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Seeing the Nucleus in 4-D


We know about genes and genomes, and how over six feet of DNA is crammed into a tiny nucleus within a cell. Decades of detailed research have given us the static, 3-D view of the nucleus. What’s new is the frenetic activity going on inside the nucleus as chromosomes move into position and genes switch on and off. The addition of the time dimension is turning our snapshots of the genome into a movie, and it’s a blockbuster.

Two groundbreaking papers in Cell explain how Caltech scientists have peered into the moment-by-moment transcription of genes, watching portions of the genome light up as they become active. What they are finding reveals new levels of design. Who could think of chance after seeing what these scientists witnessed? 

Nuclear Organization

The first paper by Quinodoz et al., “Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus,” reports on work done in the lab of Mitchell Guttman. The results are summarized in the news from Caltech, “The Cartography of the Nucleus.” Notice the design implications in the opening sentences:

Nestled deep in each of your cells is what seems like a magic trick: Six feet of DNA is packaged into a tiny space 50 times smaller than the width of a human hair. Like a long, thin string of genetic spaghetti, this DNA blueprint for your whole body is folded, twisted, and compacted to fit into the nucleus of each cell.

Now, Caltech researchers have shown how cells organize the seemingly immense genome in a clever manner so that they can conveniently find and access important genes.

Nuclear bodies are regions where genes associate with the protein machines that will transcribe and edit them. Next to a rotating 3-D image of chromosomes associating with the nucleolus and other nuclear bodies, the news item describes how the team developed a new imaging tool called SPRITE to watch how genes switch on differently in different types of cells.

Though the vast majority of cells in every human body contain identical genomes, different types of cells are able to have diverse functions because genes can be expressed at varying levels — in other words, they can be turned on or off. For example, when a stem cell is developing into a neuron, a flurry of activity happens in the nucleus to dial up and down levels of gene expression. These levels would be different, for example, if the stem cell was turning into a muscle cell or if the cell were making the decision to self-destruct.

Next we learn about nuclear bodies. Notice the machine language and the efficiency: this is rapid, precision work!

In addition to the genome, the nucleus also contains structures called nuclear bodies, which are like miniature factories in the nucleus that contain a high concentration of cellular machinery all working to accomplish similar tasks, such as turning on specific sets of genes or modifying RNA molecules to produce proteins in the cell. This cellular machinery needs to be able to efficiently search through six feet of DNA — approximately 20,000 total genes, in mammals — in order to precisely find and control its targets. This is made possible because DNA is organized into three-dimensional structures that make certain genes more or less accessible.

Figures in the paper show a high degree of organization, indeed. SPRITE places barcode tags on genes that allow scientists to follow chromosome strands as they organize around nuclear bodies. Some nuclear bodies, called nuclear speckles, are where genomic DNA is organized, and where RNA Polymerase II, spliceosomes and lncRNAs transcribe and edit them. Inactive parts of the chromosome associate with the nucleolus, which contains repressive proteins on DNA that keep genes turned off. “Moreover,” they say, “our results suggest that multiple actively transcribed DNA regions can arrange simultaneously around nuclear speckles to form higher-order inter-chromosomal interactions. 

Together, these results suggest an integrated and global picture of genome organization where individual genomic regions across chromosomes organize around nuclear bodies to shape the overall packaging of genomic DNA in a highly regulated and dynamic manner (Figure 7).

Quinodoz explains what is significant about this advancement:

“With SPRITE, we were able to see thousands of molecules — DNAs and RNAs — coming together at various ‘hubs’ around the nucleus in single cells,” says Quinodoz, the study’s first author. “Previously, researchers theorized that each chromosome is kind of on its own, occupying its own ‘territory’ in the nucleus. But now we see that multiple genes on different chromosomes are clustering together around these bodies of cellular machinery. We think these ‘hubs’ may help the cell keep DNA that are all turned on or turned off neatly organized in different parts of the nucleus to allow cellular machinery to easily access specific genes within the nucleus.”

