Small RNA
Small RNA are <200 nt (nucleotide) in length, and are usually non-coding RNA molecules.[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 can be selected by MicroRNA sequencing, a technique that selects small RNA molecules, then sequences those of 21–25 bp size. The first analysis of small RNAs using miRNA-seq methods examined approximately 1.4 million small RNAs from the model plant Arabidopsis thaliana using Lynx Therapeutics' Massively Parallel Signature Sequencing (MPSS) sequencing platform. This study demonstrated the potential of novel, high-throughput sequencing technologies for the study of small RNAs, and it showed that genomes generate large numbers of small RNAs with plants as particularly rich sources of small RNAs.[4] Later studies used other sequencing technologies, such as a study in C. elegans which identified 18 novel miRNA genes as well as a new class of nematode small RNAs termed 21U-RNAs.[5] Another study comparing small RNA profiles of human cervical tumours and normal tissue, utilized the Illumina (company) Genome Analyzer to identify 64 novel human miRNA genes as well as 67 differentially expressed miRNAs.[6] Applied Biosystems SOLiD sequencing platform has also been used to examine the prognostic value of miRNAs in detecting human breast cancer.[7] Small RNA is useful for certain kinds of study because its molecules "do not need to be fragmented prior to library preparation".[8]
Kinds of small RNA include:
- microRNA (miRNA)
- Piwi-interacting RNA (piRNA)
- small interfering RNA (siRNA)
- small nucleolar RNA (snoRNAs)
- tRNA-derived small RNA (tsRNA)[9]
- small rDNA-derived RNA (srRNA)[10]
- small nuclear RNA, also commonly referred to as U-RNA
References
- ^ Storz, G (17 May 2002). "An expanding universe of noncoding RNAs". Science (New York, N.Y.). 296 (5571): 1260–3. PMID 12016301.
- ^ Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, Siomi H, Siomi MC (Mar 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.
- ^ Robert A. Meyers, Epigenetic Regulation and Epigenomics (2012), p. 366.
- ^ Lu, C; Tej, SS; Luo, S; Haudenschild, CD; Meyers, BC; Green, PJ (Sep 2, 2005). "Elucidation of the small RNA component of the transcriptome". Science. 309 (5740): 1567–9. doi:10.1126/science.1114112. PMID 16141074.
- ^ Ruby, J. Graham; Jan, Calvin; Player, Christopher; Axtell, Michael J.; Lee, William; Nusbaum, Chad; Ge, Hui; Bartel, David P. (2006). "Large-Scale Sequencing Reveals 21U-RNAs and Additional MicroRNAs and Endogenous siRNAs in C. elegans". Cell. 127 (6): 1193–1207. doi:10.1016/j.cell.2006.10.040. ISSN 0092-8674. PMID 17174894.
- ^ Witten, Daniela; Tibshirani, Robert; Gu, Sam; Fire, Andrew; Lui, Weng-Onn (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. ISSN 1741-7007.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Wu, Qian; Lu, Zuhong; Li, Hailing; Lu, Jiafeng; Guo, Li; Ge, Qinyu (2011). "Next-Generation Sequencing of MicroRNAs for Breast Cancer Detection". Journal of Biomedicine and Biotechnology. 2011: 1–7. doi:10.1155/2011/597145. ISSN 1110-7243.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Robert A. Meyers, Epigenetic Regulation and Epigenomics (2012), p. 162.
- ^ Chen, Q; Yan, M; Cao, Z; Li, X; Zhang, Y; Shi, J; Feng, GH; Peng, H; Zhang, X; Zhang, Y; Qian, J; Duan, E; Zhai, Q; Zhou, Q (22 January 2016). "Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder". Science (New York, N.Y.). 351 (6271): 397–400. PMID 26721680.
- ^ 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. PMID 23418607.
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