiyama, Steven Gygi, Shiv I. S. Grewal & Danesh Moazed, “RNAi-Mediated Targeting of Heterochromatin by the RITS Complex,” Science 303 (2004): 672–676.
• Mohammad R. Motamedi, André Verdel, Serafin U. Colmenares, Scott A. Gerber, Steven P. Gygi & Danesh Moazed, “Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs,” Cell 119 (2004): 789–802.
• Hiroaki Kato, Derek B. Goto, Robert A. Martienssen, Takeshi Urano, Koichi Furukawa & Yota Murakami, “RNA Polymerase II Is Required for RNAiDependent Heterochromatin Assembly,” Science 309 (2005): 467–469.
• Pavel Neumann, Huihuang Yan & Jiming Jiang, “The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference,” Genetics 176 (2007): 749–761. 
• Angeline Eymery, Mary Callanan & Claire Vourc’h, “The secret message of heterochromatin: new insights into the mechanisms and function of centromeric and pericentric repeat sequence transcription,” International Journal of Developmental Biology 53 (2009): 259–268. 
• Jonathan C. Lamb & James A. Birchler, “The role of DNA sequence in centromere formation,” Genome Biology 4:5 (2003): 214. 
• Mary G. Schueler & Beth A. Sullivan, “Structural and functional dynamics of human centromeric chromatin,” Annual Review of Genomics and Human Genetics 7 (2006): 301–313.
• Beth A. Sullivan, Michael D. Blower & Gary H. Karpen, “Determining centromere identity: cyclical stories and forking paths,” Nature Reviews Genetics 2 (2001): 584–596.
• Peter E. Warburton, Carol A. Cooke, Sylvie Bourassa, Omid Vafa, Beth A. Sullivan, Gail Stetten, Giorgio Gimelli, Dorothy Warburton, Chris Tyler-Smith, Kevin F. Sullivan, Guy G. Poirier & William C. Earnshaw, “Immunolocalization of CENP-A suggests a distinct nucleosome structure at the inner kinetochore plate of active centromeres,” Current Biology 7 (1997): 901–904.
• Aaron A. Van Hooser, Michael A. Mancini, C. David Allis, Kevin F. Sullivan & B. R. Brinkley, “The mammalian centromere: structural domains and the attenuation of chromatin modeling,” FASEB Journal 13 Supplement (1999): S216-S220.
• Kinya Yoda, Satoshi Ando, Setsuo Morishita, Kenichi Houmura, Keiji Hashimoto, Kunio Takeyasu & Tuneko Okazaki, “Human centromere protein A (CENP-A) can replace histone H3 in nucleosome reconstitution in vitro,” Proceedings of the National Academy of Sciences USA 97 (2000): 7266–7271. 
• Ben E. Black, Melissa A. Brock, Sabrina Bédard, Virgil L. Woods, Jr. & Don W. Cleveland, “An epigenetic mark generated by the incorporation of CENP-A into centromeric nucleosomes,” Proceedings of the National Academy of Sciences USA 104 (2007): 5008–5013.
• Mònica Torras-Llort, Olga MorenoMoreno & Fernando Azorín, “Focus on the centre: the role of chromatin on the regulation of centromere identity and function,” EMBO Journal 28 (2009): 2337–2348.
• Aaron A. Van Hooser, Ilia I. Ouspenski, Heather C. Gregson, Daniel A. Starr, Tim J. Yen, Michael L. Goldberg, Kyoko Yokomori, William C. Earnshaw, Kevin F. Sullivan & B. R. Brinkley, “Specification of kinetochore-forming chromatin by the histone H3 variant CENP-A,” Journal of Cell Science 114 (2001): 3529–3542.
• Larissa J. Vos, Jakub K. Famulski & Gordon K.T. Chan, “How to build a centromere: from centromeric and pericentromeric chromatin to kinetochore assembly,” Biochemistry and Cell Biology 84 (2006): 619–639.
• Deborah L. Grady, Robert L. Ratliff, Donna L. Robinson, Erin C. McCanlies, Julianne Meyne & Robert K. Moyzis, “Highly conserved repetitive DNA sequences are present at human centromeres,” Proceedings of the National Academy of Sciences USA 89 (1992): 1695–1699.
• Jiming Jiang, Shuhei Nasuda, Fenggao Dong, Christopher W. Sherrer, Sung-Sick Woo, Rod A. Wing, Bikram S. Gill & David C. Ward, “A conserved repetitive DNA element located in the centromeres of cereal chromosomes,” Proceedings of the National Academy of Sciences USA 93 (1996): 14210–14213.
• Huntington F. Willard, “Chromosome-Specific Organization of Human Alpha Satellite DNA,” American Journal of Human Genetics 37 (1985): 524–532.
• John S. Waye & Huntington F. Willard, “Chromosome-specific alpha satellite DNA: nucleotide sequence analysis of the 2.0 kilobasepair repeat from the human X chromosome,” Nucleic Acids Research 13 (1985): 2731–2743.
• R. Heller, K. E. Brown, C. Burgtorf & W. R. A. Brown, “Mini-chromosomes derived from the human Y chromosome by telomere directed chromosome breakage,” Proceedings of the National Academy of Sciences USA 93 (1996): 7125–7130.
• Terence D. Murphy and Gary H. Karpen, “Centromeres Take Flight: Alpha Satellite and the Quest for the Human Centromere,” Cell 93 (1998): 317–320.
• Brenda R. Grimes, Angela A. Rhoades & Huntington F. Willard, “Alpha-satellite DNA and vector composition influence rates of human artificial chromosome formation,” Molecular Therapy 5 (2002): 798–805.
• M. Katharine Rudd, Robert W. Mays, Stuart Schwartz & Huntington F. Willard, “Human Artificial Chromosomes with Alpha Satellite-Based De Novo Centromeres Show Increased Frequency of Nondisjunction and Anaphase Lag,” Molecular and Cellular Biology 23 (2003): 7689–7697.
• Hartley G. and O‘Neill R.J. (2019) Centromere repeats: Hidden gems of the genome. Genes 10: 223.
• Whitelaw E. and Martin D.I. (2001) Retrotransposons as epigenetic mediators of phenotypic variation in mammals. Nature Genetics 27: 361–5.
• Schramke V. and Allshire R. (2003) Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 301: 1069–74.
• Lippman Z. et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471–6.
• Slotkin R.K. and Martienssen R. (2007) Transposable elements and the epigenetic regulation of the genome. Nature Reviews Genetics 8: 272–85.
• Gehring M., Bubb K.L. and Henikoff S. (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: 1447–51.

6. Transposons

• Okhovat M, VanCampen J, Nevonen KA, Harshman L, Li W, Layman CE, Ward S, Herrera J, Wells J, Sheng RR, Mao Y, Ndjamen B, Lima AC, Vigh-Conrad KA, Stendahl AM, Yang R, Fedorov L, Matthews IR, Easow SA, Chan DK, Jan TA, Eichler EE, Rugonyi S, Conrad DF, Ahituv N, Carbone L. TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function. Nat Commun. 2023 Dec 7;14(1):8111. 
• Sturm Á, Saskői É, Hotzi B, Tarnóci A, Barna J, Bodnár F, Sharma H, Kovács T, Ari E, Weinhardt N, Kerepesi C, Perczel A, Ivics Z, Vellai T. Downregulation of transposable elements extends lifespan in Caenorhabditis elegans. Nat Commun. 2023 Aug 29;14(1):5278.
• Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet. 2021 Nov;22(11):691-711.
• Ladias P, Markopoulos G, Lazaros L, Markoula S, Tzavaras T, Georgiou I. Holliday Junctions Are Associated with Transposable Element Sequences in the Human Genome. J Mol Biol. 2016 Feb 13;428(3):658-667.
• Glinsky GV. Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells. Chromosome Res. 2018 Mar;26(1-2):61-84.
• Lowe C.B., Bejerano G. and Haussler D. (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proceedings of the National Academy of Sciences USA 104: 8005–10.
• Faulkner G.J. et al. (2009) The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics 41: 563–71.
• Xu A.G. et al. (2010) Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA- Seq. PLOS Computational Biology 6: e1000843.
• Skryabin B.V. et al. (1998) The BC200 RNA gene and its neural expression are conserved in Anthropoidea (Primates). Journal of Molecular Evolution 47: 677–85.
• Xie X., Kamal M. and Lander E.S. (2006) A family of conserved noncoding elements derived from an ancient transposable element. Proceedings of the National Academy of Sciences USA 103: 11659–64.
• Jordan I.K., Rogozin I.B., Glazko G.V. and Koonin E.V. (2003) Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends in Genetics 19: 68–72.
• M. Morgante, “Plant genome organisation and diversity: the year of the junk!,” Current Opinion in Biotechnology, Vol. 17:168–173 (2006).
• C. B. Lowe et al., “Thousands of human mobile element fragments undergo strong purifying selection near developmental genes,” Proceedings of the National Academy of Sciences USA, Vol. 104(19):8005-8010 (May 8, 2007).
• Geoffrey J. Faulkner, Yasumasa Kimura, Carsten O. Daub, Shivangi Wani, Charles Plessy, Katharine M. Irvine, Kate Schroder, Nicole Cloonan, Anita L. Steptoe, Timo Lassmann, Kazunori Waki, Nadine Hornig, Takahiro Arakawa, Hazuki Takahashi, Jun Kawai, Alistair R. R. Forrest, Harukazu Suzuki, Yoshihide Hayashizaki, David A. Hume, Valerio Orlando, Sean M. Grimmond & Piero Carninci, “The regulated retrotransposon transcriptome of mammalian cells,” Nature Genetics 41 (2009): 563–571.
• Amar Kumar & Jeffrey L. Bennetzen, “Retrotransposons: central players in the structure, evolution and function of plant genomes,” Trends in Plant Science 5 (2000): 509–510.
• Craig B. Lowe, Gill Bejerano & David Haussler, “Thousands of human mobile element fragments undergo strong purifying selection near developmental genes,” Proceedings of the National Academy of Sciences USA 104 (2007): 8005–8010.
• Mangiavacchi A, Liu P, Della Valle F, Orlando V. New insights into the functional role of retrotransposon dynamics in mammalian somatic cells. Cell Mol Life Sci. 2021 Jul;78(13):5245-5256.
• Hsu PS, Yu SH, Tsai YT, Chang JY, Tsai LK, Ye CH, Song NY, Yau LC, Lin SP. More than causing (epi)genomic instability: emerging physiological implications of transposable element modulation. J Biomed Sci. 2021 Aug 7;28(1):58.

