Small RNA explained

See also: Bacterial small RNA. Small RNA (sRNA) are polymeric RNA molecules that are less than 200 nucleotides in length, and are usually non-coding.[1] RNA silencing is often a function of these molecules, with the most common and well-studied example being RNA interference (RNAi), in which endogenously expressed microRNA (miRNA) or exogenously derived small interfering RNA (siRNA) induces the degradation of complementary messenger RNA. Other classes of small RNA have been identified, including piwi-interacting RNA (piRNA) and its subspecies repeat associated small interfering RNA (rasiRNA).[2] 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".[3]

Small RNA have been detected or sequenced using a range of techniques, including directly by MicroRNA sequencing on several sequencing platforms,[4] [5] [6] or indirectly through genome sequencing and analysis.[7] Identification of miRNAs has been evaluated in detecting human disease, such as breast cancer. Peripheral blood mononuclear cell (PBMC) miRNA expression has been studied as potential biomarker for different neurological disorders such as Parkinson's disease,[8] Multiple sclerosis.[9] Evaluating small RNA is useful for certain kinds of study because its molecules "do not need to be fragmented prior to library preparation".

Types of small RNA include:

In plants

The first known function in plants was discovered in mutants of Arabidopsis. Specifically with decline in function mutations for RNA-dependent RNA polymerase and DICER-like production. This impairment actually enhanced Arabidopsis 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.[14]

Notes and References

  1. Storz G . An expanding universe of noncoding RNAs . Science . 296 . 5571 . 1260–3 . May 2002 . 12016301 . 10.1126/science.1072249 . 35295924 . 2002Sci...296.1260S .
  2. Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, Siomi H, Siomi MC . 6 . A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila . Science . 315 . 5818 . 1587–90 . March 2007 . 17322028 . 10.1126/science.1140494 . 11513777 . free .
  3. Book: Meyers RA . Epigenetic Regulation and Epigenomics . 2012 . Wiley-Blackwell . 978-3-527-66861-8.
  4. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ . Elucidation of the small RNA component of the transcriptome . Science . 309 . 5740 . 1567–9 . September 2005 . 16141074 . 10.1126/science.1114112 . 1651848 . 2005Sci...309.1567L .
  5. Wu Q, Lu Z, Li H, Lu J, Guo L, Ge Q . Next-generation sequencing of microRNAs for breast cancer detection . Journal of Biomedicine & Biotechnology . 2011 . 597145 . 2011 . 21716661 . 3118289 . 10.1155/2011/597145 . free .
  6. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP . 6 . Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans . Cell . 127 . 6 . 1193–207 . December 2006 . 17174894 . 10.1016/j.cell.2006.10.040 . 16838469 . free .
  7. Witten D, Tibshirani R, Gu SG, Fire A, Lui WO . Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls . BMC Biology . 8 . 1 . 58 . May 2010 . 20459774 . 2880020 . 10.1186/1741-7007-8-58 . free .
  8. Gui Y, Liu H, Zhang L, Lv W, Hu X . Altered microRNA profiles in cerebrospinal fluid exosome in Parkinson disease and Alzheimer disease . Oncotarget . 6 . 35 . 37043–53 . November 2015 . 26497684 . 4741914 . 10.18632/oncotarget.6158 .
  9. Keller A, Leidinger P, Lange J, Borries A, Schroers H, Scheffler M, Lenhof HP, Ruprecht K, Meese E . 6 . Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls . PLOS ONE . 4 . 10 . e7440 . October 2009 . 19823682 . 2757919 . 10.1371/journal.pone.0007440 . 2009PLoSO...4.7440K . free .
  10. Green . D . Dalmay . T . Chapman . T . Microguards and micromessengers of the genome . Heredity . February 2016 . 116 . 2 . 125–134 . 10.1038/hdy.2015.84. 26419338 . 4806885 . free .
  11. Wei H, Zhou B, Zhang F, Tu Y, Hu Y, Zhang B, Zhai Q . Profiling and identification of small rDNA-derived RNAs and their potential biological functions . PLOS ONE . 8 . 2 . e56842 . 2013 . 23418607 . 3572043 . 10.1371/journal.pone.0056842 . 2013PLoSO...856842W . free .
  12. Green . Darrell . Fraser . William D. . Dalmay . Tamas . Transfer RNA-derived small RNAs in the cancer transcriptome . Pflügers Archiv: European Journal of Physiology . June 2016 . 468 . 6 . 1041–1047 . 10.1007/s00424-016-1822-9. 27095039 . 4893054 . free .
  13. Billmeier . Martina . Green . Darrell . Hall . Adam E. . Turnbull . Carly . Singh . Archana . Xu . Ping . Moxon . Simon . Dalmay . Tamas . Mechanistic insights into non-coding Y RNA processing . RNA Biology . 31 December 2022 . 19 . 1 . 468–480 . 10.1080/15476286.2022.2057725 . 35354369 . 8973356 . free .
  14. Hewezi T . Epigenetic Mechanisms in Nematode–Plant Interactions . . . 58 . 1 . 2020-08-25 . 0066-4286 . 10.1146/annurev-phyto-010820-012805 . 119–138. 32413274 . 218658491 .

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