How is it that the human genome, with about 23,000 protein coding genes, can produce such a complicated organism as the human being, when the laboratory flatworm (C. elegans, a relatively simple organism) has about 20,000 coding genes? It seems fairly obvious that there must be something else at work in more complex organisms that vastly augments the basic genes. Probing that inference has led to a massive expansion of what is loosely called epigenetics, which these days seems headed in the direction of covering everything that transcribes, translates, regulates, and implements the genetic code.
Recently, in work discussed in the June 24, 2010 issue of the journal Nature some possibly major new pieces were added to the epigenetics puzzle. (I call it a puzzle, because though molecular biologists have done a great deal of research in various aspects, it seems the overall picture remains subject to uncertainty and frequent redefinition.) This research, performed by a consortium of institutions led by the Beth Israel Deaconess Medical Center of Harvard Medical School (USA), focused on the role of RNA in the expression of specific genes and their pseudogenes that are related to cancer.
Pseudogenes, as the name seems to imply, are segments of the genome that look like genes but have no known function, that is, they don’t code for protein. It’s thought that most pseudogenes are relics from once active genes but now comprise part of the so called ‘junk DNA’ of the human genome. One pair of genes/pseudogenes the research studied is called the PTEN (gene) and PTENP1 (pseudogene). The gene PTEN is known to have an important role in tumor suppression. Its ability to do this is regulated by a form of RNA known as microRNA, which binds to the messenger RNA (mRNA) that carries the DNA code for specific proteins to the locations in the cell where the protein is manufactured. When mRNA binds to microRNA, the mRNA is ‘turned off’ – no longer able to carry out its function.
It has long been thought that microRNA is the active party, with levels of microRNA corresponding to suppression of mRNA activity. The researchers thought otherwise, that in fact, RNA might be what regulates the levels of microRNA. To demonstrate this they experimented with the PTEN gene, showing that its production of microRNA was related to the activity of the PTENP1 pseudogene. In effect, the pseudogene competed with the ‘real’ gene to bind with its microRNA, thus reducing the suppression of the PTEN gene. What seemed to be involved was the active participation of PTENP1 produced RNA in ‘sequestering’ microRNA, what the researchers called competitive endogenous RNA (ceRNA).
This was an important finding: It shows that RNA does more than carry the DNA code for proteins. It has another mode, a complex chemically interactive mode that regulates the function of microRNA and through it the expression of genes. It also showed rather conclusively that at least some pseudogenes are active biologically.
Further experiments with mice involving the development of cancerous tumors showed that even 20% changes in the activity of PTEN or PTENP1 had demonstrable effect on the probability of tumors. This linkage indicates that the relationships between gene, pseudogene, and RNA can be highly significant in the development of cancer and probably other diseases.
“Because this new function does not depend on the blueprint that RNAs harbor in their protein-encoding nucleotide sequence, the discovery additionally holds true for the thousands of noncoding RNA molecules in the cell,” explains senior author Pier Paolo Pandolfi, MD, PhD, Director of Research at the BIDMC Cancer Center and George C. Reisman Professor of Medicine at Harvard Medical School.”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.”
There is a strong ‘tip of the iceberg’ vibe to this research. Phrases are thrown around such as “We now understand how these RNA units talk with one another” like this was the discovery of a new mode for RNA behavior…which in a way, it may be. The paper itself makes modest claims; it sticks to the experiments at hand that involve the PTEN and PTENP1 gene/pseudogene and other combinations, and points out that the ability to predict outcomes from increase or decrease in the activity of either has impact on the occurrence of cancer (and possibly other diseases). This alone should push pseudogenes into the general forum of molecular biology research and discussion.
As I mentioned at the beginning, one of the motivations for doing epigenetic research is to answer the question ‘How can so few genes produce a human being?’ Adding the activity of pseudogenes and a previously unknown functionality to RNA to the mix increases the scope of epigenetics considerably. It will take many years and a lot more research to verify these results and extend their implications, but it continues the trend of discovery that the interface between the genetic code of DNA and the ‘real world’ of living cells is a very complex epigenetic system.