7. Pseudogenes

• Wen, Yan-Zi, Ling-Ling Zheng, Liang-Hu Qu, Francisco J. Ayala, and Zhao-Rong Lun. 2012. Pseudogenes Are Not Pseudo Any More. RNA Biology 9: 27-32. DOI:10.4161/rna.9.1.18277.
• Feng Y, Wang Z, Chien KY, Chen HL, Liang YH, Hua X, Chiu CH. “Pseudo-pseudogenes” in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica. Nucleic Acids Res. 2022 May 20;50(9):5158-5170.
• H.-H. M. Dahl, R. M. Brown, W. M. Hutchison, C. Maragos & G. K. Brown, “A testis-specific form of the human pyruvate dehydrogenase E1 alpha subunit is coded for by an intronless gene on chromosome 4,” Genomics 8 (1990): 225–232.
• J. Sorge, E. Gross, C. West & E. Beutlert, “High level transcription of the glucocerebrosidase pseudogene in normal subjects and patients with Gaucher disease,” Journal of Clinical Investigation 86 (1990): 1137–1141.
• Fiddes, Ian T. et al. 2018. Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis. Cell 173: 1356-1369. 
• Habib, Adella M. et al. 2019. Microdeletion in a FAAH pseudogene identified in a patient with high anandamide concentrations and pain insensitivity. British Journal of Anaesthesia 123 (2): e249-e253. DOI:10.1016/j.bja.2019.02.019.
• Suzuki, Ikuo K. et al. 2018. Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation. Cell 173: 1370-1384. DOI:10.1016/j.cell.2018.03.067.
• Prieto-Godino, Lucia L., Raphael Rytz, Benoîte Bargeton, Liliane Abuin, J. Roman Arguello, Matteo Dal Peraro, and Richard Benton. 2016. Olfactory receptor pseudo-pseudogenes. Nature 539: 93-97. 
• Touitou, Q. Q. Cai & H. Rochefort, “17 beta Hydroxysteroid dehydrogenase 1 ‘pseudogene’ is differentially transcribed: still a candidate for the breast-ovarian cancer susceptibility gene (BRCA1),” Biochemical and Biophysical Research Communications 201 (1994): 1327–1332.
• Cornelia Schmutzler & Hans J. Gross, “Genes, variant genes, and pseudogenes of the human tRNAVal gene family are differentially expressed in HeLa cells and in human placenta,” Nucleic Acids Research 18 (1990): 5001–5008.
• Yasemin Kaçar, Hildburg Beier & Hans J. Gross, “The presence of tRNA pseudogenes in mammalia and plants and their absence in yeast may account for different specificities of pre-tRNA processing enzymes,” Gene 156 (1995): 129–132.
• Erich T. Boger, James R. Sellers& Thomas B. Friedman, “Human myosin XVBP is a transcribed pseudogene,” Journal of Muscle Research and Cell Motility 22 (2001): 477–483.
• Richard J. Cristiano, Sara J. Giordano & Alan W. Steggles, “The Isolation and Characterization of the Bovine Cytochrome b5 Gene, and a Transcribed Pseudogene,” Genomics 17 (1993):348–354.
• Rainer Fürbass & Jens Vanselow, “An aromatase pseudogene is transcribed in the bovine placenta,” Gene 154 (1995): 287–291.
• D. Aubert, C. Nisanz-Sever & M. Herzog, “Mitochondrial rps14 is a transcribed and edited pseudogene in Arabidopsis thaliana,” Plant Molecular Biology 20 (1992): 1169–1174.

