MicroRNAs in cardiac arrhythmia: DNA sequence variation of MiR-1 and MiR-133A in long QT syndrome

Abstract

Long QT syndrome (LQTS) is a genetic cardiac condition associated with prolonged ventricular repolarization, primarily a result of perturbations in cardiac ion channels, which predisposes individuals to life-threatening arrhythmias. Using DNA screening and sequencing methods, over 700 different LQTS-causing mutations have been identified in 13 genes worldwide. Despite this, the genetic cause of 30-50% of LQTS is presently unknown. MicroRNAs (miRNAs) are small (∼ 22 nucleotides) noncoding RNAs which post-transcriptionally regulate gene expression by binding complementary sequences within messenger RNAs (mRNAs). The human genome encodes over 1800 miRNAs, which target about 60% of human genes. Consequently, miRNAs are likely to regulate many complex processes in the body, indeed aberrant expression of various miRNA species has been implicated in numerous disease states, including cardiovascular diseases. MiR-1 and MiR-133A are the most abundant miRNAs in the heart and have both been reported to regulate cardiac ion channels. We hypothesized that, as a consequence of their role in regulating cardiac ion channels, genetic variation in the genes which encode MiR-1 and MiR-133A might explain some cases of LQTS. Four miRNA genes (miR-1-1, miR-1-2, miR-133a-1 and miR-133a-2), which encode MiR-1 and MiR-133A, were sequenced in 125 LQTS probands. No genetic variants were identified in miR-1-1 or miR-133a-1; but in miR-1-2 we identified a single substitution (n.100A> G) and in miR-133a-2 we identified two substitutions (n.-19G> A and n.98C> T). None of the variants affect the mature miRNA products. Our findings indicate that sequence variants of miR-1-1, miR-1-2, miR-133a-1 and miR-133a-2 are not a cause of LQTS in this cohort.

Keywords: DNA mutational analysis; gene expression regulation; long QT syndrome; single nucleotide polymorphism.

Figure 1.

(A) Genomic structure of the miR-1 and miR-133 clusters. (B) Genomic structure of mir-1-2 and mir-133a-2, variants identified in this study are represented by a red line. The minor allele frequencies (MAF) indicated here are representative of the CEU population as reported in 1000 genomes [60], except rs200375711 (mir-133a-2:n.98C> T) which was not identified in 1000 genomes but was identified in one of 493 atherosclerosis patients of European descent from the ClinSeq whole-exome sequencing project [53]. This Figure is reproduced in colour in the online version of The Scandinavian Journal of Clinical & Laboratory Investigation.

Figure 2.

(A) Pri-miR-1-2 multiple species sequence alignment. Pre-miR-1-2 is indicated in a blue box, mature MiR-1 is indicated in a red box, the seed region is highlighted, rs9989532 is indicated by a black arrow. (B) Pre-miR-1-2 secondary structure, mature MiR-1 is indicated in red. Secondary structure was predicted using RNAfold Web Server [50]. This Figure is reproduced in colour in the online version of The Scandinavian Journal of Clinical & Laboratory Investigation.

Figure 3.

(A) Pri-miR-133a-2 multiple species sequence alignment. Pre-miR-133a-2 is indicated in a blue box, mature MiR-133A is indicated in a red box, the seed region is highlighted, rs13040413 and rs200375711 are indicated by black arrows. (B) Pre-miR-133a-2 secondary structure, mature MiR-133A is indicated in red, n.98C is indicated in blue. Secondary structure was predicted using RNAfold Web Server [50]. This Figure is reproduced in colour in the online version of The Scandinavian Journal of Clinical & Laboratory Investigation.