Nuclear Dynamics

The second paper, by Shah et al., is summarized in this from Caltech, “Ten Thousand Bursting Genes.” This team improved on an existing imaging tool called seqFISH that allowed them to watch not just four or five genes, as before, but 10,421 genes at once within individual cells by tagging them with fluorescent barcodes. The news item shows thousands of colored dots in a map of the nucleus where nascent transcription was seen to be occurring. 

Previous methods followed the messenger RNAs, which have a longer lifetime. By following short-lived introns in the genes with their tags, this team found a purpose behind those mysterious non-coding regions:

In order for genetic instructions to be turned into an actual functioning protein, a process called transcription must first occur. This process often occurs in pulses, or “bursts.” First, a gene will be read and copied into a precursor messenger RNA, or pre-mRNA, like jotting a quick, rough draft. This molecule then matures into a messenger RNA, or mRNA, akin to editing the rough draft. During the “editing” process, certain regions called introns are cut out of the pre-mRNA.

The team chose to focus on labeling introns because they are produced so early in the transcription process, giving a picture of what a cell is doing at the precise moment of gene expression.

Following the introns led to a discovery that 

the transcription of genes oscillates globally across many genes on what Cai calls a “surprisingly short” timescale — only about two hours — compared to the time it takes for a cell to divide and replicate itself, which takes from 12 to 24 hours. This means that over the course of a two-hour period, many genes within a cell will burst on and off.

It was like watching a miniature fireworks show in color. The tags reveal what the “nascent transcriptome” is doing, providing more dynamical resolution of nuclear activity. With this improved seqFISH tagging technique, scientists will be able to watch how transcription activity differs between different types of cells. 

The team also learned things about nuclear organization. They were “surprised to discover that most active, protein-encoding genes are located on the surface of the chromosome, not buried inside of it.” Additionally, “Transcriptionally active loci are positioned at the surface of chromosome territories.” This is not “spaghetti code” inside a basketball! (“Spaghetti code” was a term of derision for computer programs tangled up with “go-to” signals all over the place, making it hard to follow. Today’s modular programming is better organized. The cell had it first!)

The work by Shah et al. could lead to other exciting discoveries. In conclusion, they look ahead:

Using pulsatile and oscillatory dynamics, cells can achieve states not accessible with amplitude-based regulation schemes (Letsou and Cai, 2016). For example, cells can use fluctuations in global transcriptional activity to coordinate the stoichiometry of many transcripts in a mechanisms [sic] akin to the frequency-modulated signaling observed in yeast and mammalian pathways (Cai et al., 2008; Yissachar et al., 2013). 

Finally, an exciting recent work showed that intron-to-exon ratios across the transcriptome can be used to determine the direction of of [sic] cells on the developmental trajectory (La Manno et al., 2017). As we showed, the nascent transcriptome profiles can not only distinguish cell types and cell states, but also detect fast dynamics in single cells. Applications of intron seqFISH with signal amplification (Shah et al., 2016a), along with mRNA seq- FISH (Shah et al., 2016b, Lignell et al., 2017), can enable simultaneous profiling of nascent and mature RNAs in tissues, with spatial information preserved. It will be fascinating to explore the nascent transcriptome in single cells in many tissue settings and developmental contexts.

In short, cells could take advantage of the observed two-hour oscillation for additional levels of coordination and regulation. They can use it like signals superimposed on an FM radio carrier wave!


The really exciting work in genetics is being done with an eye to design. These researchers did not need to explicitly endorse intelligent design to show why this is the case. The message of design comes through loud and clear in the questions they ask, and in the findings that result. The absence of evolutionary speculation improves the signal-to-noise ratio.

Image credit: TheDigitalArtist, via Pixabay.

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3-D4-DCaltechcartographycellchromosomeDNAgenesgenomesimaging toolMitchell Guttmannuclear bodiesnucleusRNAseqFISHSPRITEstoichiometrytranscription