A heterozygous variant in the human cardiac miR-133 gene, MIR133A2, alters miRNA duplex processing and strand abundance

BMC Genetics

Diane Fatkin¹  Thomas Preiss³  Elizabeth Anderson²  David T Humphreys⁴  Monique Ohanian⁵ 

[1] Cardiology Department, St Vincent’s Hospital, Darlinghurst, New South Wales, Australia;Capital Cardiac Centre, Garran, Australian Capital Territory, Australia;Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia;Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia;Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia

关键词: Atrial fibrillation;    Genetics;    isomiR;    MicroRNA;   

Others  :  1087302
DOI  :  10.1186/1471-2156-14-18

 received in 2012-08-28, accepted in 2013-02-27,  发布年份 2013

【 摘 要 】

Background

MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression. Sequential cleavage of miRNA precursors results in a ~22 nucleotide duplex of which one strand, the mature miRNA, is typically loaded into the RNA-induced silencing complex (RISC) while the passenger strand is degraded. Very little is known about how genetic variation might affect miRNA biogenesis and function.

Results

We re-sequenced the MIR1-1, MIR1-2, MIR133A1, MIR133A2, and MIR133B genes, that encode the cardiac-enriched miRNAs, miR-1 and miR-133, in 120 individuals with familial atrial fibrillation and identified 10 variants, including a novel 79T > C MIR133A2 substitution. This variant lies within the duplex at the 3^′ end of the mature strand, miR-133a-3p, and is predicted to prevent base-pairing and weaken thermostability at this site, favoring incorporation of the passenger strand, miR-133a-5p, into RISC. Genomic DNA fragments containing miR-133a-2 precursor sequences with 79T and 79C alleles were transfected into HeLa cells. On Northern blotting the 79T allele showed strong expression of miR-133a-3p with weak expression of miR-133a-5p. In contrast, the 79C allele had no effect on miR-133a-3p but there was a significant increase (mean 3.6-fold) in miR-133a-5p levels. Deep sequencing of small RNA libraries prepared from normal human and murine atria confirmed that nearly all the mature miR-133a was comprised of miR-133a-3p and that levels of miR-133a-5p were very low. A number of isomiRs with variations at 5^′ and 3^′ ends were identified for both miR-133a-3p and miR-133a-5p, with 2 predominant miR-133a-3p isomiRs and one predominant miR-133a-5p isomiR. Bioinformatics analyses indicate that the major miR-133a-3p and 5p isomiRs have numerous predicted target mRNAs, only a few of which are in common.

Conclusions

Multiple miR-133a isomiRs with potential different mRNA target profiles are present in the atrium in humans and mice. We identified a human 79T > C MIR133A2 variant that alters miRNA processing and results in accumulation of the miR-133a-5p strand that is usually degraded.

