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]: 366 

See also: Bacterial small RNA

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.[5] 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".[3]: 162 

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]

References
  1. Storz G (May 2002). "An expanding universe of noncoding RNAs". Science. 296 (5571): 1260–3. Bibcode:2002Sci...296.1260S. doi:10.1126/science.1072249. PMID 12016301. S2CID 35295924.
  2. Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, et al. (March 2007). "A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila". Science. 315 (5818): 1587–90. doi:10.1126/science.1140494. PMID 17322028. S2CID 11513777.
  3. Meyers RA (2012). Epigenetic Regulation and Epigenomics. Wiley-Blackwell. ISBN 978-3-527-66861-8.
  4. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (September 2005). "Elucidation of the small RNA component of the transcriptome". Science. 309 (5740): 1567–9. Bibcode:2005Sci...309.1567L. doi:10.1126/science.1114112. PMID 16141074. S2CID 1651848.
  5. Wu Q, Lu Z, Li H, Lu J, Guo L, Ge Q (2011). "Next-generation sequencing of microRNAs for breast cancer detection". Journal of Biomedicine & Biotechnology. 2011: 597145. doi:10.1155/2011/597145. PMC 3118289. PMID 21716661.
  6. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, et al. (December 2006). "Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans". Cell. 127 (6): 1193–207. doi:10.1016/j.cell.2006.10.040. PMID 17174894. S2CID 16838469.
  7. Witten D, Tibshirani R, Gu SG, Fire A, Lui WO (May 2010). "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. doi:10.1186/1741-7007-8-58. PMC 2880020. PMID 20459774.
  8. Gui Y, Liu H, Zhang L, Lv W, Hu X (November 2015). "Altered microRNA profiles in cerebrospinal fluid exosome in Parkinson disease and Alzheimer disease". Oncotarget. 6 (35): 37043–53. doi:10.18632/oncotarget.6158. PMC 4741914. PMID 26497684.
  9. Keller A, Leidinger P, Lange J, Borries A, Schroers H, Scheffler M, et al. (October 2009). "Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls". PLOS ONE. 4 (10): e7440. Bibcode:2009PLoSO...4.7440K. doi:10.1371/journal.pone.0007440. PMC 2757919. PMID 19823682.
  10. Green, D; Dalmay, T; Chapman, T (February 2016). "Microguards and micromessengers of the genome". Heredity. 116 (2): 125–134. doi:10.1038/hdy.2015.84.
  11. Wei H, Zhou B, Zhang F, Tu Y, Hu Y, Zhang B, Zhai Q (2013). "Profiling and identification of small rDNA-derived RNAs and their potential biological functions". PLOS ONE. 8 (2): e56842. Bibcode:2013PLoSO...856842W. doi:10.1371/journal.pone.0056842. PMC 3572043. PMID 23418607.
  12. Green, Darrell; Fraser, William D.; Dalmay, Tamas (June 2016). "Transfer RNA-derived small RNAs in the cancer transcriptome". Pflügers Archiv: European Journal of Physiology. 468 (6): 1041–1047. doi:10.1007/s00424-016-1822-9.
  13. Billmeier, Martina; Green, Darrell; Hall, Adam E.; Turnbull, Carly; Singh, Archana; Xu, Ping; Moxon, Simon; Dalmay, Tamas (31 December 2022). "Mechanistic insights into non-coding Y RNA processing". RNA Biology. 19 (1): 468–480. doi:10.1080/15476286.2022.2057725. PMID 35354369.
  14. Hewezi T (2020-08-25). "Epigenetic Mechanisms in Nematode–Plant Interactions". Annual Review of Phytopathology. Annual Reviews. 58 (1): 119–138. doi:10.1146/annurev-phyto-010820-012805. ISSN 0066-4286. PMID 32413274. S2CID 218658491.


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