Editing Small RNA

{{Short description|Small, usually non-coding RNA molecule}}{{For|the RNA formerly known as sRNA|soluble RNA}}{{See also|Bacterial small RNA}}
'''Small RNA''' ('''sRNA''') are polymeric [[RNA]] molecules that are less than 200 [[nucleotide]]s in length, and are usually [[non-coding RNA|non-coding]].<ref>{{cite journal | vauthors = Storz G | title = An expanding universe of noncoding RNAs | journal = Science | volume = 296 | issue = 5571 | pages = 1260–3 | date = May 2002 | pmid = 12016301 | doi = 10.1126/science.1072249 | s2cid = 35295924 | bibcode = 2002Sci...296.1260S }}</ref> [[RNA silencing]] is often a function of these molecules, with the most common and well-studied example being [[RNA interference]] (RNAi), in which endogenously (from within the organism) expressed [[microRNA]] (miRNA) or endogenously/exogenously (from outside the organism) derived [[small interfering RNA]] (siRNA) induces the degradation of [[complementarity (molecular biology)|complementary]] [[messenger RNA]].<ref>{{Citation |last1=Billi |first1=Allison C. |title=Endogenous RNAi pathways in C. elegans |date=2018 |work=WormBook: The Online Review of C. elegans Biology [Internet] |url=https://www.ncbi.nlm.nih.gov/books/NBK206718/ |access-date=2025-05-05 |publisher=WormBook |language=en |pmid=24816713 |last2=Fischer |first2=Sylvia E. J. |last3=Kim |first3=John K.|pages=1–49 |doi=10.1895/wormbook.1.170.1 |pmc=4781133 }}</ref> Other classes of small RNA have been identified, including [[piwi-interacting RNA]] (piRNA) and its subspecies [[rasiRNA|repeat associated small interfering RNA]] (rasiRNA).<ref name=Gunawardane>{{cite journal | vauthors = Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, Siomi H, Siomi MC | display-authors = 6 | title = A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila | journal = Science | volume = 315 | issue = 5818 | pages = 1587–90 | date = March 2007 | pmid = 17322028 | doi = 10.1126/science.1140494 | s2cid = 11513777 | doi-access = free }}</ref> Small RNA "is unable to induce RNAi alone, and to accomplish the task it must form the core of the RNA–protein complex termed the RNA-induced silencing complex (RISC), specifically with Argonaute protein".<ref name = "Meyers_2012">{{cite book | vauthors = Meyers RA |title=Epigenetic Regulation and Epigenomics |url=https://books.google.com/books?id=N9QXSmgGDugC&pg=PA366 |date=2012 |publisher =  Wiley-Blackwell |isbn=978-3-527-66861-8}}</ref>{{rp|366}}
[[File:Rna interference plos.svg|thumb|A simplified overview of RNAi.]]
