Richard Peachey writes:

I’ve just added a new item to my web article “Not Junk! — An Extensive Collective of Quotes Indicating Functionality in Non-Protein-Coding DNA“.

The new section includes quotations from a lengthy technical review published just a few months ago in the premier scientific journal Cell.

That review contains a table spread out over three pages, listing a variety of functions for 54 broad categories of RNA (see pages 78 to 80 in the review article, available at UFV).

The quotations that I added to my web article are as follows:   (Bold print indicates my emphasis.)

“The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones” (Thomas R. Cech and Joan A. Steitz, Cell, Vol. 157 [Mar 27, 2014], pp. 77-94)

[ABSTRACT:] “Noncoding RNAs (ncRNAs) accomplish a remarkable variety of biological functions. They regulate gene expression at the levels of transcription, RNA processing, and translation. They protect genomes from foreign nucleic acids. They can guide DNA synthesis or genome rearrangement. For ribozymes and riboswitches, the RNA structure itself provides the biological function, but most ncRNAs operate as RNA-protein complexes, including ribosomes, snRNPs, snoRNPs, telomerase, microRNAs, and long ncRNAs. Many, though not all, ncRNAs exploit the power of base pairing to selectively bind and act on other nucleic acids. Here, we describe the pathway of ncRNA research, where every established ‘rule’ seems destined to be overturned.” (p. 77)

Today, the ncRNA revolution has engulfed all living organisms, as deep sequencing has uncovered the existence of thousands of long (l)ncRNAs with a breaktaking variety of roles in both gene expression and remodeling of the eukaryotic genome.” (p. 77)

The discovery of introns sparked a lively debate about the evolutionary nature of noncoding (then considered ‘junk’) DNA. . . .
Relegating introns to the junk pile turned out to be premature. A clear-cut ‘use’ of intronic sequences that redefines them as not-junk is in alternative splicing . . ., whereby sequences that are sometimes eliminated from the mRNA appear instead as exonic (coding) regions. This occurs through the selection of alternative 5′- or 3′-splice sites or by cassette exons being included (or not) during the splicing process. Alternative splicing is pervasive with the latest estimates from deep-sequencing data assigning detectable alternatively-spliced transcripts to 95% of human genes. . . .
Most small nucleolar (sno)RNAs are pieces of intron (~70 nt) that lead a second life after their release from excised introns through exonucleolytic processing. . . . SnoRNPs use intermolecular base pairing to direct the modification of ribose 2′-hydroxyl groups or the isomerization of uridines to pseudouridines within pre-rRNAs. . . .
A recent revelation concerning intronic ‘junk’ is the discovery that entire introns or portions thereof, called stable intronic sequence (sis)RNAs, can sometimes accumulate to significant levels, rather than undergo rapid turnover. In the Xenopus oocyte, such sequences dominate the nuclear transcriptome. . . . Some sisRNAs are selectively nuclear and others cytoplasmic, hinting at special functions in early development.” (p. 83)

“Early work on transcription in mammalian cells identified hnRNA, a heterogeneous population of huge nuclear RNAs that were short-lived. . . . the pendulum of scientific opinion has now swung away from the idea that much of this RNA could be ‘transcriptional noise’ or junk RNA transcribed from junk DNA. . . .
Reviewing the biological functions and mechanisms of lncRNAs is a daunting task for several reasons. New lncRNA papers are published daily, and entire new categories and paradigms are proposed annually. And although our human penchant for categorization drives a desire to assign individual functions to individual lncRNAs, a single 1 kb lncRNA is long enough to carry out a large number of functions with perhaps different subsets of these functions being active in different tissues and at different stages of development.” (p. 87)

“Notwithstanding the fact that there are definable classes of ncRNAs that work by similar principles (e.g., tRNAs, riboswitches, miRNAs), it could be argued that every ncRNA studied has a different function.Certainly no two mammalian lncRNAs appear to have the same function. Thus, with perhaps 10,000 lncRNAs yet to be studied in the human genome alone, it seems safe to predict that many new functions of ncRNAs will be identified—perhaps thousands of functions.” (p. 89)