• V. Quiñones, S. Zanlungo, A. Moenne, I. Gómez, L. Holuigue, S. Litvak & X. Jordana, “The rpl5-rps14-cob gene arrangement in Solanum tuberosum: rps14 is a transcribed and unedited pseudogene,” Plant Molecular Biology 31 (1996) 937–943.
• Deyou Zheng, Zhaolei Zhang, Paul M. Harrison, John Karro, Nick Carriero & Mark Gerstein, “Integrated pseudogene annotation for human chromosome 22: evidence for transcription,” Journal of Molecular Biology 349 (2005): 27–45
• D. Zheng and M. B. Gerstein, “The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?,” Trends in Genetics, Vol. 23(5):219-224 (2007).
• Paul M. Harrison, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero & Mark Gerstein, “Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability,” Nucleic Acids Research 33 (2005): 2374–2383.
• Deyou Zheng, Adam Frankish, Robert Baertsch, Philipp Kapranov, Alexandre Reymond, Siew Woh Choo, Yontao Lu, France Denoeud, Stylianos E. Antonarakis, Michael Snyder, Yijun Ruan, Chia-Lin Wei, Thomas R. Gingeras, Roderic Guigó, Jennifer Harrow & Mark B. Gerstein, “Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution,” Genome Research 17 (2007): 839–851.
• Michael J. Chorney, Ikuhisa Swada, Gerald A. Gillespie, Rakesh Srivastava, Julian Pan & Sherman M. Weissman, “Transcription Analysis, Physical Mapping, and Molecular Characterization of a Nonclassical Human Leukocyte Antigen Class I Gene,” Molecular and Cellular Biology 10 (1990): 243–253.
• Tuan Nguyen, Roger Sunahara, Adriano Marchese, Hubert H. M. Van Tol, Philip Seeman & Brian F. O’Dowd, “Transcription of a human dopamine D5 pseudogene,” Biochemical and Biophysical Research Communications 181 (1991): 16–21.
• Jonathan A. Bard, Stanley P. Nawoschik, Brian F. O’Dowd, Susan R. George, Theresa A. Branchek & Richard L. Weinshank, “The human serotonin 5-hydroxytryptamine1D receptor pseudogene is transcribed,” Gene 153 (1995): 295–296.
• Christine Pourcel, Jean Jaubert, Michelle Hadchouel, Xue Wu & Johannes Schweizer, “A new family of genes and pseudogenes potentially expressing testisand brain-specific leucine zipper proteins in man and mouse,” Gene 249 (2000): 105–113.
• Mustapha Kandouz, Andrew Bier, George D. Carystinos, Moulay A. AlaouiJamali and Gerald Batist, “Connexin43 pseudogene is expressed in tumor cells and inhibits growth,” Oncogene 23 (2004): 4763–4770.
• Paul Yaswen, Amy Smoll, Junko Hosoda, Gordon Parry & Martha R. Stampfer, “Protein product of a human intronless calmodulin-like gene shows tissue-specific expression and reduced abundance in transformed cells,” Cell Growth & Differentiation 3 (1992): 335–345.
• Manyuan Long & Charles H. Langley, “Natural Selection and the Origin of jingwei, a Chimeric Processed Functional Gene in Drosophila,” Science 260 (1993): 91–95.
• Evgeniy S. Balakirev & Francisco J. Ayala, “Is Esterase-P Encoded by a Cryptic Pseudogene in Drosophila melanogaster?” Genetics 144 (1996): 1511–1518.
• M. M. Dumancic, J. G. Oakeshott, R. J. Russell & M. J. Healy, “Characterization of the EstP protein in Drosophila melanogaster and its conservation in drosophilids,” Biochemical Genetics 35 (1997): 251–271.
• Esther Betrán, Wen Wang, Li Jin & Manyuan Long, “Evolution of the Phosphoglycerate Mutase Processed Gene in Human and Chimpanzee Revealing the Origin of a New Primate Gene,” Molecular Biology and Evolution 19 (2002): 654–663.
• Agnès Moreau-Aubry, Soizic Le Guiner, Nathalie Labarrière, Marie-Claude Gesnel, Francine Jotereau & Richard Breathnach, “A Processed Pseudogene Codes for a New Antigen Recognized by a CD8+ T Cell Clone on Melanoma,” Journal of Experimental Medicine 191 (2000): 1617–1624.
• Bing-Sen Zhou, David R. Beidler & Yung-Chi Cheng, “Identification of Antisense RNA Transcripts from a Human DNA Topoisomerase I Pseudogene,” Cancer Research 52 (1992): 4280–4285.
• Dominique Weil, Mary-Anne Power, Graham C. Webb & Chung Leung Li, “Antisense transcription of a murine FGFR3 pseudogene during fetal development,” Gene 187 (1997): 115–122.
• Sergei A. Korneev, Ji-Ho Park & Michael O’Shea, “Neuronal Expression of Neural Nitric Oxide Synthase (nNOS) Protein Is Suppressed by an Antisense RNA Transcribed from an NOS Pseudogene,” Journal of Neuroscience 19 (1999): 7711–7720.
• D. Pain et al., “Multiple Retropseudogenes from Pluripotent Cell-specific Gene Expression Indicates a Potential Signature for Novel Gene Identification,” The Journal of Biological Chemistry, Vol. 280(8):6265–6268 (February 25, 2005).
• Toshiaki Watanabe, Yasushi Totoki, Atsushi Toyoda, Masahiro Kaneda, Satomi Kuramochi-Miyagawa, Yayoi Obata, Hatsune Chiba, Yuji Kohara, Tomohiro Kono, Toru Nakano, M. Azim Surani, Yoshiyuki Sakaki & Hiroyuki Sasaki, “Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes,” Nature 453 (2008): 539–543.
• Oliver H. Tam, Alexei A. Aravin, Paula Stein, Angelique Girard, Elizabeth P. Murchison, Sihem Cheloufi, Emily Hodges, Martin Anger, Ravi Sachidanandam, Richard M. Schultz & Gregory J. Hannon, “Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes,” Nature 453 (2008): 534–538.
• Xingyi Guo, Zhaolei Zhang, Mark B. Gerstein & Deyou Zheng, “Small RNAs Originated from Pseudogenes: cis- or trans-Acting?” PLos Computational Biology 5:7 (2009): e1000449.
• Shinji Hirotsune, Noriyuki Yoshida, Amy Chen, Lisa Garrett, Fumihiro Sugiyama, Satoru Takahashi, Ken-ichi Yagami, Anthony Wynshaw-Boris & Atsushi Yoshiki, “An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene,” Nature 423 (2003): 91–96.
• Yoshihisa Yano, Rintaro Saito, Noriyuki Yoshida, Atsushi Yoshiki, Anthony Wynshaw-Boris, Masaru Tomita & Shinji Hirotsune, “A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene,” Journal of Molecular Medicine 82 (2004): 414–422.
• Ondrej Podlaha and Jianzhi Zhang, “Nonneutral Evolution of the Transcribed Pseudogene Makorin1-p1 in Mice,” Molecular Biology and Evolution 21 (2004): 2202–2209.
• Satoko Kaneko, Ikuko Aki, Kaoru Tsuda, Kazuyuki Mekada, Kazuo Moriwaki, Naoyuki Takahata & Yoko Satta,“Origin and Evolution of Processed Pseudogenes That Stabilize Functional Makorin1 mRNAs in Mice, Primates and Other Mammals,” Genetics 172 (2006): 2421– 2429.
• José Manuel Franco-Zorrilla, Adrián Valli, Marco Todesco, Isabel Mateos, María Isabel Puga, Ignacio Rubio-Somoza, Antonio Leyva, Detlef Weigel, Juan Antonio García & Javier Paz-Ares, “Target mimicry provides a new mechanism for regulation of microRNA activity,” Nature Genetics 39 (2007): 1033–1037.
• Armin P. Piehler, Marit Hellum, Jürgen J. Wenzel, Ellen Kaminski, Kari Bente Foss Haug, Peter Kierulf & Wolfgang E. Kaminski, “The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference,” BMC Genomics 9 (2008): 165.
• Muro, Enrique M., Nancy Mah, and Miguel A. Andrade-Navarro. 2011. Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie 93: 1916-1921.
• Poliseno, Laura. 2012. Pseudogenes: Newly Discovered Players in Human Cancer. Science Signaling 5 (242): re5. DOI:10.1126/scisignal.2002858.
• Salmena, Leonardo, Laura Poliseno, Yvonne Tay, Lev Kats, and Pier Paolo Pandolfi. 2011. A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? Cell 146 (3): 353-358. DOI:10.1016/j.cell.2011.07.014.
• Laura Poliseno, Leonardo Salmena, Jiangwen Zhang, Brett Carver, William J. Haveman & Pier Paolo Pandolfi, “A coding-independent function of gene and pseudogene mRNAs regulates tumour biology,” Nature 465 (2010): 1033–1038.
• Örjan Svensson, Lars Arvestad & Jens Lagergren, “Genome-Wide Survey for Biologically Functional Pseudogenes,” PLoS Computational Biology 2:5 (2006): e46. 
• Evgeniy S. Balakirev & Francisco J. Ayala, “Pseudogenes: Are They ‘Junk’ or Functional DNA?” Annual Review of Genetics 37 (2003): 123–51.
• Ma, Yanni et al. 2021. Genome-wide Analysis of Pseudogenes Reveals HBBP1’s Human-specific Essentiality in Erythropoiesis and Implication in β-Thalassemia. Developmental Cell 56 (4): 478-493. DOI:10.1016/j.devcel.2020.12.019.
• Amit N. Khachane & Paul M. Harrison, “Assessing the genomic evidence for conserved transcribed pseudogenes under selection,” BMC Genomics 10 (2009): 435.
• Amit N. Khachane & Paul M. Harrison, “Assessing the genomic evidence for conserved transcribed pseudogenes under selection,” BMC Genomics 10 (2009): 435.

