Junk DNA goodbye!: Look for short RNA's (Introduction)

by David Turell , Thursday, June 02, 2016, 15:12 (3097 days ago) @ David Turell

As study of DNA becomes more refined, short segments in open reading frames are found to code small peptides:-http://www.the-scientist.com/?articles.view/articleNo/46150/title/Noncoding-RNAs-Not-So-Noncoding/&utm_campaign=NEWSLETTER_TS_The-Scientist-Daily_2016&utm_source=hs_email&utm_medium=email&utm_content=30186776&_hsenc=p2ANqtz--qrPQXRxBG6mcSqI8C5S11sCRe8FyHrl_pzT0ug0glBuJuXgm2GmXWsqwhpGO72phj5KxFMZFt3_ZxS91gUxsIT8_ckA&_hsmi=30186776/-"In 2002, a group of plant researchers studying legumes at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, discovered that a 679-nucleotide RNA believed to function in a noncoding capacity was in fact a protein-coding messenger RNA (mRNA).1 It had been classified as a long (or large) noncoding RNA (lncRNA) by virtue of being more than 200 nucleotides in length. The RNA, transcribed from a gene called early nodulin 40 (ENOD40), contained short open reading frames (ORFs)—putative protein-coding sequences bookended by start and stop codons—but the ORFs were so short that they had previously been overlooked. When the Cologne collaborators examined the RNA more closely, however, they found that two of the ORFs did indeed encode tiny peptides: one of 12 and one of 24 amino acids. Sampling the legumes confirmed that these micropeptides were made in the plant, where they interacted with a sucrose-synthesizing enzyme.-***-"Turning his attention to how the RNA functioned, Kageyama thought he should first rule out the possibility that it encoded proteins. But he couldn't. “We actually found it was a protein-coding gene,” he says. “It was an accident—we are RNA people!” The pri gene turned out to encode four tiny peptides—three of 11 amino acids and one of 32—that Kageyama and colleagues showed are important for activating a key developmental transcription factor.4-"Since then, a handful of other lncRNAs have switched to the mRNA ranks after being found to harbor micropeptide-encoding short ORFs (sORFs)—those less than 300 nucleotides in length. And given the vast number of documented lncRNAs—most of which have no known function—the chance of finding others that contain micropeptide codes seems high.-***-"ORFs can exist in practically any stretch of RNA sequence by chance, but many do not encode actual proteins. Because the chance that an ORF encodes a protein increases with its length, most ORF-finding algorithms had a size cut-off of 300 nucleotides—translating to 100 amino acids. This allowed researchers to “filter out garbage—that is, meaningless ORFs that exist randomly in RNAs,” says Eric Olson of the University of Texas Southwestern Medical Center in Dallas.-"Of course, by excluding all ORFs less than 300 nucleotides in length, such algorithms inevitably missed those encoding genuine small peptides. “I'm sure that the people who came up with [the cut-off] understood that this rule would have to miss anything that was shorter than 100 amino acids,” says Nicholas Ingolia of the University of California, Berkeley. “As people applied this rule more and more, they sort of lost track of that caveat.” Essentially, sORFs were thrown out with the computational trash and forgotten.-***-"That paper was really a milestone in terms of showing that there is a lot of translation outside of [known] coding regions,” says Pauli.-"But just how much is still unclear. While Ingolia and Weissman's findings could have pointed to a transcriptome littered with micropeptide-encoding sORFs, they also found some fully characterized lncRNAs with well-known nuclear functions to be associated with ribosomes in their analysis. Classical noncoding RNAs such as telomerase RNA, which acts as a template for telomeric DNA replication, for example, and small nuclear RNAs known to be involved in splicing “come up as very highly translated” in ribosome profiling assays, says Caltech's Mitch Guttman. “That's what originally clued us in to the fact that . . . this ribosome-occupancy measure is not [always] indicative of real translation.”-***-"And as researchers continue to more carefully comb small snippets of genomes, it's likely that even more cellular roles for micropeptides will be uncovered. Their diminutive size may have caused these peptides to be overlooked, their sORFs to be buried in statistical noise, and their RNAs to be miscategorized, but it does not prevent them from serving important, often essential functions, as the micropeptides characterized to date demonstrate.-"In short, size isn't everything. Indeed, says Pauli, the only reason researchers haven't identified more peptide-encoding sORFs to date is “because one just didn't know that these things existed.'”-Comment: Same point. Not much DNA is junk, and a major Darwinian theory goes out the window.