Small RNA have been detected or sequenced using a range of techniques, including directly by [[MicroRNA sequencing]] on several sequencing platforms,<ref>{{cite journal | vauthors = Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ | title = Elucidation of the small RNA component of the transcriptome | journal = Science | volume = 309 | issue = 5740 | pages = 1567–9 | date = September 2005 | pmid = 16141074 | doi = 10.1126/science.1114112 | s2cid = 1651848 | bibcode = 2005Sci...309.1567L }}</ref><ref name="WuLu2011">{{cite journal | vauthors = Wu Q, Lu Z, Li H, Lu J, Guo L, Ge Q | title = Next-generation sequencing of microRNAs for breast cancer detection | journal = Journal of Biomedicine & Biotechnology | volume = 2011 | pages = 597145 | year = 2011 | pmid = 21716661 | pmc = 3118289 | doi = 10.1155/2011/597145 | doi-access = free }}</ref><ref name="RubyJan2006">{{cite journal | vauthors = Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP | display-authors = 6 | title = Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans | journal = Cell | volume = 127 | issue = 6 | pages = 1193–207 | date = December 2006 | pmid = 17174894 | doi = 10.1016/j.cell.2006.10.040 | s2cid = 16838469 | doi-access = free }}</ref> or indirectly through genome sequencing and analysis.<ref name="WittenTibshirani2010">{{cite journal | vauthors = Witten D, Tibshirani R, Gu SG, Fire A, Lui WO | title = Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls | journal = BMC Biology | volume = 8 | issue = 1 | pages = 58 | date = May 2010 | pmid = 20459774 | pmc = 2880020 | doi = 10.1186/1741-7007-8-58 | doi-access = free }}</ref>  Identification of miRNAs has been evaluated in detecting human disease, such as breast cancer.<ref name="WuLu2011" /> [[Peripheral blood mononuclear cell]] (PBMC) miRNA expression has been studied as potential biomarker for different neurological disorders such as [[Parkinson's disease]],<ref>{{cite journal | vauthors = Gui Y, Liu H, Zhang L, Lv W, Hu X | title = Altered microRNA profiles in cerebrospinal fluid exosome in Parkinson disease and Alzheimer disease | journal = Oncotarget | volume = 6 | issue = 35 | pages = 37043–53 | date = November 2015 | pmid = 26497684 | pmc = 4741914 | doi = 10.18632/oncotarget.6158 }}</ref> [[Multiple sclerosis]].<ref>{{cite journal | vauthors = Keller A, Leidinger P, Lange J, Borries A, Schroers H, Scheffler M, Lenhof HP, Ruprecht K, Meese E | display-authors = 6 | title = Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls | journal = PLOS ONE | volume = 4 | issue = 10 | pages = e7440 | date = October 2009 | pmid = 19823682 | pmc = 2757919 | doi = 10.1371/journal.pone.0007440 | bibcode = 2009PLoSO...4.7440K | doi-access = free }}</ref>  Evaluating small RNA is useful for certain kinds of study because its molecules "do not need to be fragmented prior to library preparation".<ref name = "Meyers_2012" />{{rp|162}}

== Discovery ==
The first sRNA discovered was in 1984 where [[MicF RNA|MicF]] was found to regulate the outer cell membrane in ''[[Escherichia coli|E. Coli]]'' by inhibiting the production of the protein ompF and ompC.<ref>{{Cite journal |last1=Mizuno |first1=T |last2=Chou |first2=M Y |last3=Inouye |first3=M |date=April 1984 |title=A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). |journal=Proceedings of the National Academy of Sciences |volume=81 |issue=7 |pages=1966–1970 |doi=10.1073/pnas.81.7.1966 |doi-access=free |pmc=345417 |pmid=6201848|bibcode=1984PNAS...81.1966M }}</ref> The use of sRNA in regulation of gene expression was found alongside it's discovery. It was later discovered to be present across all eukaryotic organisms. In 1998 it was discovered that the sRNA can be transferred between organisms. It was later discovered in 2011 that sRNA are transferred from cell to cell inside an organism as well.