Deciphering the miRNA transcriptome of breast muscle from the embryonic to post-hatching periods in chickens

Jie Liu,Fuwei Li,Dingguo Cao,Haixia Han,Wei Liu,Yan Zhou,Qiuxia Lei,Xin Hu

doi:10.1186/s12864-021-07374-y

Abstract

BackgroundmiRNAs play critical roles in growth and development. Various studies of chicken muscle development have focused on identifying miRNAs that are important for embryo or adult muscle development. However, little is known about the role of miRNAs in the whole muscle development process from embryonic to post-hatching periods. Here, we present a comprehensive investigation of miRNA transcriptomes at 12-day embryo (E12), E17, and day 1 (D1), D14, D56 and D98 post-hatching stages.ResultsWe identified 337 differentially expressed miRNAs (DE-miRNAs) during muscle development. A Short Time-Series Expression Miner analysis identified two significantly different expression profiles. Profile 4 with downregulated pattern contained 106 DE-miRNAs, while profile 21 with upregulated pattern contained 44 DE-miRNAs. The DE-miRNAs with the upregulated pattern mainly played regulatory roles in cellular turnover, such as pyrimidine metabolism, DNA replication, and cell cycle, whereas DE-miRNAs with the downregulated pattern directly or indirectly contributed to protein turnover metabolism such as glycolysis/gluconeogenesis, pyruvate metabolism and biosynthesis of amino acids.ConclusionsThe main functional miRNAs during chicken muscle development differ between embryonic and post-hatching stages. miRNAs with an upregulated pattern were mainly involved in cellular turnover, while miRNAs with a downregulated pattern mainly played a regulatory role in protein turnover metabolism. These findings enrich information about the regulatory mechanisms involved in muscle development at the miRNA expression level, and provide several candidates for future studies concerning miRNA-target function in regulation of chicken muscle development.

Highlights

MiRNAs play critical roles in growth and development
Our previous study showed that there were distinct gene regulatory mechanisms of chicken muscle development between the embryonic and post-hatching periods, based on RNA sequencing of breast muscle tissue obtained from Shouguang chickens at 12-day embryo (E12), E17 and day 1 (D1), D14, D56 and D98 post-hatching stages [14]
Differential expression of miRNAs We identified 615 mature miRNAs corresponding to 401 precursor sequences based on the 18 small RNA libraries (Table S1), in which 337 miRNAs were differentially expressed during muscle development (Table S2)

Summary

Introduction

MiRNAs play critical roles in growth and development. Various studies of chicken muscle development have focused on identifying miRNAs that are important for embryo or adult muscle development. Little is known about the role of miRNAs in the whole muscle development process from embryonic to post-hatching periods. Postnatal muscle hypertrophy is mainly associated with accumulation of muscle-specific proteins [13] In addition to these complex cell developmental processes during myofiber formation and hypertrophy, the fine-tuned regulation of numerous myogenic genes is important for the development of skeletal muscle [4]. Our previous study showed that there were distinct gene regulatory mechanisms of chicken muscle development between the embryonic and post-hatching periods, based on RNA sequencing of breast muscle tissue obtained from Shouguang chickens at 12-day embryo (E12), E17 and day 1 (D1), D14, D56 and D98 post-hatching stages [14]. A comprehensive study of the dynamics of miRNAs during chicken muscle development is lacking, especially from embryonic to post-hatching period. Jebessa et al explored the miRNA expression profile during chicken leg muscle development at E11, E16 and D1 [15], while Li et al analyzed miRNA and mRNA expression profiles during chicken breast muscle development at 6, 14, 22 and 30 weeks of age [16]

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Conclusion