8. ERVs / Retrotransposons

• Ogaki Y, Fukuma M, Shimizu N. Repeat induces not only gene silencing, but also gene activation in mammalian cells. PLoS One. 2020 Jun 24;15(6):e0235127.
• Turelli P, Playfoot C, Grun D, Raclot C, Pontis J, Coudray A, Thorball C, Duc J, Pankevich EV, Deplancke B, Busskamp V, Trono D. Primate-restricted KRAB zinc finger proteins and target retrotransposons control gene expression in human neurons. Sci Adv. 2020 Aug 28;6(35):eaba3200.
• R. Sternberg and J. A. Shapiro, “How repeated retroelements format genome function,” Cytogenetic and Genome Research, Vol.110:108–116 (2005).
• Jönsson, Marie E et al. 2021. Activation of endogenous retroviruses during braindevelopment causes an inflammatory response. The EMBO Journal 40: e106423. DOI:10.15252/embj.2020106423.
• Koks S, Pfaff AL, Bubb VJ, Quinn JP. Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome. Int J Mol Sci. 2021 Jun 12;22(12):6319.
• Ferrari R, Grandi N, Tramontano E, Dieci G. Retrotransposons as Drivers of Mammalian Brain Evolution. Life (Basel). 2021 Apr 22;11(5):376.
• Mangiavacchi A, Liu P, Della Valle F, Orlando V. New insights into the functional role of retrotransposon dynamics in mammalian somatic cells. Cell Mol Life Sci. 2021 Jul;78(13):5245-5256.
• J. Zhang et al., “NANOGP8 is a retrogene expressed in cancers,” FEBS Journal Vol. 273:1723–1730 (2006).
• Jian Yang, Lauryn Cook, Zhiyuan Chen, “Systematic evaluation of retroviral LTRs as cis-regulatory elements in mouse embryos,” Cell Reports, 43: 113775 (March 26, 2024).
• Akihiko Sakashita, Tomohiro Kitano, Hirotsugu Ishizu, Youjia Guo, Harumi Masuda, Masaru Ariura, Kensaku Murano, and Haruhiko Siomi, “Transcription of MERVL retrotransposons is required for preimplantation embryo development,” Nature Genetics, 55: 484-495 (2023).
• Hossain MJ, Nyame P, Monde K. Species-Specific Transcription Factors Associated with Long Terminal Repeat Promoters of Endogenous Retroviruses: A Comprehensive Review. Biomolecules. 2024 Feb 26;14(3):280.
• Di Giorgio E, Ranzino L, Tolotto V, Dalla E, Burelli M, Gualandi N, Brancolini C. Transcription of endogenous retroviruses in senescent cells contributes to the accumulation of double-stranded RNAs that trigger an anti-viral response that reinforces senescence. Cell Death Dis. 2024 Feb 21;15(2):157.
• Torre D, Fstkchyan YS, Ho JSY, Cheon Y, Patel RS, Degrace EJ, Mzoughi S, Schwarz M, Mohammed K, Seo JS, Romero-Bueno R, Demircioglu D, Hasson D, Tang W, Mahajani SU, Campisi L, Zheng S, Song WS, Wang YC, Shah H, Francoeur N, Soto J, Salfati Z, Weirauch MT, Warburton P, Beaumont K, Smith ML, Mulder L, Villalta SA, Kessenbrock K, Jang C, Lee D, De Rubeis S, Cobos I, Tam O, Hammell MG, Seldin M, Shi Y, Basu U, Sebastiano V, Byun M, Sebra R, Rosenberg BR, Benner C, Guccione E, Marazzi I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Mol Cell. 2023 Dec 7;83(23):4255-4271.e9.
• Lu X. Regulation of endogenous retroviruses in murine embryonic stem cells and early embryos. J Mol Cell Biol. 2024 Jan 17;15(8):mjad052.
• Elissa D Pastuzyn, Cameron E Day, Rachel B Kearns, Madeleine Kyrke-Smith, Andrew V Taibi, John McCormick, Nathan Yoder, David M Belnap, Simon Erlendsson, Dustin R Morado, John A G Briggs, Cédric Feschotte, Jason D Shepherd, “The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer,” Cell, 172(1-2): 275-288.e18 (2018)
• Zhang J, Hou W, Zhao Q, Xiao S, Linghu H, Zhang L, Du J, Cui H, Yang X, Ling S, Su J, Kong Q. Deep annotation of long noncoding RNAs by assembling RNA-seq and small RNA-seq data. J Biol Chem. 2023 Sep;299(9):105130.
• Otsuka K, Sakashita A, Maezawa S, Schultz RM, Namekawa SH. KRAB-zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution. bioRxiv [Preprint]. 2023 Jun 26:2023.06.24.546405.
• Pal D, Patel M, Boulet F, Sundarraj J, Grant OA, Branco MR, Basu S, Santos SDM, Zabet NR, Scaffidi P, Pradeepa MM. H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function. Nat Struct Mol Biol. 2023 Jul;30(7):935-947.
• Frost JM, Amante SM, Okae H, Jones EM, Ashley B, Lewis RM, Cleal JK, Caley MP, Arima T, Maffucci T, Branco MR. Regulation of human trophoblast gene expression by endogenous retroviruses. Nat Struct Mol Biol. 2023 Apr;30(4):527-538.
• Ghosh et al., “A retroviral link to vertebrate myelination through retrotransposon-RNA-mediated control of myelin gene expression,” Cell, 187, 814–830 (2024).
• Jin L, He J, Feng H, Li S, Liu H, Dong H, Hu M, Huang J, Wu H, Chen J, Qi L, Wu K. Transposable elements activation triggers necroptosis in mouse embryonic stem cells. Cell Death Dis. 2023 Mar 7;14(3):184. 
• Yu M, Hu X, Pan Z, Du C, Jiang J, Zheng W, Cai H, Wang Y, Deng W, Wang H, Lu J, Sun MA, Cao B. Endogenous retrovirus-derived enhancers confer the transcriptional regulation of human trophoblast syncytialization. Nucleic Acids Res. 2023 Jun 9;51(10):4745-4759.
• Du C, Jiang J, Li Y, Yu M, Jin J, Chen S, Fan H, Macfarlan TS, Cao B, Sun MA. Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells. Genome Res. 2023 Feb;33(2):197-207.
• Li C, Zhang Y, Leng L, Pan X, Zhao D, Li X, Huang J, Bolund L, Lin G, Luo Y, Xu F. The single-cell expression profile of transposable elements and transcription factors in human early biparental and uniparental embryonic development. Front Cell Dev Biol. 2022 Nov 11;10:1020490.
• Shikata D, Matoba S, Hada M, Sakashita A, Inoue K, Ogura A. Suppression of endogenous retroviral enhancers in mouse embryos derived from somatic cell nuclear transfer. Front Genet. 2022 Nov 8;13:1032760.
• She J, Du M, Xu Z, Jin Y, Li Y, Zhang D, Tao C, Chen J, Wang J, Yang E. The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites. Genome Biol. 2022 Nov 3;23(1):231.
• Yang X, Ji J, Cui H, Zhao Q, Ding C, Xu C. Functional evaluation of LTR-derived lncRNAs in porcine oocytes and zygotes with RNA-seq and small RNA-seq. Front Genet. 2022 Oct 13;13:1023041.
• Du AY, Zhuo X, Sundaram V, Jensen NO, Chaudhari HG, Saccone NL, Cohen BA, Wang T. Functional characterization of enhancer activity during a long terminal repeat’s evolution. Genome Res. 2022 Oct;32(10):1840-1851.
• Lee DH, Bae WH, Ha H, Park EG, Lee YJ, Kim WR, Kim HS. Z-DNA-Containing Long Terminal Repeats of Human Endogenous Retrovirus Families Provide Alternative Promoters for Human Functional Genes. Mol Cells. 2022 Aug 31;45(8):522-530.
• Calvet S, Sallis S, Saksouk N, Rebouissou C, Teyssier C, Lesne A, Cammas F, Forné T. Endogenous Retroviral Sequences Behave as Putative Enhancers Controlling Gene Expression through HP1-Regulated Long-Range Chromatin Interactions. Cells. 2022 Aug 3;11(15):2392.
