Non-coding RNA: Difference between revisions

Revision as of 09:15, 18 January 2024

Revision as of 09:21, 18 January 2024

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A '''non-coding RNA''' ('''ncRNA''') is a functional [[RNA]] molecule that is not [[Translation (genetics)|translated]] into a [[protein]]. The [[DNA]] sequence from which a functional non-coding RNA is transcribed is often called an RNA [[gene]]. Abundant and functionally important [[list of RNAs|types of non-coding RNAs]] include [[transfer RNA]]s (tRNAs) and [[ribosomal RNA]]s (rRNAs), as well as small RNAs such as [[microRNA]]s, [[siRNA]]s, [[piRNA]]s, [[snoRNA]]s, [[snRNA]]s, [[Extracellular RNA|exRNAs]], [[scaRNAs]] and the [[long noncoding RNA|long ncRNA]]s such as [[Xist]] and [[HOTAIR]].

The number of non-coding RNAs within the human genome is unknown; however, recent [[Transcriptomics|transcriptomic]] and [[Bioinformatics|bioinformatic]] studies suggest that there are thousands of non-coding transcripts.<ref name="pmid15790807">{{cite journal | vauthors = Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR | display-authors = 6 | title = Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution | journal = Science | volume = 308 | issue = 5725 | pages = 1149–1154 | date = May 2005 | pmid = 15790807 | doi = 10.1126/science.1108625 | s2cid = 13047538 | bibcode = 2005Sci...308.1149C }}</ref><ref name="pmid17571346" /><ref name="Thind">{{cite journal | vauthors = Thind AS, Monga I, Thakur PK, Kumari P, Dindhoria K, Krzak M, Ranson M, Ashford B | display-authors = 6 | title = Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology | journal = Briefings in Bioinformatics | volume = 22 | issue = 6 | date = November 2021 | pmid = 34329375 | doi = 10.1093/bib/bbab259 }}</ref><ref name="pmid17568003">{{cite journal | vauthors = Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF | display-authors = 6 | title = Structured RNAs in the ENCODE selected regions of the human genome | journal = Genome Research | volume = 17 | issue = 6 | pages = 852–864 | date = June 2007 | pmid = 17568003 | pmc = 1891344 | doi = 10.1101/gr.5650707 }}</ref><ref name= MorrisKV>{{cite book | veditors = Morris KV | year=2012 | title=Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection | publisher=[[Caister Academic Press]] | isbn= 978-1-904455-94-3}}</ref><ref name="Shahrouki P 2012">{{cite journal | vauthors = Shahrouki P, Larsson E | title = The non-coding oncogene: a case of missing DNA evidence? | journal = Frontiers in Genetics | volume = 3 | pages = 170 | date = 2012 | pmid = 22988449 | pmc = 3439828 | doi = 10.3389/fgene.2012.00170 | doi-access = free }}</ref><!--^{but see}--><ref>{{cite journal | vauthors = van Bakel H, Nislow C, Blencowe BJ, Hughes TR | title = Most "dark matter" transcripts are associated with known genes | journal = PLoSPLOS Biology | volume = 8 | issue = 5 | pages = e1000371 | date = May 2010 | pmid = 20502517 | pmc = 2872640 | doi = 10.1371/journal.pbio.1000371 | veditors = Eddy SR | doi-access = free }}</ref>

Many of the newly identified ncRNAs have not been validated for their function.<ref name="pmid15851066">{{cite journal | vauthors = Hüttenhofer A, Schattner P, Polacek N | title = Non-coding RNAs: hope or hype? | journal = Trends in Genetics | volume = 21 | issue = 5 | pages = 289–297 | date = May 2005 | pmid = 15851066 | doi = 10.1016/j.tig.2005.03.007 }}</ref>

There is no consensus in the literature on how much of non-coding transcription is functional. Some researchers have argued that many ncRNAs are non-functional (sometimes referred to as "junk RNA"), spurious transcriptions.<ref name="waste">{{cite journal | vauthors = Brosius J | title = Waste not, want not--transcript excess in multicellular eukaryotes | journal = Trends in Genetics | volume = 21 | issue = 5 | pages = 287–288 | date = May 2005 | pmid = 15851065 | doi = 10.1016/j.tig.2005.02.014 }}</ref><ref name="PalazzoLee2015">{{cite journal | vauthors = Palazzo AF, Lee ES | title = Non-coding RNA: what is functional and what is junk? | journal = Frontiers in Genetics | volume = 6 | pages = 2 | year = 2015 | pmid = 25674102 | pmc = 4306305 | doi = 10.3389/fgene.2015.00002 | doi-access = free }}</ref>

