A novel mutation within the MIR96 gene causes non-syndromic inherited hearing loss in an Italian family by altering pre-miRNA processing

Abstract

The miR-96, miR-182 and miR-183 microRNA (miRNA) family is essential for differentiation and function of the vertebrate inner ear. Recently, point mutations within the seed region of miR-96 were reported in two Spanish families with autosomal dominant non-syndromic sensorineural hearing loss (NSHL) and in a mouse model of NSHL. We screened 882 NSHL patients and 836 normal-hearing Italian controls and identified one putative novel mutation within the miR-96 gene in a family with autosomal dominant NSHL. Although located outside the mature miR-96 sequence, the detected variant replaces a highly conserved nucleotide within the companion miR-96*, and is predicted to reduce the stability of the pre-miRNA hairpin. To evaluate the effect of the detected mutation on miR-96/mir-96* biogenesis, we investigated the maturation of miR-96 by transient expression in mammalian cells, followed by real-time reverse-transcription polymerase chain reaction (PCR). We found that both miR-96 and miR-96* levels were significantly reduced in the mutant, whereas the precursor levels were unaffected. Moreover, miR-96 and miR-96* expression levels could be restored by a compensatory mutation that reconstitutes the secondary structure of the pre-miR-96 hairpin, demonstrating that the mutation hinders precursor processing, probably interfering with Dicer cleavage. Finally, even though the mature miR-96 sequence is not altered, we demonstrated that the identified mutation significantly impacts on miR-96 regulation of selected targets. In conclusion, we provide further evidence of the involvement of miR-96 mutations in human deafness and demonstrate that a quantitative defect of this miRNA may contribute to NSHL.

Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation

“…Previously, it was speculated that this minor allele affects DICER1 processing of the miRNA (Solda et al 2012). We predicted that there was an increase of the bulge size in a bulge-depleted region, which should reduce pri-miRNA processing (Fig.…”

MiR-204 is responsible for inherited retinal dystrophy associated with ocular coloboma

“…The resulting mutations directly affected the miR-96 biogenesis and resulted in a significant reduction in the silencing of target genes. Soldà et al reported a mutation in the 3p arm of MIR96 in a family with nonsyndromic inherited hearing loss (15). This mutation was found to impair correct maturation of miR-96, leading to a significant decrease in the expression level of the mature 3p and 5p microRNA arms.…”

microRNAs and inherited retinal dystrophies

“…In PNAS, Conte et al report a dominant mutation in miR-204 that causes IRD associated with ocular coloboma in a large five-generation family (8). This paper is the first report to show that a point mutation in an individual miRNA results in significant functional consequence and causes IRD in humans, and the third miRNA in which mutations cause Mendelian inherited disorders in humans, after miR-96, which causes nonsyndromic hearing loss (9,10), and miR-184 (5, 6). Conte et al's report (8) provides a new molecular mechanism of IRD and underscores the importance of miRNA in IRD.…”