Junk DNA: goodbye!: Review article (Introduction)

by David Turell , Tuesday, March 31, 2015, 15:09 (3313 days ago) @ David Turell

Another review article of the latest findings:-http://www.evolutionnews.org/2015/03/these_sequences094801.html-"A "News & Views" piece in Nature, "Coding in non-coding RNAs," states: "The discovery of peptides encoded by what were thought to be non-coding -- or 'junk' -- regions of precursors to microRNA sequences reveals a new layer of gene regulation. These sequences may not be junk, after all." It then describes a new study just published in Nature which finds that precursors of microRNAs can in fact encode proteins. The news article tells a familiar story: Evolutionary biologist meets new type of DNA. Evolutionary biologist doesn't know what DNA does. Evolutionary biologists assumes DNA is junk and ignores it. Molecular biologist comes along, doesn't think about evolution, and finds out DNA isn't junk and does something important. Here's how the Nature piece puts it:-"In the 1970s, as it started to become clear that the genomic regions that encode proteins (the genes) swim in a sea of non-protein- coding sequences, the idea of meaningless, or 'junk', DNA became a hot topic of discussion. Biologists are now well aware of introns, the sequences within genes that separate the coding regions (exons) and which are spliced out at the messenger-RNA level, as well as their notable regulatory roles. However, the term junk DNA has survived and is used loosely to describe genomic sequences between genes, giving them an implied lack of importance.-"The debate about the usefulness of non-protein-coding DNA sequences continues to rage. However, within these intergenic regions of a genome are the sequences that produce most plant and many animal pri-miRs. Clearly, these sequences are not useless. Yet the regions of a pri-miR that do not generate the miRNA or the highly structured adjacent sequences have suffered the similar fate of being largely ignored and possibly thought of as junk RNA lacking function.
Essentially, pri-miRs are RNAs from which microRNAs are derived. Researchers have long known that microRNAs can regulate gene expression, but most thought that the pri-miR DNA didn't do anything if it didn't help generate microRNAs. Now it turns out that they are actually a class of DNA that can encode functional proteins, called miPEpS: "Lauressergues and colleagues identified short open reading frames (ORFs) -- sequences that can potentially encode proteins -- in many different pri-miRs of two plant species." Indeed, the proteins generated by pri-miR transcripts also have the ability to promote transcription, ensuring that these proteins stay at certain levels within the cytoplasm. So add a gene-regulation function to these pri-miR sequences. The article concludes:
The experimental discovery of miPEPs and other small peptides such as these raises an inconvenient question: are we missing a vast library of biologically important peptide signals...?"