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[[Image:010 large subunit-1FFK.gif|thumb|left|Atomic structure of the 50S Subunit from ''[[Haloarcula|Haloarcula marismortui]]''. Proteins are shown in blue and the two RNA strands in orange and yellow.<ref name=Ban>{{cite journal | vauthors = Ban N, Nissen P, Hansen J, Moore PB, Steitz TA | title = The complete atomic structure of the large ribosomal subunit at 2.4 A resolution | journal = Science | volume = 289 | issue = 5481 | pages = 905–920 | date = August 2000 | pmid = 10937989 | doi = 10.1126/science.289.5481.905 | citeseerx = 10.1.1.58.2271 | bibcode = 2000Sci...289..905B }}</ref> The small patch of green in the center of the subunit is the active site.]]

Many of the conserved, essential and abundant ncRNAs are involved in [[Translation (genetics)|translation]]. [[Ribonucleoprotein]] (RNP) particles called [[ribosome]]s are the 'factories' where translation takes place in the cell. The ribosome consists of more than 60% [[rRNA|ribosomal RNA]]; these are made up of 3 ncRNAs in [[prokaryotes]] and 4 ncRNAs in [[eukaryotes]]. Ribosomal RNAs catalyse the translation of nucleotide sequences to protein. Another set of ncRNAs, [[Transfer RNA]]s, form an 'adaptor molecule' between [[mRNA]] and protein. The [[snoRNA|H/ACA box and C/D box snoRNAs]] are ncRNAs found in archaea and eukaryotes. [[RNase MRP]] is restricted to eukaryotes. Both groups of ncRNA are involved in the maturation of rRNA. The snoRNAs guide covalent modifications of rRNA, tRNA and [[snRNA]]s; RNase MRP cleaves the [[internal transcribed spacer 1]] between 18S and 5.8S rRNAs. The ubiquitous ncRNA, [[RNase P]], is an evolutionary relative of RNase MRP.<ref name="PMID16540690">{{cite journal | vauthors = Zhu Y, Stribinskis V, Ramos KS, Li Y | title = Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA | journal = RnaRNA | volume = 12 | issue = 5 | pages = 699–706 | date = May 2006 | pmid = 16540690 | pmc = 1440897 | doi = 10.1261/rna.2284906 }}</ref> RNase P matures tRNA sequences by generating mature 5'-ends of tRNAs through cleaving the 5'-leader elements of precursor-tRNAs. Another ubiquitous RNP called [[Signal recognition particle|SRP]] recognizes and transports specific nascent proteins to the [[endoplasmic reticulum]] in [[eukaryote]]s and the [[plasma membrane]] in [[prokaryote]]s. In bacteria, [[tmRNA|Transfer-messenger RNA]] (tmRNA) is an RNP involved in rescuing stalled ribosomes, tagging incomplete [[Peptide|polypeptides]] and promoting the degradation of aberrant mRNA.{{citation needed|date=June 2017}}

===In RNA splicing===

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===Bifunctional RNA===

''Bifunctional RNAs'', or ''dual-function RNAs'', are RNAs that have two distinct functions.<ref name="pmid18042713">{{cite journal | vauthors = Wadler CS, Vanderpool CK | title = A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 51 | pages = 20454–20459 | date = December 2007 | pmid = 18042713 | pmc = 2154452 | doi = 10.1073/pnas.0708102104 | doi-access = free | bibcode = 2007PNAS..10420454W }}</ref><ref name="pmid19043537">{{cite journal | vauthors = Dinger ME, Pang KC, Mercer TR, Mattick JS | title = Differentiating protein-coding and noncoding RNA: challenges and ambiguities | journal = PLoSPLOS Computational Biology | volume = 4 | issue = 11 | pages = e1000176 | date = November 2008 | pmid = 19043537 | pmc = 2518207 | doi = 10.1371/journal.pcbi.1000176 | veditors = McEntyre J | doi-access = free | bibcode = 2008PLSCB...4E0176D }}</ref> The majority of the known bifunctional RNAs are mRNAs that encode both a protein and ncRNAs. However, a growing number of ncRNAs fall into two different ncRNA categories; e.g., [[snoRNA|H/ACA box snoRNA]] and [[miRNA]].<ref name="pmid19043559">{{cite journal | vauthors = Saraiya AA, Wang CC | title = snoRNA, a novel precursor of microRNA in Giardia lamblia | journal = PLoSPLOS Pathogens | volume = 4 | issue = 11 | pages = e1000224 | date = November 2008 | pmid = 19043559 | pmc = 2583053 | doi = 10.1371/journal.ppat.1000224 | veditors = Goldberg DE | doi-access = free }}</ref><ref name="pmid19026782">{{cite journal | vauthors = Ender C, Krek A, Friedländer MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G | display-authors = 6 | title = A human snoRNA with microRNA-like functions | journal = Molecular Cell | volume = 32 | issue = 4 | pages = 519–528 | date = November 2008 | pmid = 19026782 | doi = 10.1016/j.molcel.2008.10.017 | doi-access = free }}</ref>