【 授权许可】

   
2013 Ohanian et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

【 参考文献 】

• [1]Fabian MR, Sonenberg N, Filipowicz W: Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 2010, 79:351-379.
• [2]Kozomara A, Griffiths-Jones S: miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39(Suppl 1):D152-D157.
• [3]Mendell JT, Olson EN: MicroRNAs in stress signaling and human disease. Cell 2012, 148:1172-1187.
• [4]Winter J, Jung S, Keller S, Gregory RI, Diederichs S: Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 2009, 11:228-234.
• [5]Fernandez-Valverde SL, Taft RJ, Mattick JS: Dynamic isomiR regulation in Drosophila development. RNA 2010, 16:1881-1888.
• [6]Lee LW, Zhang S, Etheridge A, Ma L, Martin D, Galas D, Wang K: Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 2010, 16:2170-2180.
• [7]Cloonan N, Wani S, Xu Q, Gu J, Lea K, Heater S, Barbacioru C, Steptoe AL, Martin HC, Nourbaksh E, Krishnan K, Gardiner B, Wang X, Nones K, Steen JA, Matigian NA, Wood DL, Kassahn KS, Waddell N, Shepherd J, Lee C, Ichikawa J, McKernan K, Bramlett K, Kuersten S, Grimmond SM: MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biol 2011, 12:R126. BioMed Central Full Text
• [8]Humphreys DT, Hynes CJ, Patel HR, Wei GH, Cannon L, Fatkin D, Suter CM, Clancy JL, Preiss T: Complexity of murine cardiomyocyte miRNA biogenesis, sequence variant expression and function. PLoS One 2012, 7:e30933.
• [9]Liang Y, Ridzon D, Wong L, Chen C: Characterization of microRNA expression in normal human tissues. BMC Genomics 2007, 8:166. BioMed Central Full Text
• [10]Luo X, Zhang H, Xiao J, Wang Z: Regulation of human cardiac ion channel genes by microRNAs: theoretical perspective and pathophysiological implications. Cell Physiol Biochem 2010, 25:571-586.
• [11]Zhao Y, Ransom JF, Li A, Vedantham V, Von Drehle M, Muth AN, Tsuchihashi T, McManus MT, Schwartz RJ, Srivastava D: Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 2007, 129:303-317.
• [12]Care A, Catalucci D, Felicetti F, Bonci D, Addario A, Gallo P, Bang ML, Segnalini P, Gu Y, Dalton ND, Elia L, Latronico MV, Høydal M, Autore C, Russo MA, Dorn GW II, Ellingsen O, Ruiz-Lozano P, Peterson KL, Croce CM, Peschle C, Condorelli G: MicroRNA-133 controls cardiac hypertrophy. Nat Med 2007, 13:613-618.
• [13]Duisters RF, Tijsen AJ, Schroen B, Leenders JJ, Lentink V, van der Made I, Herias V, Van Leeuwen RE, Schellings MW, Barenbrug F, Maessen JG, Heymans S, Pinto YM, Creemers EE: MiR-133 and miR-30 regulate connective tissue growth factor: implications for a role of microRNAs in myocardial matrix remodeling. Circ Res 2009, 104:170-178.
• [14]Matkovich SJ, Wang W, Tu Y, Eschenbacher WH, Dorn LE, Condorelli G, Diwan A, Nerboone JM, Dorn GW II: MicroRNA-133a protects against myocardial fibrosis and modulates electrical repolarization without affecting hypertrophy in pressure-overloaded adult hearts. Circ Res 2010, 106:166-175.
• [15]Belevych AE, Sansom SE, Terentyeva R, Ho HT, Nishijima Y, Martin MM, Jindal HK, Rochira JA, Kunitomo Y, Abdellatif M, Carnes CA, Elton TS, Györke S, Terentyev D: MicroRNA-1 and-133 increase arrhythmogenesis in heart failure by dissociating phosphatase activity from RyR2 complex. PLoS One 2011, 6:e28324.
• [16]Matkovich SJ, Van Booven DJ, Eschenbacher WH, Dorn GW: RISC RNA sequencing for context-specific identification of in vivo microRNA targets. Circ Res 2011, 108:18-26.
• [17]Girmatsion Z, Biliczki P, Bonauer A, Wimmer-Greinecker G, Scherer M, Moritz A, Bukowska A, Goette A, Nattel S, Hohnloser SH, Ehrlich JR: Changes in microRNA-1 expression and IK1 up-regulation in human atrial fibrillation. Heart Rhythm 2009, 6:1802-1809.
• [18]Xiao J, Liang D, Zhang Y, Liu Y, Zhang H, Liu Y, Li L, Liang X, Sun Y, Chen YH: MicroRNA expression signature in atrial fibrillation with mitral stenosis. Physiol Genomics 2011, 43:655-664.
• [19]Cooley N, Cowley MJ, Lin RC, Marasco S, Wong C, Kaye DM, Dart AM, Woodcock EA: Influence of atrial fibrillation on microRNA expression profiles in left and right atria from patients with valvular heart disease. Physiol Genomics 2012, 44:211-219.
• [20]De Mena L, Coto E, Cardo LF, Diaz M, Blazquez M, Ribacoba R, Salvador C, Pastor P, Samaranch L, Moris G, Menéndez M, Corao AI, Alvarez V: Analysis of the Micro-RNA-133 and PITX3 genes in Parkinson’s disease. Am J Med Genet 2010, 153B:1234-1239.
• [21]Liu N, Bezprozvannaya S, Williams AH, Qi X, Richardson JA, Bassel-Duby R, Olson EN: MicroRNA-133a regulates cardiomyocyte proliferation and suppresses smooth muscle gene expression in the heart. Genes Dev 2008, 22:3242-3254.
• [22]Saunders MA, Liang H, Li WH: Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci 2007, 104:3300-3305.
• [23]Borel C, Antonarakis SE: Functional genetic variation of human miRNAs and phenotypic consequences. Mamm Genome 2008, 19:503-509.
• [24]Kim J, Bartel DP: Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression. Nat Biotechnol 2009, 27:472-477.
• [25]Ryan BM, Robles AI, Harris CC: Genetic variation in microRNA networks: the implications for cancer research. Nat Rev Cancer 2010, 10:389-402.
• [26]Mencia A, Modamio-Hoybjor S, Redshaw N, Morin M, Mayo-Merino F, Olavarrieta L, Aguirre LA, Del Castillo I, Steel KP, Dalmay T, Moreno F, Moreno-Pelayo MA: Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat Genet 2009, 41:609-613.
• [27]Dorn GW II, Matkovich SJ, Eschenbacher WH, Zhang Y: A human 3’ miR-499 mutation alters cardiac mRNA targeting and function. Circ Res 2012, 110:958-967.
• [28]Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC: Widespread regulatory activity of vertebrate microRNA* species. RNA 2011, 17:312-326.
• [29]Starega-Roslan J, Krol J, Koscianska E, Kozlowski P, Szlachcic WJ, Sobczak K, Krzyzosiak WJ: Structural basis of miRNA length variety. Nucleic Acids Res 2011, 39:257-268.
• [30]Marti E, Pantano L, Banez-Coronel M, Llorens F, Minones-Moyano E, Porta S, Sumoy L, Ferrer I, Estivill X: A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing. Nucleic Acids Res 2010, 38:7219-7235.
• [31]Bostjancic E, Zidar N, Stajer D, Glavac D: MicroRNAs miR-1, miR-133a, miR-133b, and miR-208 are dysregulated in human myocardial infarction. Cardiology 2010, 115:163-169.
• [32]Beilharz TH, Humphreys DT, Clancy JL, Thermann R, Martin DI, Hentze MW, Preiss T: MicroRNA-mediated messenger RNA deadenylation contributes to translational repression in mammalian cells. PLoS One 2009, 4:e6783.
• [33]Lewis BP, Burge CB, Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.