• Asimi V, Sampath Kumar A, Niskanen H, Riemenschneider C, Hetzel S, Naderi J, Fasching N, Popitsch N, Du M, Kretzmer H, Smith ZD, Weigert R, Walther M, Mamde S, Meierhofer D, Wittler L, Buschow R, Timmermann B, Cisse II, Ameres SL, Meissner A, Hnisz D. Hijacking of transcriptional condensates by endogenous retroviruses. Nat Genet. 2022 Aug;54(8):1238-1247.
• Ito J, Seita Y, Kojima S, Parrish NF, Sasaki K, Sato K. A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells. PLoS Genet. 2022 May 12;18(5):e1009846.
• Bakoulis S, Krautz R, Alcaraz N, Salvatore M, Andersson R. Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells. Nucleic Acids Res. 2022 Feb 28;50(4):2111-2127.
• Xiang X, Tao Y, DiRusso J, Hsu FM, Zhang J, Xue Z, Pontis J, Trono D, Liu W, Clark AT. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nat Commun. 2022 Jan 24;13(1):463.
• Durnaoglu S, Lee SK, Ahnn J. Human Endogenous Retroviruses as Gene Expression Regulators: Insights from Animal Models into Human Diseases. Mol Cells. 2021 Dec 31;44(12):861-878.
• Chandrasekaran S, Espeso-Gil S, Loh YE, Javidfar B, Kassim B, Zhu Y, Zhang Y, Dong Y, Bicks LK, Li H, Rajarajan P, Peter CJ, Sun D, Agullo-Pascual E, Iskhakova M, Estill M, Lesch BJ, Shen L, Jiang Y, Akbarian S. Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions. Nat Commun. 2021 Dec 13;12(1):7243.
• Chuong, Edward B. 2018. The placenta goes viral: Retroviruses control gene expression in pregnancy. PLoS Biology 16(10): e3000028. https://doi.org/10.1371/journal.pbio.3000028.
• Robson, Michael I., and Stefan Mundlos. 2019. Jumping retroviruses nudge TADs apart. Nature Genetics 51: 1304-1305. https://doi.org/10.1038/s41588-019-0491-y.
• Buttler CA, Chuong EB. Emerging roles for endogenous retroviruses in immune epigenetic regulation. Immunol Rev. 2022 Jan;305(1):165-178.
• Kitao K, Nakagawa S, Miyazawa T. An ancient retroviral RNA element hidden in mammalian genomes and its involvement in co-opted retroviral gene regulation. Retrovirology. 2021 Nov 10;18(1):36.
• Kinisu M, Choi YJ, Cattoglio C, Liu K, Roux de Bezieux H, Valbuena R, Pum N, Dudoit S, Huang H, Xuan Z, Kim SY, He L. Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes. Cell Rep. 2021 Nov 9;37(6):109982.
• Yu H, Sun Z, Tan T, Pan H, Zhao J, Zhang L, Chen J, Lei A, Zhu Y, Chen L, Xu Y, Liu Y, Chen M, Sheng J, Xu Z, Qian P, Li C, Gao S, Daley GQ, Zhang J. rRNA biogenesis regulates mouse 2C-like state by 3D structure reorganization of peri-nucleolar heterochromatin. Nat Commun. 2021 Nov 9;12(1):6365.
• Andergassen D, Smith ZD, Kretzmer H, Rinn JL, Meissner A. Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages. Dev Cell. 2021 Nov 8;56(21):2995-3005.e4.
• Low Y, Tan DEK, Hu Z, Tan SYX, Tee WW. Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems. Stem Cells Int. 2021 Oct 15;2021:1624669.
• Puri D, Koschorz B, Engist B, Onishi-Seebacher M, Ryan D, Soujanya M, Montavon T. Foxd3 controls heterochromatin-mediated repression of repeat elements and 2-cell state transcription. EMBO Rep. 2021 Dec 6;22(12):e53180.
• Nathalie de Parseval, Hanan Alkabbani & Thierry Heidmann, “The long terminal repeats of the HERV-H human endogenous retrovirus contain binding sites for transcriptional regulation by the Myb protein,” Journal of General Virology 80 (1999): 841–845.
• Patrik Medstrand, Josette-Renée Landry & Dixie L. Mager, “Long Terminal Repeats Are Used as Alternative Promoters for the Endothelin B Receptor and Apolipoprotein C-I Genes in Humans,” Journal of Biological Chemistry 276 (2001): 1896– 1903.
• Anne E. Peaston, Alexei V. Evsikov, Joel H. Graber, Wilhelmine N. de Vries, Andrea E. Holbrook, Davor Solter & Barbara B. Knowles, “Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos,” Developmental Cell 7 (2004): 597–606.
• James A. Shapiro, “Retrotransposons and regulatory suites,” BioEssays 27 (2005): 122–125.
• Jianhua Ling, Wenhu Pi, Roni Bollag, Shan Zeng, Meral Keskintepe, Hatem Saliman, Sanford Krantz, Barry Whitney & Dorothy Tuan, “The Solitary Long Terminal Repeats of ERV-9 Endogenous Retrovirus Are Conserved during Primate Evolution and Possess Enhancer Activities in Embryonic and Hematopoietic Cells,” Journal of Virology 76 (2002): 2410–2423.
• Elena Gogvadze, Elena Stukacheva, Anton Buzdin & Eugene Sverdlov, “HumanSpecific Modulation of Transcriptional Activity Provided by Endogenous Retroviral Insertions,” Journal of Virology 83 (2009): 6098–6105.
• Catherine A. Dunn, Patrik Medstrand & Dixie L. Mager, “An endogenous retroviral long terminal repeat is the dominant promoter for human b1,3-galactosyltransferase 5 in the colon,” Proceedings of the National Academy of Sciences USA 100 (2003): 12841–12846.
• Catherine A. Dunn & Dixie L. Mager, “Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus,” BMC Genomics 6 (2005): 47.
• Anton Buzdin, Elena KovalskayaAlexandrova, Elena Gogvadze & Eugene Sverdlov, “At Least 50% of Human-Specific HERV-K (HML-2) Long Terminal Repeats Serve in Vivo as Active Promoters for Host Nonrepetitive DNA Transcription,” Journal of Virology 80 (2006): 10752– 10762.
• Woo Jung Lee, Hyun Jin Kwun & Kyung Lib Jang, “Analysis of transcriptional regulatory sequences in the human endogenous retrovirus W long terminal repeat,” Journal of General Virology 84 (2003): 2229– 2235. 
• Andrew B. Conley, Jittima Piriyapongsa & I. King Jordan, “Retroviral promoters in the human genome,” Bioinformatics 24 (2008): 1563–1567. 
• Ulrike Schön, Olivia Diem, Laura Leitner, Walter H. Günzburg, Dixie L. Mager, Brian Salmons & Christine Leib-Mösch, “Human Endogenous Retroviral Long Terminal Repeat Sequences as Cell TypeSpecific Promoters in Retroviral Vectors,” Journal of Virology 83 (2009): 12643– 12650. 
• Patrick J. W. Venables, Sharon M. Brookes, David Griffiths, Robin A. Weiss & Mark T. Boyd, “Abundance of an endogenous retroviral envelope protein in placental trophoblasts suggests a biological function.” Virology 211 (1995): 589–592.
• Sha Mi, Xinhua Lee, Xiang-ping Li, Geertruida M. Veldman, Heather Finnerty, Lisa Racie, Edward LaVallie, Xiang-Yang Tang, Philippe Edouard, Steve Howes, James C. Keith Jr. & John M. McCoy, “Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis,” Nature 403 (2000): 785–789.
• Jean-Luc Blond, Dimitri Lavillette, Valérie Cheynet, Olivier Bouton, Guy Oriol, Sylvie Chapel-Fernandes, Bernard Mandrand, François Mallet & FrançoisLoïc Cosset, “An Envelope Glycoprotein of the Human Endogenous Retrovirus HERV-W Is Expressed in the Human Placenta and Fuses Cells Expressing the Type D Mammalian Retrovirus Receptor,” Journal of Virology 74 (2000): 3321–3329.
• Jean-Louis Frendo, Delphine Olivier, Valérie Cheynet, Jean-Luc Blond, Olivier Bouton, Michel Vidaud, Michèle Rabreau, Danièle Evain-Brion & François Mallet, “Direct Involvement of HERV-W Env Glycoprotein in Human Trophoblast Cell Fusion and Differentiation,” Molecular and Cellular Biology 23 (2003): 3566–3574.