<ref>{{Cite journal |last1=Zeng |first1=Jun |last2=Gupta |first2=Vijai Kumar |last3=Jiang |first3=Yueming |last4=Yang |first4=Bao |last5=Gong |first5=Liang |last6=Zhu |first6=Hong |date=2019-04-23 |title=Cross-Kingdom Small RNAs Among Animals, Plants and Microbes |journal=Cells |volume=8 |issue=4 |pages=371 |doi=10.3390/cells8040371 |doi-access=free |issn=2073-4409 |pmc=6523504 |pmid=31018602}}</ref>

== Types of Small RNA ==
* [[microRNA]] (miRNA) - an [[RNA]] involved in [[RNA interference|RNAi]] through gene regulation as well as [[Messenger RNA|mRNA]] degradation<ref>{{Cite journal |last1=Lim |first1=Lee P. |last2=Lau |first2=Nelson C. |last3=Garrett-Engele |first3=Philip |last4=Grimson |first4=Andrew |last5=Schelter |first5=Janell M. |last6=Castle |first6=John |last7=Bartel |first7=David P. |last8=Linsley |first8=Peter S. |last9=Johnson |first9=Jason M. |date=2005-02-17 |title=Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs |url=https://pubmed.ncbi.nlm.nih.gov/15685193 |journal=Nature |volume=433 |issue=7027 |pages=769–773 |doi=10.1038/nature03315 |issn=1476-4687 |pmid=15685193|bibcode=2005Natur.433..769L }}</ref><ref>{{cite journal |last1=Green |first1=D |last2=Dalmay |first2=T |last3=Chapman |first3=T |title=Microguards and micromessengers of the genome |journal=Heredity |date=February 2016 |volume=116 |issue=2 |pages=125–134 |doi=10.1038/hdy.2015.84|pmid=26419338 |pmc=4806885 |doi-access=free |bibcode=2016Hered.116..125G }}</ref><ref>{{Cite journal |last1=Iwakawa |first1=Hiro-oki |last2=Tomari |first2=Yukihide |date=2022-01-06 |title=Life of RISC: Formation, action, and degradation of RNA-induced silencing complex |url=https://www.sciencedirect.com/science/article/pii/S1097276521010285 |journal=Molecular Cell |volume=82 |issue=1 |pages=30–43 |doi=10.1016/j.molcel.2021.11.026 |pmid=34942118 |issn=1097-2765}}</ref>
* [[File:Functions of Small RNAs.jpg|thumb|Lists the multiple functions of the types of small RNA]][[Piwi-interacting RNA]] (piRNA) - an [[RNA]] that regulates the germ line, [[Transposable element|transposons]], as well as [[Histone|histones]]. It also participates in the argonaute complex.<ref>{{Cite journal |last1=Wu |first1=Xi |last2=Pan |first2=Yutian |last3=Fang |first3=Yuan |last4=Zhang |first4=Jingxin |last5=Xie |first5=Mengyan |last6=Yang |first6=Fengming |last7=Yu |first7=Tao |last8=Ma |first8=Pei |last9=Li |first9=Wei |last10=Shu |first10=Yongqian |date=2020-09-04 |title=The Biogenesis and Functions of piRNAs in Human Diseases |journal=Molecular Therapy - Nucleic Acids |volume=21 |pages=108–120 |doi=10.1016/j.omtn.2020.05.023 |pmid=32516734 |pmc=7283962 |issn=2162-2531}}</ref>
* QDE-2 interfering RNA (qiRNA) - an [[RNA]] that regulates gene expression after [[DNA]] damage<ref>{{Cite journal |last1=Lee |first1=Heng-Chi |last2=Chang |first2=Shwu-Shin |last3=Choudhary |first3=Swati |last4=Aalto |first4=Antti P. |last5=Maiti |first5=Mekhala |last6=Bamford |first6=Dennis H. |last7=Liu |first7=Yi |date=2009-05-14 |title=qiRNA is a new type of small interfering RNA induced by DNA damage |journal=Nature |volume=459 |issue=7244 |pages=274–277 |doi=10.1038/nature08041 |issn=1476-4687 |pmc=2859615 |pmid=19444217|bibcode=2009Natur.459..274L }}</ref>
