Editing Non-coding RNA (section)

==Distinction between functional RNA (fRNA) and ncRNA==

Scientists have started to distinguish ''functional RNA'' (''fRNA'') from ncRNA, to describe regions functional at the RNA level that may or may not be stand-alone RNA transcripts.<ref>{{cite journal | vauthors = Carter RJ, Dubchak I, Holbrook SR | title = A computational approach to identify genes for functional RNAs in genomic sequences | journal = Nucleic Acids Research | volume = 29 | issue = 19 | pages = 3928–3938 | date = October 2001 | pmid = 11574674 | pmc = 60242 | doi = 10.1093/nar/29.19.3928 }}</ref><ref>{{cite journal | vauthors = Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D | display-authors = 6 | title = Identification and classification of conserved RNA secondary structures in the human genome | journal = PLOS Computational Biology | volume = 2 | issue = 4 | pages = e33 | date = April 2006 | pmid = 16628248 | pmc = 1440920 | doi = 10.1371/journal.pcbi.0020033 | doi-access = free | bibcode = 2006PLSCB...2...33P }}</ref><ref>{{cite journal | vauthors = Thomas JM, Horspool D, Brown G, Tcherepanov V, Upton C | title = GraphDNA: a Java program for graphical display of DNA composition analyses | journal = BMC Bioinformatics | volume = 8 | pages = 21 | date = January 2007 | pmid = 17244370 | pmc = 1783863 | doi = 10.1186/1471-2105-8-21 | doi-access = free }}</ref> This implies that fRNA (such as riboswitches, [[SECIS element]]s, and other cis-regulatory regions) is not ncRNA. Yet fRNA could also include [[Messenger RNA|mRNA]], as this is RNA coding for protein, and hence is functional.  Additionally [[Systematic Evolution of Ligands by Exponential Enrichment|artificially evolved RNAs]] also fall under the fRNA umbrella term.  Some publications<ref name="Edd01" /> state that ''ncRNA'' and ''fRNA'' are nearly synonymous, however others have pointed out that a large proportion of annotated ncRNAs likely have no function.<ref name="waste"/><ref name="PalazzoLee2015"/> It also has been suggested to simply use the term ''RNA'', since the distinction from a protein coding RNA ([[messenger RNA]]) is already given by the qualifier ''mRNA''.<ref>{{cite journal | vauthors = Brosius J, Raabe CA | title = What is an RNA? A top layer for RNA classification | journal = RNA Biology | volume = 13 | issue = 2 | pages = 140–144 | date = February 2015 | pmid = 26818079 | pmc = 4829331 | doi = 10.1080/15476286.2015.1128064 }}</ref> This eliminates the ambiguity when addressing a gene "encoding a non-coding" RNA. Besides, there may be a number of ncRNAs that are misannoted in published literature and datasets.<ref>{{cite journal | vauthors = Ji Z, Song R, Regev A, Struhl K | title = Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins | journal = eLife | volume = 4 | pages = e08890 | date = December 2015 | pmid = 26687005 | pmc = 4739776 | doi = 10.7554/eLife.08890 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Tosar JP, Rovira C, Cayota A | title = Non-coding RNA fragments account for the majority of annotated piRNAs expressed in somatic non-gonadal tissues | language = En | journal = Communications Biology | volume = 1 | issue = 1 | pages = 2 | date = 2018-01-22 | pmid = 30271890 | pmc = 6052916 | doi = 10.1038/s42003-017-0001-7 }}</ref><ref>{{cite journal | vauthors = Housman G, Ulitsky I | title = Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs | journal = Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms | volume = 1859 | issue = 1 | pages = 31–40 | date = January 2016 | pmid = 26265145 | doi = 10.1016/j.bbagrm.2015.07.017 }}</ref>