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Open Access Research article

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

Monique Ohanian1, David T Humphreys23, Elizabeth Anderson4, Thomas Preiss5 and Diane Fatkin1236*

Author affiliations

1 Molecular Cardiology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia

2 Molecular Genetics Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia

3 Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia

4 Capital Cardiac Centre, Garran, Australian Capital Territory, Australia

5 Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia

6 Cardiology Department, St Vincent’s Hospital, Darlinghurst, New South Wales, Australia

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Citation and License

BMC Genetics 2013, 14:18  doi:10.1186/1471-2156-14-18

Published: 6 March 2013

Abstract

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.

Keywords:
MicroRNA; isomiR; Genetics; Atrial fibrillation