* [[Short hairpin RNA]] (shRNA) - an [[RNA]] that acts similarly to [[MicroRNA|miRNA]], regulating gene expression via RISC<ref>{{Cite journal |last1=Silva |first1=Jose M. |last2=Li |first2=Mamie Z. |last3=Chang |first3=Ken |last4=Ge |first4=Wei |last5=Golding |first5=Michael C. |last6=Rickles |first6=Richard J. |last7=Siolas |first7=Despina |last8=Hu |first8=Guang |last9=Paddison |first9=Patrick J. |last10=Schlabach |first10=Michael R. |last11=Sheth |first11=Nihar |last12=Bradshaw |first12=Jeff |last13=Burchard |first13=Julia |last14=Kulkarni |first14=Amit |last15=Cavet |first15=Guy |date=November 2005 |title=Second-generation shRNA libraries covering the mouse and human genomes |url=https://www.nature.com/articles/ng1650 |journal=Nature Genetics |language=en |volume=37 |issue=11 |pages=1281–1288 |doi=10.1038/ng1650 |pmid=16200065 |issn=1546-1718|url-access=subscription }}</ref>
* [[small interfering RNA]] (siRNA) - an [[RNA]] that regulates both gene expression with RISC<ref>{{Cite journal |last1=Tiwari |first1=Deepti |last2=Patel |first2=Manoj Kumar |date=May 7, 2024 |title=22 Nucleotide siRNAs: Emerging Players in Plant Stress Adaptation |url=https://bioticapublications.com/journal-backend/articlePdf/5c11d2d246.pdf |journal=Biotica Research Today |volume=6 |issue=5 |pages=249–251}}</ref> and by [[histone]] modifications.<ref>{{Cite journal |last1=Weinberg |first1=Marc S. |last2=Morris |first2=Kevin V. |date=2016-08-19 |title=Transcriptional gene silencing in humans |journal=Nucleic Acids Research |volume=44 |issue=14 |pages=6505–6517 |doi=10.1093/nar/gkw139 |issn=1362-4962 |pmc=5001580 |pmid=27060137}}</ref>
* [[small nuclear RNA]] (snRNA), also commonly referred to as U-RNA  - an [[RNA]] integral to the [[Spliceosome|splicosome]], that also stabilizes [[Messenger RNA|mRNA]]<ref>{{Cite journal |last1=Valadkhan |first1=Saba |last2=Gunawardane |first2=Lalith S. |date=2013-04-30 |editor-last=Lindsay |editor-first=Mark A. |editor2-last=Griffiths-Jones |editor2-first=Sam |title=Role of small nuclear RNAs in eukaryotic gene expression |journal=Essays in Biochemistry |volume=54 |pages=79–90 |doi=10.1042/bse0540079 |pmid=23829528 |pmc=11246792 |issn=0071-1365}}</ref>
* [[small nucleolar RNA]] (snoRNA) - an [[RNA]] regulates the [[Ribosomal RNA|rRNA]] as well as aiding [[alternative splicing]]. It also aids in [[Messenger RNA|mRNA]] degradation.<ref>{{Cite journal |last1=Huang |first1=Zheng-hao |last2=Du |first2=Yu-ping |last3=Wen |first3=Jing-tao |last4=Lu |first4=Bing-feng |last5=Zhao |first5=Yang |date=2022-05-12 |title=snoRNAs: functions and mechanisms in biological processes, and roles in tumor pathophysiology |journal=Cell Death Discovery |language=en |volume=8 |issue=1 |page=259 |doi=10.1038/s41420-022-01056-8 |pmid=35552378 |pmc=9098889 |issn=2058-7716}}</ref>
* small rDNA-derived RNA (srRNA) - an [[RNA]] involved in multiple signaling pathways as well as the formation of Argonaute protein complexes.<ref>{{Cite journal |last1=Wei |first1=Haibin |last2=Zhou |first2=Ben |last3=Zhang |first3=Fang |last4=Tu |first4=Yanyang |last5=Hu |first5=Yanan |last6=Zhang |first6=Baoguo |last7=Zhai |first7=Qiwei |date=2013 |title=Profiling and identification of small rDNA-derived RNAs and their potential biological functions |journal=PLOS ONE |volume=8 |issue=2 |pages=e56842 |doi=10.1371/journal.pone.0056842 |doi-access=free |issn=1932-6203 |pmc=3572043 |pmid=23418607|bibcode=2013PLoSO...856842W }}</ref>