Two well known examples of bifunctional RNAs are [[SgrS RNA]] and [[RNAIII]]. However, a handful of other bifunctional RNAs are known to exist (e.g., steroid receptor activator/SRA,<ref name="pmid17710122">{{cite journal | vauthors = Leygue E | title = Steroid receptor RNA activator (SRA1): unusual bifaceted gene products with suspected relevance to breast cancer | journal = Nuclear Receptor Signaling | volume = 5 | pages = e006 | date = August 2007 | pmid = 17710122 | pmc = 1948073 | doi = 10.1621/nrs.05006 }}</ref> VegT RNA,<ref name="pmid9012531">{{cite journal | vauthors = Zhang J, King ML | title = Xenopus VegT RNA is localized to the vegetal cortex during oogenesis and encodes a novel T-box transcription factor involved in mesodermal patterning | journal = Development | volume = 122 | issue = 12 | pages = 4119–4129 | date = December 1996 | pmid = 9012531 | doi = 10.1242/dev.122.12.4119 | s2cid = 28462527 }}</ref><ref name="pmid16000384">{{cite journal | vauthors = Kloc M, Wilk K, Vargas D, Shirato Y, Bilinski S, Etkin LD | title = Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes | journal = Development | volume = 132 | issue = 15 | pages = 3445–3457 | date = August 2005 | pmid = 16000384 | doi = 10.1242/dev.01919 | doi-access = free }}</ref>

Oskar RNA,<ref name="pmid16835436">{{cite journal | vauthors = Jenny A, Hachet O, Závorszky P, Cyrklaff A, Weston MD, Johnston DS, Erdélyi M, Ephrussi A | display-authors = 6 | title = A translation-independent role of oskar RNA in early Drosophila oogenesis | journal = Development | volume = 133 | issue = 15 | pages = 2827–2833 | date = August 2006 | pmid = 16835436 | doi = 10.1242/dev.02456 | doi-access = free }}</ref> [[ENOD40]],<ref name="pmid17452360">{{cite journal | vauthors = Gultyaev AP, Roussis A | title = Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants | journal = Nucleic Acids Research | volume = 35 | issue = 9 | pages = 3144–3152 | year = 2007 | pmid = 17452360 | pmc = 1888808 | doi = 10.1093/nar/gkm173 }}</ref> p53 RNA<ref name="pmid19160491">{{cite journal | vauthors = Candeias MM, Malbert-Colas L, Powell DJ, Daskalogianni C, Maslon MM, Naski N, Bourougaa K, Calvo F, Fåhraeus R | display-authors = 6 | title = P53 mRNA controls p53 activity by managing Mdm2 functions | journal = Nature Cell Biology | volume = 10 | issue = 9 | pages = 1098–1105 | date = September 2008 | pmid = 19160491 | doi = 10.1038/ncb1770 | s2cid = 5122088 }}</ref> [[SR1 RNA]]<ref>{{cite journal | vauthors = Gimpel M, Preis H, Barth E, Gramzow L, Brantl S | title = SR1--a small RNA with two remarkably conserved functions | journal = Nucleic Acids Research | volume = 40 | issue = 22 | pages = 11659–11672 | date = December 2012 | pmid = 23034808 | pmc = 3526287 | doi = 10.1093/nar/gks895 }}</ref>, and [[Spot 42 RNA]].<ref name="pmid35239441">{{cite journal | vauthors = Aoyama JJ, Raina M, Zhong A, Storz G | title = Dual-function Spot 42 RNA encodes a 15-amino acid protein that regulates the CRP transcription factor | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 119 | issue = 10 | pages = e2119866119 | date = March 2022 | pmid = 35239441 | pmc = 8916003 | doi = 10.1073/pnas.2119866119 | doi-access = free | bibcode = 2022PNAS..11919866A }}</ref>) Bifunctional RNAs were the subject of a 2011 special issue of [[Biochimie]].<ref>{{cite journal | vauthors = Francastel C, Hubé F | title = Coding or non-coding: Need they be exclusive? | journal = Biochimie | volume = 93 | issue = 11 | pages = vi-vii | date = November 2011 | pmid = 21963143 | doi = 10.1016/S0300-9084(11)00322-1 | url = https://zenodo.org/record/889579 }}</ref>

