title: Role of miRNAs and alternative mRNA 3'-end cleavage and polyadenylation of their mRNA targets in cardiomyocyte hypertrophy.
abstract: miRNAs play critical roles in heart disease. In addition to differential miRNA expression, miRNA-mediated control is also affected by variable miRNA processing or alternative 3'-end cleavage and polyadenylation (APA) of their mRNA targets. To what extent these phenomena play a role in the heart remains unclear. We sought to explore miRNA processing and mRNA APA in cardiomyocytes, and whether these change during cardiac hypertrophy. Thoracic aortic constriction (TAC) was performed to induce hypertrophy in C57BL/6J mice. RNA extracted from cardiomyocytes of sham-treated, pre-hypertrophic (2 days post-TAC), and hypertrophic (7 days post-TAC) mice was subjected to small RNA- and poly(A)-test sequencing (PAT-Seq). Differential expression analysis matched expectations; nevertheless we identified ~400 mRNAs and hundreds of noncoding RNA loci as altered with hypertrophy for the first time. Although multiple processing variants were observed for many miRNAs, there was little change in their relative proportions during hypertrophy. PAT-Seq mapped ~48,000 mRNA 3'-ends, identifying novel 3' untranslated regions (3'UTRs) for over 7000 genes. Importantly, hypertrophy was associated with marked changes in APA with a net shift from distal to more proximal mRNA 3'-ends, which is predicted to decrease overall miRNA repression strength. We independently validated several examples of 3'UTR proportion change and showed that alternative 3'UTRs associate with differences in mRNA translation. Our work suggests that APA contributes to altered gene expression with the development of cardiomyocyte hypertrophy and provides a rich resource for a systems-level understanding of miRNA-mediated regulation in physiological and pathological states of the heart.
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia.
authors.forename: R
authors.initials: R
authors.lastname: Soetanto
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia.
authors.forename: C J
authors.initials: CJ
authors.lastname: Hynes
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia.
authors.forename: H R
authors.initials: HR
authors.lastname: Patel
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.
authors.forename: D T
authors.initials: DT
authors.lastname: Humphreys
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia.
authors.forename: M
authors.initials: M
authors.lastname: Evers
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia.
authors.forename: G
authors.initials: G
authors.lastname: Duan
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia.
authors.forename: B J
authors.initials: BJ
authors.lastname: Parker
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia; Monash Bioinformatics Platform, Monash University, Melbourne, Victoria 3800, Australia.
authors.forename: S K
authors.initials: SK
authors.lastname: Archer
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia.
authors.forename: J L
authors.initials: JL
authors.lastname: Clancy
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.
authors.forename: R M
authors.initials: RM
authors.lastname: Graham
authors.affiliation: Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia.
authors.forename: T H
authors.initials: TH
authors.lastname: Beilharz
authors.affiliation: Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia.
authors.forename: N J
authors.initials: NJ
authors.lastname: Smith
authors.affiliation: EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia. Electronic address: thomas.preiss@anu.edu.au.
authors.forename: T
authors.initials: T
authors.lastname: Preiss
mesh_terms: D000818:Animals; D005786:Gene Expression Regulation; D006801:Humans; D006984:Hypertrophy / Q000235:genetics*; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D032383:Myocytes, Cardiac / Q000378:metabolism* / Q000473:pathology; D026723:Polyadenylation / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D012323:RNA Processing, Post-Transcriptional
chemical_list: D035683:MicroRNAs
keywords: APA; Cardiac hypertrophy; RNA-seq; mRNA 3′UTR; microRNA