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A map of human microRNA variation uncovers unexpectedly high levels of variability

José Carbonell1, Eva Alloza1, Pablo Arce2, Salud Borrego34, Javier Santoyo2, Macarena Ruiz-Ferrer24, Ignacio Medina1, Jorge Jiménez-Almazán15, Cristina Méndez-Vidal34, María González-del Pozo34, Alicia Vela2, Shomi S Bhattacharya26, Guillermo Antiñolo234* and Joaquín Dopazo1257*

Author Affiliations

1 Institute of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain

2 Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain

3 Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, Avda. Manuel Siurot s/n, Sevilla, 41013, Spain

4 Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Avda. Manuel Siurot s/n, Sevilla, 41013, Spain

5 BIER, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), CIPF, C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain

6 Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Avda. Americo Vespucio s/n, Sevilla, 41092, Spain

7 Functional Genomics Node (INB), CIPF, C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain

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Genome Medicine 2012, 4:62  doi:10.1186/gm363

Published: 24 August 2012

Abstract

Background

MicroRNAs (miRNAs) are key components of the gene regulatory network in many species. During the past few years, these regulatory elements have been shown to be involved in an increasing number and range of diseases. Consequently, the compilation of a comprehensive map of natural variability in a healthy population seems an obvious requirement for future research on miRNA-related pathologies.

Methods

Data on 14 populations from the 1000 Genomes Project were analyzed, along with new data extracted from 60 exomes of healthy individuals from a population from southern Spain, sequenced in the context of the Medical Genome Project, to derive an accurate map of miRNA variability.

Results

Despite the common belief that miRNAs are highly conserved elements, analysis of the sequences of the 1,152 individuals indicated that the observed level of variability is double what was expected. A total of 527 variants were found. Among these, 45 variants affected the recognition region of the corresponding miRNA and were found in 43 different miRNAs, 26 of which are known to be involved in 57 diseases. Different parts of the mature structure of the miRNA were affected to different degrees by variants, which suggests the existence of a selective pressure related to the relative functional impact of the change. Moreover, 41 variants showed a significant deviation from the Hardy-Weinberg equilibrium, which supports the existence of a selective process against some alleles. The average number of variants per individual in miRNAs was 28.

Conclusions

Despite an expectation that miRNAs would be highly conserved genomic elements, our study reports a level of variability comparable to that observed for coding genes.