The Diversity of Small Non-coding RNA

Abstract

Abstract: RNA is a ubiquitous family of large biological molecules that perform multiple vital roles. There are many RNA types with different structure. RNA has many important biological functions for the diversity and structure. Non-coding RNA（ncRNA）show unprecedented complexity and diversity along with further research on ncRNA. This paper mainly introduced the structure and function of two categories, housekeeping ncRNA and regulation ncRNA, such as tRNA, snRNA, scRNA, rRNA, siRNA, miRNA, piRNA and nat-siRNA, in order to understand the small ncRNA diversity in vivo. It provides accessible reference source of further mining and utilization of ncRNAs and new insights on RNA recognition and status.

Key words: ncRNA , Small molecules , Diversity , Structure, Function

Huang Junjun, Wang Huahua, Liang Weihong. The Diversity of Small Non-coding RNA[J]. Biotechnology Bulletin, 2014, 0(11): 79-83.

References

[1] Holly RW. Structure of an alanine transfer ribonucleic acid[J]. JAMA, 1965, 194（8）：868-871.
[2] Frank DN, Roiha H, Guthrie C. Architecture of the U5 small nuclear RNA[J]. Molecular Cell Biology, 1994, 14（3）：2180-2190.
[3]Hüttenhofer A, Brosius J, Bachellerie JP. RNomics：identification and function of small, non-messenger RNAs[J]. Current Opinion in Chemical Biology, 2002, 6（6）：835-843.
[4]Bachellerie JP, Cavaillé J, Hüttenhofer A. The expanding snoRNA world[J]. Biochimie, 2002, 84（8）：775-790.
[5]Li X, Frank DN, Pace N, et al. Phylogenetic analysis of the structure of RNase MRP RNA in yeasts[J]. RNA, 2002, 8（6）：740-751.
[6]Michel CI, Holley CL, Scruggs BS, et al. Small nucleolar RNAs U32a, U33, and U35a are critical mediators of metabolic stress[J]. Cell Metabolism, 2011, 14（1）：33-44.
[7]Hamilton A, Baulcombe D. A species of small antisense RNA in posttranscriptional gene silencing in plants[J]. Science, 1999, 286（5441）：950-952.
[8]Zhang Z, Weinschenk T, Guo K, et al. siRNA binding proteins of microglial cells：PKR is an unanticipated ligand[J]. Journal of Cellular Biochemistry, 2006, 97（6）：1217-1229.
[9]Gaur A, Jewell DA, Liang Y, et al. Characterization of microRNA expression levels and their biological correlates in human cancer cell lines[J]. Cancer Research, 2007, 67（6）：2456-2468.
[10]王岷, 刘红雨, 陈军. 微小RNA研究进展[J]. 中国肺癌杂志, 2008, 11（4）：582-586.
[11] Saito K, Sakaquchi Y, Suzuki T, et al. Pimet, the Drosophila homolog of HEN1, mediates2'-O-methylation of Piwi-interacting RNAs at their 3' ends[J]. Genes Dev, 2007, 21（13）：1603-1608.
[12]Aravin A, Gaidatzis D, Pfeffer S, et al. A novel class of small RNAs bind to MILI protein in mouse testes[J]. Nature, 2006, 442（7099）：203-207.
[13]Sai Lakshmi S, Agrawal S. piRNABank：a web resource on classified and clustered Piwi-interacting RNAs[J]. Nucleic Acids Research, 2008, 36：173-177.
[14]Seto AG, Kingston RE, Lau NC. The coming of age for Piwi proteins[J]. Molecular Cell, 2007, 26（5）：603-609.
[15]Lin HF. piRNAs in the germ line[J]. Science, 2007, 316（5823）：397.
[16] Dueck A, Meister G. Assembly and function of small RNA-argona-ute protein complexes[J]. Biol Chem, 2014, 395（6）：611-629.
[17]Aravin AA, Lagos-Quintana M, Yalcin A, et al. The small RNA profile during Drosophila melanogaster development[J]. Dev Cell, 2003, 5（2）：337-350.
[18] Chen PY, Manninga H, Slanchev K, et al. The developmental miRNA profiles of Zebrafish as determined by small RNA cloning[J]. Genes & Dev, 2005, 19（11）：1288-1293.
[19]Vagin VV, Sigova A, Li C, et al. Adistinct small RNA path way silences selfish genetic elements in the germline[J]. Science, 2006, 313（5785）：320-324.
[20]Gunawardane LS, Saito K, Nishida KM, et al. Aslicer mediated mechanism for repeat associated siRNA 5' end formation in Drosophila[J]. Science, 2007, 315（5818）：1587-1590.
[21]Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants[J]. Cell, 2005, 121（2）：207-221.
[22]Axtell MJ, Jan C, Rajagopalan R, Bartel DP. A two-hit trigger for siRNA biogenesis in plants[J]. Cell, 2006, 127（3）：565-577.
[23]Peragine A, Yoshikawa M, Wu G, et al. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis[J]. Genes Dev, 2004, 18（19）：2368-2379.
[24]Vazquez F, Vaucheret H, Rajagopalan R, et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs[J]. Mol Cell, 2004, 16（1）：69-79.
[25]Fahlgren N, Montgomery TA, Howell MD, et al. Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis[J]. Curr Biol, 2006, 16（9）：939-944.
[26]Liu B, Chen Z, Song X, et al. Oryza sativa dicer-like4 reveals a key role for small interfering RNA silencing in plant development[J]. Plant Cell, 2007, 19（9）：2705-2718.
[27]Grant-Downton R, Le Trionnaire G, Schmid R, et al. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana[J]. BMC Genomics, 2009, 10：643.
[28]Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana[J]. Genes Dev, 2006, 20（24）：3407-3425.
[29]Nogueira FT, Madi S, Chitwood DH, et al. Two small regulatory RNAs establish opposing fates of a developmental axis[J]. Genes Dev, 2007, 21（7）：750-755.
[30] Wu L, Mao L, Qi Y. Roles of dicer-like and argonaute proteins in TAS-derived small interfering RNA-triggered DNA methylation[J]. Plant Physiol, 2012, 160（2）：990-999.
[31] Cho SH, Coruh C, Axtell MJ. miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens[J]. The Plant Cell, 2012, 24（12）：4837-4849.
[32]Axtell MJ. Classification and comparison of small RNAs from plants[J]. Annu Rev Plant Biol, 2013, 64：137-159.