• Knerr, B. Huppertz, C. Weigel, J. Dötsch, C. Wich, R. L. Schild, M. W. Beckmann & W. Rascher, “Endogenous retroviral syncytin: compilation of experimental research on syncytin and its possible role in normal and disturbed human placentogenesis,” Molecular Human Reproduction 10 (2004): 581–588.
• Kathrin A. Dunlap, Massimo Palmarini, Mariana Varela, Robert C. Burghardt, Kanako Hayashi, Jennifer L. Farmer & Thomas E. Spencer, “Endogenous retroviruses regulate periimplantation placental growth and differentiation,” Proceedings of the National Academy of Sciences USA 103 (2006): 14390–14395.
• Ina Knerr, Ernst Beinder & Wolfgang Rascher, “Syncytin, a novel human endogenous retroviral gene in human placenta: Evidence for its dysregulation in preeclampsia and HELLP syndrome,” American Journal of Obstetrics and Gynecology 186 (2002): 210–213.
• Joseph M. Antony, Kristofor K. Ellestad, Robert Hammond, Kazunori Imaizumi, Francois Mallet, Kenneth G. Warren & Christopher Power, “The Human Endogenous Retrovirus Envelope Glycoprotein, Syncytin-1, Regulates Neuroinflammation and its Receptor Expression in Multiple Sclerosis: A Role for Endoplasmic Reticulum Chaperones in Astrocytes,” Journal of Immunology 179 (2007): 1210–1224.
• Sandra Blaise, Nathalie de Parseval, Laurence Bénit & Thierry Heidmann, “Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution,” Proceedings of the National Academy of Sciences USA 100 (2003): 13013–13018. 
• Cécile Esnault, Stéphane Priet, David Ribet, Cécile Vernochet, Thomas Bruls, Christian Lavialle, Jean Weissenbach & Thierry Heidmann, “A placenta-specific receptor for the fusogenic, endogenous retrovirus-derived, human syncytin-2,” Proceedings of the National Academy of Sciences USA 105 (2008): 17532–17537. 
• Anne Dupressoir, Geoffroy Marceau, Cécile Vernochet, Laurence Bénit, Colette Kanellopoulos, Vincent Sapin & Thierry Heidmann, “Syncytin-A and syncytin-B, two fusogenic placenta-specific murine envelope genes of retroviral origin conserved in Muridae,” Proceedings of the National Academy of Sciences USA 102 (2005): 725– 730.
• Anne Dupressoir, Cécile Vernochet, Olivia Bawa, Francis Harper, Gérard Pierron, Paule Opolon & Thierry Heidmann, “Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene,” Proceedings of the National Academy of Sciences USA 106 (2009): 12127–12132. 
• Odile Heidmann, Cécile Vernochet, Anne Dupressoir & Thierry Heidmann, “Identification of an endogenous retroviral envelope gene with fusogenic activity and placenta-specific expression in the rabbit: a new ‘syncytin’ in a third order of mammals,” Retrovirology 6 (2009): 107.
• Jonathan P. Stoye, “Proviral protein provides placental function,” Proceedings of the National Academy of Sciences USA 106 (2009): 11827–11828.
• Sarah Prudhomme, Guy Oriol & François Mallet, “A Retroviral Promoter and a Cellular Enhancer Define a Bipartite Element which Controls env ERVWE1 Placental Expression,” Journal of Virology 78 (2004): 12157–12168.
• You-Hong Cheng, Brian D. Richardson, Michael A. Hubert & Stuart Handwerger, “Isolation and Characterization of the Human Syncytin Gene Promoter,” Biology of Reproduction 70 (2004): 694–701.
• François Mallet, Olivier Bouton, Sarah Prudhomme, Valérie Cheynet, Guy Oriol, Bertrand Bonnaud, Gérard Lucotte, Laurent Duret & Bernard Mandrand, “The endogenous retroviral locus ERVWE-1 is a bona fide gene involved in hominoid placental physiology,” Proceedings of the National Academy of Sciences USA 101 (2004): 1731–1736.   
• Bogutz A.B. et al. (2019) Evolution of imprinting via lineage-specific insertion of retroviral promoters. Nature Communications 10: 5674.
• Kigami D., Minami N., Takayama H. and Imai H. (2003) MuERV-L is one of the earliest transcribed genes in mouse one- cell embryos. Biology of Reproduction 68: 651–4.
• Tora L, Vincent SD. What defines the maternal transcriptome? Biochem Soc Trans. 2021 Nov 1;49(5):2051-2062.
• Sexton CE, Tillett RL, Han MV. The essential but enigmatic regulatory role of HERVH in pluripotency. Trends Genet. 2022 Jan;38(1):12-21.
• Sun MA, Wolf G, Wang Y, Senft AD, Ralls S, Jin J, Dunn-Fletcher CE, Muglia LJ, Macfarlan TS. Endogenous Retroviruses Drive Lineage-Specific Regulatory Evolution across Primate and Rodent Placentae. Mol Biol Evol. 2021 Oct 27;38(11):4992-5004.
• Clapes T, Polyzou A, Prater P, Sagar, Morales-Hernández A, Ferrarini MG, Kehrer N, Lefkopoulos S, Bergo V, Hummel B, Obier N, Maticzka D, Bridgeman A, Herman JS, Ilik I, Klaeylé L, Rehwinkel J, McKinney-Freeman S, Backofen R, Akhtar A, Cabezas-Wallscheid N, Sawarkar R, Rebollo R, Grün D, Trompouki E. Chemotherapy-induced transposable elements activate MDA5 to enhance haematopoietic regeneration. Nat Cell Biol. 2021 Jul;23(7):704-717. doi: 10.1038/s41556-021-00707-9.
• Fu B, Ma H, Liu D. Functions and Regulation of Endogenous Retrovirus Elements during Zygotic Genome Activation: Implications for Improving Somatic Cell Nuclear Transfer Efficiency. Biomolecules. 2021 Jun 2;11(6):829.
• Srinivasachar Badarinarayan S, Sauter D. Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections. J Virol. 2021 May 24;95(12):e02299-20.
• Xiang Y, Liang H. The Regulation and Functions of Endogenous Retrovirus in Embryo Development and Stem Cell Differentiation. Stem Cells Int. 2021 Feb 27;2021:6660936.
• Akashita A, Maezawa S, Takahashi K, Alavattam KG, Yukawa M, Hu YC, Kojima S, Parrish NF, Barski A, Pavlicev M, Namekawa SH. Endogenous retroviruses drive species-specific germline transcriptomes in mammals. Nat Struct Mol Biol. 2020 Oct;27(10):967-977.
• Göke J, Ng HH. CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome. EMBO Rep. 2016 Aug;17(8):1131-44.
• Robbez-Masson L, Rowe HM. Retrotransposons shape species-specific embryonic stem cell gene expression. Retrovirology. 2015 May 29;12:45.
• Wang C, Liu X, Gao Y, Yang L, Li C, Liu W, Chen C, Kou X, Zhao Y, Chen J, Wang Y, Le R, Wang H, Duan T, Zhang Y, Gao S. Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat Cell Biol. 2018 May;20(5):620-631.
• Mamillapalli A, Pathak RU, Garapati HS, Mishra RK. Transposable element ‘roo’ attaches to nuclear matrix of the Drosophila melanogaster. J Insect Sci. 2013;13:111.
• Harding EF, Russo AG, Yan GJH, Waters PD, White PA. Ancient viral integrations in marsupials: a potential antiviral defence. Virus Evol. 2021 Sep 2;7(2):veab076. doi: 10.1093/ve/veab076. PMID: 34548931; PMCID: PMC8449507.
• Yang F, Su W, Chung OW, Tracy L, Wang L, Ramsden DA, Zhang ZZZ. Retrotransposons hijack alt-EJ for DNA replication and eccDNA biogenesis. Nature. 2023 Aug;620(7972):218-225.

