Evolutionary comparisons of miRNA regulation system in six model organisms
- 416 Downloads
miRNAs are a class of endogenous small non-coding regulatory RNAs, that can mediate the transcriptional gene silencing as well as gene expression activation. miRNAs, which are found in a wide range of species, participate in cell differentiation, proliferation, development, apoptosis, tumorigenesis, metabolism, immune system, and signaling pathways. Here, we focused on the relationship between evolution and the miRNA system, with an emphasis on both miRNAs and their target genes. Six species from the evolutionary ladder were selected as a focus of this study. Public data were retrieved and combined to compare miRNAs abundance, miRNA families, molecular functions of target genes, biological processes of target genes, protein families of target gene products, transcription factors regulated by the miRNAs, signaling pathways and tissues across the six species. We found that the expansion rate of miRNAs was significantly higher compared to other genes in human evolution. Newborn miRNA families, which were quantitatively larger than dead miRNA families, seem to be closely related to the species complexity and tissue specificity. Additionally, miRNAs in higher order species were more likely to target genes related to signaling and the immune system, while miRNAs from lower order species preferred to target genes related to the embryonic development process, reproduction and growth. Meanwhile, miRNA systems displayed diversity in regulating transcription factors, signaling pathways and tissues. Our research suggested that the miRNA system might promote evolution, especially in higher species.
KeywordsmicroRNA Evolution Target genes Model organisms
We would like to extend our thanks to Professor Cao who directly instructed us for this research.
Conflict of interests
The authors declare no conflict of interests.
- Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36 (database issue):D149–D153. doi: 10.1093/nar/gkm995
- Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T (2005) The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 19(11):1288–1293. doi: 10.1101/gad.1310605 PubMedCrossRefGoogle Scholar
- Dorsett Y, McBride KM, Jankovic M, Gazumyan A, Thai TH, Robbiani DF, Di Virgilio M, Reina San-Martin B, Heidkamp G, Schwickert TA, Eisenreich T, Rajewsky K, Nussenzweig MC (2008) MicroRNA-155 suppresses activation-induced cytidine deaminase-mediated Myc-Igh translocation. Immunity 28(5):630–638. doi: 10.1016/j.immuni.2008.04.002 PubMedCentralPubMedCrossRefGoogle Scholar
- Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, Huang HD (2008) miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res 36 (Database issue):D165–D169. doi: 10.1093/nar/gkm1012
- Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 39 (database issue):D163–D169. doi: 10.1093/nar/gkq1107
- Hu HY, Guo S, Xi J, Yan Z, Fu N, Zhang X, Menzel C, Liang H, Yang H, Zhao M, Zeng R, Chen W, Paabo S, Khaitovich P (2011) MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genet 7(10):e1002327. doi: 10.1371/journal.pgen.1002327 PubMedCentralPubMedCrossRefGoogle Scholar
- Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic acids research 40 (database issue):D306–D312. doi: 10.1093/nar/gkr948
- Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic acids research 39 (database issue):D152–D157. doi: 10.1093/nar/gkq1027
- Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7):1401–1414. doi: 10.1016/j.cell.2007.04.040 PubMedCentralPubMedCrossRefGoogle Scholar
- Larroux C, Fahey B, Liubicich D, Hinman VF, Gauthier M, Gongora M, Green K, Worheide G, Leys SP, Degnan BM (2006) Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity. Evol Develop 8(2):150–173. doi: 10.1111/j.1525-142X.2006.00086.x CrossRefGoogle Scholar
- Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic acids research 37 (database issue):D155–D158. doi: 10.1093/nar/gkn809
- Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic acids research 40 (database issue):D290–D301. doi: 10.1093/nar/gkr1065
- Somel M, Liu X, Tang L, Yan Z, Hu H, Guo S, Jiang X, Zhang X, Xu G, Xie G, Li N, Hu Y, Chen W, Paabo S, Khaitovich P (2011) MicroRNA-driven developmental remodeling in the brain distinguishes human from other primates. PLoS Biol 9(12):e1001214. doi: 10.1371/journal.pbio.1001214 PubMedCentralPubMedCrossRefGoogle Scholar
- Technau U, Rudd S, Maxwell P, Gordon PM, Saina M, Grasso LC, Hayward DC, Sensen CW, Saint R, Holstein TW, Ball EE, Miller DJ (2005) Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians. Trends Genet 21(12):633–639. doi: 10.1016/j.tig.2005.09.007 PubMedCrossRefGoogle Scholar
- Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37 (database issue):D105–D110. doi: 10.1093/nar/gkn851