* tRNA-derived stress induced RNA (tiRNA) - an [[RNA]] that regulates translation by binding to [[Ribosome|ribosomes]].<ref name=":0">{{Cite journal |last1=Xie |first1=Yaoyao |last2=Yao |first2=Lipeng |last3=Yu |first3=Xiuchong |last4=Ruan |first4=Yao |last5=Li |first5=Zhe |last6=Guo |first6=Junming |date=2020-06-30 |title=Action mechanisms and research methods of tRNA-derived small RNAs |journal=Signal Transduction and Targeted Therapy |language=en |volume=5 |issue=1 |page=109 |doi=10.1038/s41392-020-00217-4 |pmid=32606362 |pmc=7326991 |issn=2059-3635}}</ref>
* tRNA fragment (tRF) - an [[RNA]] fragment that regulates translation by binding to [[Ribosome|ribosomes]] and altering mRNA's caps. It can also combine with Argonaute protein complexes to degrade mRNA.<ref name=":0" /><ref>{{cite journal |last1=Green |first1=Darrell |last2=Fraser |first2=William D. |last3=Dalmay |first3=Tamas |title=Transfer RNA-derived small RNAs in the cancer transcriptome |journal=Pflügers Archiv: European Journal of Physiology |date=June 2016 |volume=468 |issue=6 |pages=1041–1047 |doi=10.1007/s00424-016-1822-9|pmid=27095039 |pmc=4893054 |doi-access=free }}</ref>
* Y RNA-derived small RNA (ysRNA) - an [[RNA]] that aids in initiaion of [[DNA replication]] as well as preventing [[Messenger RNA|mRNA]] from degrading.<ref>{{Cite book |last1=Valkov |first1=Nedyalka |last2=Das |first2=Saumya |title=Non-coding RNAs in Cardiovascular Diseases |date=2020 |chapter=Y RNAs: Biogenesis, Function and Implications for the Cardiovascular System |series=Advances in Experimental Medicine and Biology |volume=1229 |pages=327–342 |doi=10.1007/978-981-15-1671-9_20 |issn=0065-2598 |pmc=7363058 |pmid=32285422|isbn=978-981-15-1670-2 }}</ref><ref>{{cite journal |last1=Billmeier |first1=Martina |last2=Green |first2=Darrell |last3=Hall |first3=Adam E. |last4=Turnbull |first4=Carly |last5=Singh |first5=Archana |last6=Xu |first6=Ping |last7=Moxon |first7=Simon |last8=Dalmay |first8=Tamas |title=Mechanistic insights into non-coding Y RNA processing |journal=RNA Biology |date=31 December 2022 |volume=19 |issue=1 |pages=468–480 |doi=10.1080/15476286.2022.2057725 |pmid=35354369 |pmc=8973356 |doi-access=free }}</ref>

==In plants==
The first known function in plants was discovered in mutants of ''[[Arabidopsis thaliana#Use as a model organism|Arabidopsis]]''. Specifically with decline in function [[mutation]]s for [[RNA-dependent RNA polymerase]] and [[DICER-like]] production. This impairment actually enhanced ''Arabidopsis'' [[plant disease resistance|resistance]] against ''[[Heterodera schachtii]]'' and ''[[Meloidogyne javanica]]''. Similarly, mutants with reduced [[Argonaute]] function - ''[[ago1-25]]'', ''[[ago1-27]]'', ''[[ago2-1]]'', and combined mutants with ''ago1-27'' and ''ago2-1'' - had greater resistance to ''[[Meloidogyne incognita]]''. Altogether this demonstrates great dependence of [[nematode]] parasitism on plants' own small RNAs.<ref name="Hewezi-2020">{{cite journal | vauthors = Hewezi T | title=Epigenetic Mechanisms in Nematode–Plant Interactions | journal=[[Annual Review of Phytopathology]] | publisher=[[Annual Reviews (publisher)|Annual Reviews]] | volume=58 | issue=1 | date=2020-08-25 | issn=0066-4286 | doi=10.1146/annurev-phyto-010820-012805 | pages=119–138| pmid=32413274 | bibcode=2020AnRvP..58..119H | s2cid=218658491 }}</ref>

== References ==
{{reflist|32em}}

[[Category:Non-coding RNA]]


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