Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression

Guan-Zheng Luo,Zhimin Shi,Thomas Tuschl,Miguel Brown,Xiu-Jie Wang,Xiaoching Li,Markus Hafner,Gui-Hai Feng

doi:10.1186/1471-2164-13-727

Abstract

BackgroundMicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes. The zebra finch (Taeniopygia guttata), an oscine songbird with characteristic learned vocal behavior, provides biologists a unique model system for studying vocal behavior, sexually dimorphic brain development and functions, and comparative genomics.ResultsWe deep sequenced small RNA libraries made from the brain, heart, liver, and muscle tissues of adult male and female zebra finches. By mapping the sequence reads to the zebra finch genome and to known miRNAs in miRBase, we annotated a total of 193 miRNAs. Among them, 29 (15%) are avian specific, including three novel zebra finch specific miRNAs. Many of the miRNAs exhibit sequence heterogeneity including length variations, untemplated terminal nucleotide additions, and internal substitution events occurring at the uridine nucleotide within a GGU motif. We also identified seven Z chromosome-encoded miRNAs. Among them, miR-2954, an avian specific miRNA, is expressed at significantly higher levels in males than in females in all tissues examined. Target prediction analysis reveals that miR-2954, but not other Z-linked miRNAs, preferentially targets Z chromosome-encoded genes, including several genes known to be expressed in a sexually dimorphic manner in the zebra finch brain.ConclusionsOur genome-wide systematic analysis of mature sequences, genomic locations, evolutionary sequence conservation, and tissue expression profiles of the zebra finch miRNA repertoire provides a valuable resource to the research community. Our analysis also reveals a miRNA-mediated mechanism that potentially regulates sex-biased gene expression in avian species.

Highlights

MicroRNAs are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes
MiRNAs function by binding to the 3 -untranslated regions (UTRs) of target mRNAs via sequence complementarity to induce mRNA degradation or repress protein translation [14,15,16]. miRNAs have been found in most eukaryotes and many of them are conserved through evolution
Following the general criteria for miRNA annotation [37], we identified three novel zebra finch specific miRNA candidates, which are supported by good hairpin-like precursor structures, presence of corresponding star sequences, and relatively high expression (Figure 1A)

Summary

Introduction

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes. MicroRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression post-transcriptionally [1]. MiRNAs function by binding to the 3 -untranslated regions (UTRs) of target mRNAs via sequence complementarity to induce mRNA degradation or repress protein translation [14,15,16]. It is estimated that over 60% of human protein-coding genes might be regulated by miRNAs [22]. MiRNAs regulate many biological processes ranging from cell proliferation, cell fate specification, cell differentiation, apoptosis, animal development, metabolism, to various disease conditions [1,16,23]

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