9. lncRNAs

• Johnsson P, Ziegenhain C, Hartmanis L, Hendriks GJ, Hagemann-Jensen M, Reinius B, Sandberg R. Transcriptional kinetics and molecular functions of long noncoding RNAs. Nat Genet. 2022 Mar;54(3):306-317.
• Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL, Speck-Martins CE, Carvalho DR, Farage L, Lourenço CM, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson MI, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Pescini-Gobert R, Unger S, Bonafé L, Grote P, Rivolta C, Mundlos S, Superti-Furga A. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature. 2021 Apr;592(7852):93-98.
• Wei W, Zhao Q, Wang Z, Liau WS, Basic D, Ren H, Marshall PR, Zajaczkowski EL, Leighton LJ, Madugalle SU, Musgrove M, Periyakaruppiah A, Shi J, Zhang J, Mattick JS, Mercer TR, Spitale RC, Li X, Bredy TW. ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3. Cell Rep. 2022 Mar 22;38(12):110546.
• Jasmina Ponjavic, Chris P. Ponting & Gerton Lunter, “Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs,” Genome Research 17 (2007): 556–565.
• Mitchell Guttman, Ido Amit, Manuel Garber, Courtney French, Michael F. Lin, David Feldser, Maite Huarte, Or Zuk, Bryce W. Carey, John P. Cassady, Moran N. Cabili, Rudolf Jaenisch, Tarjei S. Mikkelsen, Tyler Jacks, Nir Hacohen, Bradley E. Bernstein, Manolis Kellis, Aviv Regev, John L. Rinn & Eric S. Lander, “Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals,” Nature 458 (2009): 223–227.
• Moleirinho, Ana, Susana Seixas, Alexandra M Lopes, Celeste Bento, Maria J Prata, and António Amorim. 2013. Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation. Genome Biology and Evolution 5 (3): 559-571. DOI:10.1093/gbe/evt029.
• Tim R. Mercer, Marcel E. Dinger, Susan M. Sunkin, Mark F. Mehler & John S. Mattick, “Specific expression of long noncoding RNAs in the mouse brain,” Proceedings of the National Academy of Sciences USA 105 (2008): 716–721.
• Kovalenko, T.F. and L.I. Patrushev. 2018. Pseudogenes as Functionally Significant Elements of the Genome. Biochemistry (Moscow) 83(11): 1332-1349. DOI:10.1134/S0006297918110044.
• Cheetham, Seth W., Geoffrey J. Faulkner, and Marcel E. Dinger. 2020. Overcoming challenges and dogmas to understand the functions of pseudogenes. Nature Reviews Genetics 21: 191-201. https://doi.org/10.1038/s41576-019-0196-1.
• Troskie, Robin-Lee, Geoffrey J. Faulkner, and Seth W. Cheetham. 2021. Processed pseudogenes: A substrate for evolutionary innovation. BioEssays 43 (11): 2100186. https://doi.org/10.1002/bies.202100186.
• Archa H. Fox, Yun Wah Lam, Anthony K. L. Leung, Carol E. Lyon, Jens Andersen, Matthias Mann & Angus I. Lamond, “Paraspeckles: a novel nuclear domain,” Current Biology 12 (2002): 13–25.
• Charles S. Bond & Archa H. Fox, “Paraspeckles: nuclear bodies built on long noncoding RNA,” Journal of Cell Biology 186 (2009): 637–644.
• Pink, Ryan Charles, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Raul Francisco Carter. 2011. Pseudogenes: Pseudo-functional or key regulators in health and disease? RNA 17: 792-798. DOI:10.1261/rna.2658311.
• Daniel P. Caley, Ryan C. Pink, Daniel Trujillano & David R. F. Carter, “Long noncoding RNAs, chromatin, and development,” ScientificWorldJournal 10 (2010): 90–102.
• Archa H. Fox & Angus I. Lamond, “Paraspeckles,” Cold Spring Harbor Perspectives in Biology 2 (2010): a000687.
• Christine M. Clemson, John N. Hutchinson, Sergio A. Sara, Alexander W. Ensminger, Archa H. Fox, Andrew Chess & Jeanne B. Lawrence, “An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles,” Molecular Cell 33 (2009): 717–726.
• Yasnory T. F. Sasaki, Takashi Ideue, Miho Sano, Toutai Mituyama & Tetsuro Hirose, “MENe/b noncoding RNAs are essential for structural integrity of nuclear paraspeckles,” Proceedings of the National Academy of Sciences USA 106 (2009): 2525–2530.
• Yasnory T. F. Sasaki & Tetsuro Hirose, “How to build a paraspeckle,” Genome Biology 10 (2009): 227.
• Sylvie Souquere, Guillaume Beauclair, Francis Harper, Archa Fox & Gérard Pierron, “Highly-ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies,” Molecular Biology of the Cell (September 2010). 
• Marcel E. Dinger, Paulo P. Amaral, Timothy R. Mercer & John S. Mattick, “Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications,” Briefings in Functional Genomics and Proteomics 8 (2009): 407–423.
• Jeremy E. Wilusz, Hongjae Sunwoo & David L. Spector, “Long noncoding RNAs: functional surprises from the RNA world,” Genes & Development 23 (2009): 1494–1504.
• Jeannie T. Lee, “Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome,” Genes & Development 23 (2009): 1831–1842.
• Park EG, Ha H, Lee DH, Kim WR, Lee YJ, Bae WH, Kim HS. Genomic Analyses of Non-Coding RNAs Overlapping Transposable Elements and Its Implication to Human Diseases. Int J Mol Sci. 2022 Aug 11;23(16):8950.
• John S. Mattick, Paulo P. Amaral, Piero Carninci, Susan Carpenter, Howard Y. Chang, Ling-Ling Chen, Runsheng Chen, Caroline Dean, Marcel E. Dinger, Katherine A. Fitzgerald, Thomas R. Gingeras, Mitchell Guttman, Tetsuro Hirose, Maite Huarte, Rory Johnson, Chandrasekhar Kanduri, Philipp Kapranov, Jeanne B. Lawrence, Jeannie T. Lee, Joshua T. Mendell, Timothy R. Mercer, Kathryn J. Moore, Shinichi Nakagawa, John L. Rinn, David L. Spector, Igor Ulitsky, Yue Wan, Jeremy E. Wilusz, and Mian Wu, “Long non-coding RNAs: definitions, functions, challenges and recommendations,” Nature Reviews Molecular Cell Biology, 24: 430-447 (June, 2023).
• Liu S, Huang J, Zhou J, Chen S, Zheng W, Liu C, Lin Q, Zhang P, Wu D, He S, Ye J, Liu S, Zhou K, Li B, Qu L, Yang J. NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions. Nat Commun. 2024 Mar 18;15(1):2425.
• John L. Rinn, Michael Kertesz, Jordon K. Wang, Sharon L. Squazzo, Xiao Xu, Samantha A. Brugmann, Henry Goodnough, Jill A. Helms, Peggy J. Farnham, Eran Segal & Howard Y. Chang, “Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs,” Cell 129 (2007): 1311–1323.
• Miao-Chih Tsai, Ohad Manor, Yue Wan, Nima Mosammaparast, Jordon K. Wang, Fei Lan, Yang Shi, Eran Segal & Howard Y. Chang, “Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes,” Science 329 (2010): 689–693.
• Hezroni H. et al. (2015) Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Reports 11: 1110–22.
• Kelley D. and Rinn J. (2012) Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biology 13: R107.
• Yin Y, Lu JY, Zhang X, Shao W, Xu Y, Li P, Hong Y, Cui L, Shan G, Tian B, Zhang QC, Shen X. U1 snRNP regulates chromatin retention of noncoding RNAs. Nature. 2020 Apr;580(7801):147-150.
• Booy EP, McRae EK, Ezzati P, Choi T, Gussakovsky D, McKenna SA. Comprehensive analysis of the BC200 ribonucleoprotein reveals a reciprocal regulatory function with CSDE1/UNR. Nucleic Acids Res. 2018 Nov 30;46(21):11575-11591.
• Awan HM, Shah A, Rashid F, Shan G. Primate-specific Long Non-coding RNAs and MicroRNAs. Genomics Proteomics Bioinformatics. 2017 Jun;15(3):187-195.
• Kelley D, Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol. 2012 Nov 26;13(11):R107.
• Bortolin-Cavaillé ML, Dance M, Weber M, Cavaillé J. C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts. Nucleic Acids Res. 2009 Jun;37(10):3464-73. [Alu associated]
• Khanam T, Rozhdestvensky TS, Bundman M, Galiveti CR, Handel S, Sukonina V, Jordan U, Brosius J, Skryabin BV. Two primate-specific small non-protein-coding RNAs in transgenic mice: neuronal expression, subcellular localization and binding partners. Nucleic Acids Res. 2007;35(2):529-39. [Alu associated]
• Nickerson JA. The ribonucleoprotein network of the nucleus: a historical perspective. Curr Opin Genet Dev. 2022 Aug;75:101940.
• Trigiante G, Blanes Ruiz N, Cerase A. Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression. Front Cell Dev Biol. 2021 Oct 6;9:735527.
• Booy EP, Gussakovsky D, Choi T, McKenna SA. The noncoding RNA BC200 associates with polysomes to positively regulate mRNA translation in tumor cells. J Biol Chem. 2021 Jan-Jun;296:100036.
• Nguyen TM, Kabotyanski EB, Reineke LC, Shao J, Xiong F, Lee JH, Dubrulle J, Johnson H, Stossi F, Tsoi PS, Choi KJ, Ellis AG, Zhao N, Cao J, Adewunmi O, Ferreon JC, Ferreon ACM, Neilson JR, Mancini MA, Chen X, Kim J, Ma L, Li W, Rosen JM. The SINEB1 element in the long non-coding RNA Malat1 is necessary for TDP-43 proteostasis. Nucleic Acids Res. 2020 Mar 18;48(5):2621-2642.

10. MicroRNAs

• Eugene V. Makeyev & Tom Maniatis, “Multilevel Regulation of Gene Expression by MicroRNAs,” Science 319 (2008): 1789–1790
• Mustafin RN, Khusnutdinova E. Perspective for Studying the Relationship of miRNAs with Transposable Elements. Curr Issues Mol Biol. 2023 Apr 5;45(4):3122-3145.

11. Large-Scale Transcription

• The ENCODE Project Consortium, “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project,” Nature, Vol. 447:799-816 (June 14, 2007).
• ENCODE Project Consortium. 2012. An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature 489: 57-74. https://doi.org/10.1038/nature11247.
• Stefano Gustincich, Albin Sandelin, Charles Plessy, Shintaro Katayama, Roberto Simone, Dejan Lazarevic, Yoshihide Hayashizaki & Piero Carninci, “The complexity of the mammalian transcriptome,” Journal of Physiology 575:2 (2006): 321–332.
• Philipp Kapranov, Aarron T. Willingham & Thomas R. Gingeras, “Genomewide transcription and the implications for genomic organization,” Nature Reviews Genetics 8 (2007): 413–423.
• Piero Carninci, “Constructing the landscape of the mammalian transcriptome,” Journal of Experimental Biology 210 (2007): 1497–1506.
• Jia Qian Wu, Jiang Du, Joel Rozowsky, Zhengdong Zhang, Alexander E. Urban,Ghia Euskirchen, ShermanWeissman, Mark Gerstein & Michael Snyder, “Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome,” Genome Biology 9:1 (2008): R3.
• Luis M. Mendes Soares & Juan Valcárcel, “The expanding transcriptome: the genome as the ‘Book of Sand,’” EMBO Journal 25 (2006): 923–931.
• Paulo P. Amaral, Marcel E. Dinger, Tim R. Mercer & John S. Mattick, “The Eukaryotic Genome as an RNA Machine,” Science 319 (2008): 1787–1789.
• Luis M. Mendes Soares & Juan Valcárcel, “The expanding transcriptome: the genome as the ‘Book of Sand,’” EMBO Journal 25 (2006): 923–931.
• Rebuzzini P, Zuccotti M, Garagna S. Building Pluripotency Identity in the Early Embryo and Derived Stem Cells. Cells. 2021 Aug 10;10(8):2049.