=== As a hormone ===

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===Prader–Willi syndrome===

The deletion of the 48 copies of the C/D box snoRNA [[Small nucleolar RNA SNORD116|SNORD116]] has been shown to be the primary cause of [[Prader&ndash;Willi syndrome]].<ref name="pmid18500341">{{cite journal | vauthors = Sahoo T, del Gaudio D, German JR, Shinawi M, Peters SU, Person RE, Garnica A, Cheung SW, Beaudet AL | display-authors = 6 | title = Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster | journal = Nature Genetics | volume = 40 | issue = 6 | pages = 719–721 | date = June 2008 | pmid = 18500341 | pmc = 2705197 | doi = 10.1038/ng.158 }}</ref><ref name="pmid18166085">{{cite journal | vauthors = Skryabin BV, Gubar LV, Seeger B, Pfeiffer J, Handel S, Robeck T, Karpova E, Rozhdestvensky TS, Brosius J | display-authors = 6 | title = Deletion of the MBII-85 snoRNA gene cluster in mice results in postnatal growth retardation | journal = PLoSPLOS Genetics | volume = 3 | issue = 12 | pages = e235 | date = December 2007 | pmid = 18166085 | pmc = 2323313 | doi = 10.1371/journal.pgen.0030235 | doi-access = free }}</ref><ref name="pmid18320030">{{cite journal | vauthors = Ding F, Li HH, Zhang S, Solomon NM, Camper SA, Cohen P, Francke U | title = SnoRNA Snord116 (Pwcr1/MBII-85) deletion causes growth deficiency and hyperphagia in mice | journal = PloSPLOS OneONE | volume = 3 | issue = 3 | pages = e1709 | date = March 2008 | pmid = 18320030 | pmc = 2248623 | doi = 10.1371/journal.pone.0001709 | veditors = Akbarian S | doi-access = free | bibcode = 2008PLoSO...3.1709D }}</ref><ref name="pmid16075369">{{cite journal | vauthors = Ding F, Prints Y, Dhar MS, Johnson DK, Garnacho-Montero C, Nicholls RD, Francke U | title = Lack of Pwcr1/MBII-85 snoRNA is critical for neonatal lethality in Prader-Willi syndrome mouse models | journal = Mammalian Genome | volume = 16 | issue = 6 | pages = 424–431 | date = June 2005 | pmid = 16075369 | doi = 10.1007/s00335-005-2460-2 | s2cid = 12256515 }}</ref> Prader–Willi is a developmental disorder associated with over-eating and learning difficulties. SNORD116 has potential target sites within a number of protein-coding genes, and could have a role in regulating alternative splicing.<ref name="pmid18160232">{{cite journal | vauthors = Bazeley PS, Shepelev V, Talebizadeh Z, Butler MG, Fedorova L, Filatov V, Fedorov A | title = snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions | journal = Gene | volume = 408 | issue = 1-21–2 | pages = 172–179 | date = January 2008 | pmid = 18160232 | pmc = 6800007 | doi = 10.1016/j.gene.2007.10.037 }}</ref>

===Autism===

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==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 = PLoSPLOS 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>

== See also ==

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== External links ==

{{Commons category|Non-coding RNA}}

* {{cite web | url = http://jsm-research.imb.uq.edu.au/rnadb/ | title = RNAdb | archive-url = https://web.archive.org/web/20070829173837/http://jsm-research.imb.uq.edu.au/rnadb/ | titlearchive-date = RNAdb2007-08-29 | quote = This database is a comprehensive mammalian noncoding RNA database (RNAdb) }}

* [http://rfam.org/ The Rfam Database] — a curated list of hundreds of families of related ncRNAs

* [http://www.noncode.org/ NONCODE.org] — a free database of all kinds of noncoding RNAs (except tRNAs and rRNAs)