“Junk DNA” Takes Yet More Heavy Blows

Jonathan McLatchie

A paper has just been published in Nature which uncovers a host of new coding-independent functions for pseudogene mRNAs, including a role in tumor regulation. More exciting is that Poliseno et al. describe an entirely new regulatory function of RNA. This stands in contrast to conventional wisdom which maintains that the only function of mRNAs is encoding for proteins.

According to the abstract,

The canonical role of messenger RNA (mRNA) is to deliver protein-coding information to sites of protein synthesis. However, given that microRNAs bind to RNAs, we hypothesized that RNAs could possess a regulatory role that relies on their ability to compete for microRNA binding, independently of their protein-coding function. As a model for the protein-coding-independent role of RNAs, we describe the functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene PTENP1 and the critical consequences of this interaction. We find that PTENP1 is biologically active as it can regulate cellular levels of PTEN and exert a growth-suppressive role. We also show that the PTENP1 locus is selectively lost in human cancer. We extended our analysis to other cancer-related genes that possess pseudogenes, such as oncogenic KRAS. We also demonstrate that the transcripts of protein-coding genes such as PTEN are biologically active. These findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs.

The authors discuss the observed interaction between the RNA encoding for the PTEN tumor suppressor gene and its corresponding pseudogene, PTENP1, demonstrating that this pseudogene acts as a tumor suppressor. A function was also assigned for the KRAS oncogene and the corresponding pseudogene, KRAS1P. As the authors explain,

We also demonstrate that pseudogenes such as PTENP1 can derepress their cognate genes, even when expressed at lower levels (Supplementary Fig. 3a and Fig. 2f–h). We propose that pseudogenes are “perfect decoys” for their ancestral genes, because they retain many of the miRNA binding sites and can compete for the binding of many miRNAs at once.

MicroRNAs are small units of RNA that can repress the expression of protein-coding genes by preventing translation of the target RNA. According to a related article on PhysOrg.com,

“Although it is conventional knowledge that microRNA can block mRNA function, we suspected that the roles of microRNA and mRNA were actually flipped,” explains Pandolfi. “In other words, instead of microRNA binding to mRNA, we thought that RNAs were actually sequestering the microRNAs, thereby protecting mRNA and rendering the microRNAs ineffective on their other targets.”

This new discovered activity of RNA is dubbed “competitive endogenous RNA” (ceRNAs).

Perhaps the most startling announcement of all is, as observed by Pier Paolo Pandolfi and George C. Reisman in an interview for Physorg.com,

This means that not only have we discovered a new language for mRNA, but we have also translated the previously unknown language of up to 17,000 pseudogenes and at least 10,000 long non-coding (lnc) RNAs. Consequently, we now know the function of an estimated 30,000 new entities, offering a novel dimension by which cellular and tumor biology can be regulated, and effectively doubling the size of the functional genome.

A News & Views page in Nature summarized the key research and findings of the paper as follows:

1. Poliseno et al. investigated the relationship between the tumour-suppressor gene PTEN and its pseudogene PTENP1.
2. They found that RNA transcripts of both have closely related 3′ untranslated regions (3′ UTRs) to which the same set of regulatory microRNA (miRNA) sequences bind.
3. By binding to miRNAs, PTENP1 transcripts reduce downregulation of PTEN messenger RNA, allowing its translation to the tumour-suppressor protein PTEN.
4. Similarly, PTEN mRNA acts as a decoy for miRNA that would otherwise downregulate PTENP1 transcripts. This hints at a regulatory role for mRNA besides their protein-coding function.
5. Cancer-related genomic mutations affect PTENP1 independently of PTEN.
6. The authors show that similar relationships exist between other cancer-related genes and their pseudogenes.

The News & Views page explains:

PTENP1 is a pseudogene: a non-synonymous mutation at the beginning of what would otherwise be the coding region of its transcript prevents its translation. But Poliseno et al. reveal that PTENP1 — along with KRAS1P, the pseudogene of the gene KRAS, and potentially other pseudogenes — is not a non-functional relic, but a modulator of gene expression.

This is profound stuff. Not only have we succeeded in effectively doubling the size of the known functional genome virtually overnight, but we have also discovered a new “RNA language.” How will Moran, Matheson, Prothero, and other believers in “junk DNA” respond to this?