Genetic variation may play a crucial role in non-coding RNA biogenesis

DOI: 10.4236/ajmb.2012.24040   PDF   HTML   XML   3,392 Downloads   7,192 Views   Citations

Abstract

Transcription, post-transcriptional modification, translation, post-translational modification, DNA replication, and signaling interaction of intra- and extra- cellular components are the relevant mechanisms in gene regulation. Transcription is one of the most important mechanisms in the control of gene expression. Further, post-transcriptional modifications play a crucial role after transcription which determine whether the transcribed gene is coding or non-coding RNA (ncRNAs). Genome-wide analysis of RNAs provides information about the coding RNAs, whereas the status of ncRNAs are still at large and must be discussed in detail as variations in the ncRNAs can lead to different phenotypes. In this short article, we discuss the role of genetic variation in ncRNA genes and how this variation may play a crucial role in ncRNA biogenesis that eventually leads to phenotypic variation and thus speciation.

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Kandhavelu, J. and Kandhavelu, M. (2012) Genetic variation may play a crucial role in non-coding RNA biogenesis. American Journal of Molecular Biology, 2, 386-389. doi: 10.4236/ajmb.2012.24040.

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1] Crick F. Central dogma of molecular biology, Nature 1970;227:561-563. doi:10.1038/227561a0
[2] Mattick JS. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms, Bioessays 2003;25:930-939. doi:10.1002/bies.10332
[3] Dignam JD, Lebovitz RM, Roeder RG. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei, Nucleic Acids Res 1983;11:1475-1489. doi:10.1093/nar/11.5.1475
[4] Eddy SR. Non-coding RNA genes and the modern RNA world, Nat Rev Genet 2001;2:919-929. doi:10.1038/35103511
[5] Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world, Genes Dev 2009;23:1494-1504. doi:10.1101/gad.1800909
[6] Mercer TR, Dinger ME, Mattick JS. Long noncoding RNAs: insights into functions, Nat Rev Genet 2009;10:155-159. doi:10.1038/nrg2521
[7] He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene regulation, Nat Rev Genet 2004;5:522-531. doi:10.1038/nrg1379
[8] McKnight SL, Kingsbury R. Transcriptional control signals of a eukaryotic protein-coding gene, Science 1982;217:316-324. doi:10.1126/science.6283634
[9] MacArthur DG, Balasubramanian S, Frankish A et al. A systematic survey of loss-of-function variants in human protein-coding genes, Science 2012;335:823-828. doi:10.1126/science.1215040
[10] Mayr E. Animal species and evolution. Cambridge,: Belknap Press of Harvard University Press, 1963.
[11] Hobolth A, Christensen OF, Mailund T et al. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model, PLoS Genet 2007;3:e7. doi:10.1371/journal.pgen.0030007
[12] Ritz J, Martin JS, Laederach A. Evaluating our ability to predict the structural disruption of RNA by SNPs, BMC Genomics 2012;13 Suppl 4:S6. doi:10.1186/1471-2164-13-S4-S6
[13] Mattick JS, Makunin IV. Non-coding RNA, Hum Mol Genet 2006;15 Spec No 1:R17-29. doi:10.1093/hmg/ddl046
[14] Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals, Nat Rev Mol Cell Biol 2009;10:126-139. doi:10.1038/nrm2632
[15] Scott MS, Avolio F, Ono M et al. Human miRNA Precursors with Box H/ACA snoRNA Features, Plos Computational Biology 2009;5.
[16] Kandhavelu M, Lammi C, Buccioni M et al. Existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens, Journal of Bioinformatics and Sequence Analysis 2009;1(2):31-40.
[17] Kandhavelu M, Kandhavelu J. prepiRNA biogenesis mimics the pathway of miRNA. Biochemical Systematics and Ecology, 2012. doi:10.1016/j.bse.2012.03.012
[18] Eddy SR. Computational genomics of noncoding RNA genes, Cell 2002;109:137-140. doi:10.1016/S0092-8674(02)00727-4
[19] Hutvagner G, McLachlan J, Pasquinelli AE et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA, Science 2001;293:834-838. doi:10.1126/science.1062961
[20] Gregory RI, Chendrimada TP, Cooch N et al. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing, Cell 2005;123:631-640. doi:10.1016/j.cell.2005.10.022
[21] Draper DE. A guide to ions and RNA structure, Rna-a Publication of the Rna Society 2004;10:335-343.
[22] Draper DE. RNA folding: thermodynamic and molecular descriptions of the roles of ions, Biophys J 2008; 95:5489-5495. doi:10.1529/biophysj.108.131813
[23] Mathews DH, Sabina J, Zuker M et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, J Mol Biol 1999;288:911-940. doi:10.1006/jmbi.1999.2700
[24] Chillon M, Dork T, Casals T et al. A novel donor splice site in intron 11 of the CFTR gene, created by mutation 1811+1.6kbA-->G, produces a new exon: high frequency in Spanish cystic fibrosis chromosomes and association with severe phenotype, Am J Hum Genet 1995;56:623-629.
[25] Montgomery SB, Dermitzakis ET. From expression QTLs to personalized transcriptomics, Nat Rev Genet 2011;12:277-282. doi:10.1038/nrg2969
[26] Quintana-Murci L. Genetics. Gene losses in the human genome, Science 2012;335:806-807. doi:10.1126/science.1219299
[27] Darwin C. On the origin of species by means of natural selection. London,: J. Murray, 1859.
[28] Cairns J. Mutation selection and the natural history of cancer, Nature 1975;255:197-200. doi:10.1038/255197a0
[29] Garzon R, Calin GA, Croce CM. MicroRNAs in Cancer, Annu Rev Med 2009;60:167-179. doi:10.1146/annurev.med.59.053006.104707

  
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