12. Transposable Elements and 3D Genome Hierarchy

• Gunsalus LM, Keiser MJ, Pollard KS. In silico discovery of repetitive elements as key sequence determinants of 3D genome folding. Cell Genom. 2023 Sep 25;3(10):100410.
• Li Y, Fan H, Qin W, Wang Y, Chen S, Bao W, Sun MA. Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen. Comput Struct Biotechnol J. 2023 Sep 25;21:4580-4588.
• Choudhary MNK, Quaid K, Xing X, Schmidt H, Wang T. Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes. Nat Commun. 2023 Feb 6;14(1):634.
• Haws SA, Simandi Z, Barnett RJ, Phillips-Cremins JE. 3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome. Cell. 2022 Jul 21;185(15):2690-2707.

13. Other / General Function for “Junk” / Non-Coding DNA

• Gates, Alexander J., Deisy Morselli Gysi, Manolis Kellis, and Albert-László Barabási. 2022. A wealth of discovery built on the Human Genome Project — by the numbers. Nature 590: 212-215. https://doi.org/10.1038/d41586-021-00314-6.
• J. S. Mattick, “Non-coding RNAs: the architects of eukaryotic complexity,” European Molecular Biology Organization (EMBO) Reports, Vol. 2(11):986-991 (2001).
• Okazaki et al., “Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs,” Nature 420 (2002): 563-573.
• Philipp Kapranov, Simon E. Cawley, Jorg Drenkow, Stefan Bekiranov, Robert L. Strausberg, Stephen P. A. Fodor & Thomas R. Gingeras, “Large-Scale Transcriptional Activity in Chromosomes 21 and 22,” Science 296 (2002): 916–919.
• P. Carninci et al., “The Transcriptional Landscape of the Mammalian Genome,” Science 309 (2005): 1559–1563.
• Michael Pheasant & John S. Mattick, “Raising the estimate of functional human sequences,” Genome Research 17 (2007): 1245–1253.
• Ewan Birney et al. “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project,” Nature 447 (2007): 799–816.
• Maciej Szymanski, Miroslawa Z. Barciszewska, Marek Zywicki & Jan Barciszewski, “Noncoding RNA transcripts,” Journal of Applied Genetics 44 (2003): 1–19.
• John S. Mattick & Igor V. Makunin, “Non-coding RNA,” Human Molecular Genetics 15 (2006): R17-R29.
• John L. Rinn, Michael Kertesz, Jordon K. Wang, Sharon L. Squazzo, Xiao Xu, Samantha A. Brugmann, Henry Goodnough, Jill A. Helms, Peggy J. Farnham, Eran Segal & Howard Y. Chang, “Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Non-Coding RNAs,” Cell 129 (2007): 1311–1323. 
• Gennadi V. Glinsky, “Phenotype-defining functions of multiple non-coding RNA pathways,” Cell Cycle 7 (2008): 1630–1639.
• Johannes H. Urban & Jörg Vogel, “Two Seemingly Homologous Noncoding RNAs Act Hierarchically to Activate glmS mRNA Translation,” PLoS Biology 6:3 (2008): e64.
• Piero Carninci, Jun Yasuda & Yoshihide Hayashizaki,“Multifaceted mammalian transcriptome,” Current Opinion in Cell Biology 20 (2008): 274–280.
• Hayashi, H. et al. 2015. The OCT4 pseudogene POU5F1B is amplified and promotes an aggressive phenotype in gastric cancer. Oncogene 34: 199-208. DOI:10.1038/onc.2013.547.
• Rapicavoli, Nicole A, Kun Qu, Jiajing Zhang, Megan Mikhail, Remi-Martin Laberge, Howard Y Chang. 2013. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. eLife 2: e00762. DOI:10.7554/eLife.00762.
• Tam, Oliver H. et al. 2008. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453: 534-538. https://doi.org/10.1038/nature06904.
• Muro, Enrique M., Nancy Mah, and Miguel A. Andrade-Navarro. 2011. Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie 93: 1916-1921. DOI:10.1016/j.biochi.2011.07.024.
• Kim, Min-Sik et al. 2014. A Draft Map of the Human Proteome. Nature 509: 575-581. https://doi.org/10.1038/nature13302.
• Ji, Zhe, Ruisheng Song, Aviv Regev, and Kevin Struhl. 2015. Many lncRNAs, 5’UTRs, and Pseudogenes Are Translated and Some Are Likely to Express Functional Proteins. eLife 4: e08890.https://doi.org/10.7554/eLife.08890.
• Vittorio Sartorelli and Shannon M. Lauberth, “Enhancer RNAs are an important regulatory layer of the epigenome,” Nature Structural & Molecular Biology, 27: 521–528 (2020).
• Tam PLF, Leung D. The Molecular Impacts of Retrotransposons in Development and Diseases. Int J Mol Sci. 2023 Nov 16;24(22):16418.
• DiRusso JA, Clark AT. Transposable elements in early human embryo development and embryo models. Curr Opin Genet Dev. 2023 Aug;81:102086.
• Stamidis N, Żylicz JJ. RNA-mediated heterochromatin formation at repetitive elements in mammals. EMBO J. 2023 Apr 17;42(8):e111717.
• Pontis J, Pulver C, Playfoot CJ, Planet E, Grun D, Offner S, Duc J, Manfrin A, Lutolf MP, Trono D. Primate-specific transposable elements shape transcriptional networks during human development. Nat Commun. 2022 Nov 23;13(1):7178.
• Patoori S, Barnada SM, Large C, Murray JI, Trizzino M. Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors. Development. 2022 Oct 1;149(19):dev200413. doi: 10.1242/dev.200413.
• Modzelewski AJ, Gan Chong J, Wang T, He L. Mammalian genome innovation through transposon domestication. Nat Cell Biol. 2022 Sep;24(9):1332-1340.
• Lee HJ, Hou Y, Maeng JH, Shah NM, Chen Y, Lawson HA, Yang H, Yue F, Wang T. Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. Genome Res. 2022 Jul;32(7):1424-1436.
• Chesnokova E, Beletskiy A, Kolosov P. The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology. Int J Mol Sci. 2022 May 23;23(10):5847.
• Fueyo R, Judd J, Feschotte C, Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nat Rev Mol Cell Biol. 2022 Jul;23(7):481-497.
• Playfoot CJ, Duc J, Sheppard S, Dind S, Coudray A, Planet E, Trono D. Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain. Genome Res. 2021 Sep;31(9):1531-1545.
• Babarinde IA, Ma G, Li Y, Deng B, Luo Z, Liu H, Abdul MM, Ward C, Chen M, Fu X, Shi L, Duttlinger M, He J, Sun L, Li W, Zhuang Q, Tong G, Frampton J, Cazier JB, Chen J, Jauch R, Esteban MA, Hutchins AP. Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells. Nucleic Acids Res. 2021 Sep 20;49(16):9132-9153. 
• Emile Zuckerkandl, “Junk DNA and sectorial gene repression,” Gene 205 (1997): 323–343.
• Emile Zuckerkandl, “Why so many noncoding nucleotides? The eukaryote genome as an epigenetic machine,” Genetica 115 (2002): 105–129.
• Emile Zuckerkandl & Giacomo Cavalli, “Combinatorial epigenetics, ‘junk DNA’, and the evolution of complex organisms,” Gene 390 (2007): 232–242.
• Stephen C. J. Parker, Loren Hansen, Hatice Ozel Abaan, Thomas D. Tullius & Elliott H. Margulies, “Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome,” Science 324 (2009): 389–392.
• Antonio Rodríguez-Campos & Fernando Azorín, “RNA Is an Integral Component of Chromatin that Contributes to Its Structural Organization,” PLoS One 2:11 (2007): e1182.
• Irina Solovei, Moritz Kreysing, Christian Lanctôt, Süleyman Kösem, Leo Peichl, Thomas Cremer, Jochen Guck & Boris Joffe, “Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution,” Cell 137 (2009): 356–368.
• Caroline Kizilyaprak, Danièle Spehner, Didier Devys & Patrick Schultz, “In Vivo Chromatin Organization of Mouse Rod Photoreceptors Correlates with Histone Modifications,” PLoS One 5:6 (2010): e11039.
• Moritz Kreysing, Lars Boyde, Jochen Guck & Kevin J. Chalut, “Physical insight into light scattering by photoreceptor cell nuclei,” Optics Letters 35 (2010): 2639–2641.