A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs

Tingting Li,Dahai Zhu,Rimao Wu,Yong Zhang

doi:10.1186/1471-2164-12-186

Abstract

BackgroundFunctional studies have demonstrated that microRNAs (miRNAs or miRs) play critical roles in a wide spectrum of biological processes including development and disease pathogenesis. To investigate the functional roles that miRNAs play during chicken skeletal muscle development, the miRNA transcriptomes of skeletal muscles from broiler and layer chickens were profiled using Solexa deep sequencing.ResultsSome miRNAs have multiple isoforms and several miRNAs* are present at higher levels than their corresponding miRNAs. Thirty three novel and 189 known chicken miRNAs were identified using computational approaches. Subsequent miRNA transcriptome comparisons and real-time PCR validation experiments revealed 17 miRNAs that were differentially expressed between broilers and layers, and a number of targets of these miRNAs have been implicated in myogenesis regulation. Using integrative miRNA target-prediction and network-analysis approaches an interaction network of differentially expressed and muscle-related miRNAs and their putative targets was constructed, and miRNAs that could contribute to the divergent muscle growth of broiler and layer chickens by targeting the ACVR2B gene were identified, which can causes dramatic increases in muscle mass.ConclusionsThe present study provides the first transcriptome profiling-based evaluation of miRNA function during skeletal muscle development in chicken. Systematic predictions aided the identification of potential miRNAs and their targets, which could contribute to divergent muscle growth in broiler and layer chickens. Furthermore, these predictions generated information that can be utilized in further research investigating the involvement of interaction networks, containing miRNAs and their targets, in the regulation of muscle development.

Highlights

Functional studies have demonstrated that microRNAs play critical roles in a wide spectrum of biological processes including development and disease pathogenesis
Characterization of the miRNA transcriptome of skeletal muscle from broiler and layer chickens using deep sequencing Solexa sequencing was used to profile miRNAs expressed in layer and broiler chicken skeletal muscles
To assess the efficiency of deep sequencing for miRNA detection, all sequence reads were annotated and classified by analyzing the sequence tags in relation to the data from miRBase, RefSeq mRNA, RepeatMasker and non-protein-coding RNAs annotated by ENSEMBL

Summary

Introduction

Functional studies have demonstrated that microRNAs (miRNAs or miRs) play critical roles in a wide spectrum of biological processes including development and disease pathogenesis. Embryonic patterning and organogenesis involve coordinated differentiation, migration, proliferation and programmed cell death in metazoans. These complex cellular and developmental processes rely on precise spatiotemporal networks that regulate transcription factors at multiple levels including mRNA transcription and translation, protein stability and degradation. Evidence has demonstrated that microRNAs (miRNAs or miRs) are involved in diverse aspects of biology including developmental regulation and the pathogenesis of human diseases [1,2,3,4]. Expression of miR-181 isoforms, miR-181a and miR-181b, are induced upon initiation of myogenesis and they participate in the regulation of myoblast differentiation by repressing HoxA-11 protein levels [24]. Identifying novel miRNAs that are expressed at low levels during skeletal muscle development but are functionally important requires robust approaches such as high-throughput deep sequencing technology

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