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Genes 2018, 9(1), 34; doi:10.3390/genes9010034

Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis

College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou 225000, China
Authors to whom correspondence should be addressed.
Received: 9 November 2017 / Revised: 22 December 2017 / Accepted: 3 January 2018 / Published: 11 January 2018
(This article belongs to the Section Animal Genetics and Genomics)
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A series of elaborately regulated and orchestrated changes in gene expression profiles leads to muscle growth and development. In this study, RNA sequencing was used to profile embryonic chicken myoblasts and fused myotube transcriptomes, long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) at four stages of myoblast differentiation. Of a total of 2484 lncRNA transcripts, 2288 were long intergenic non-coding RNAs (lincRNAs) and 198 were antisense lncRNAs. Additionally, 1530 lncRNAs were neighboring 2041 protein-coding genes (<10 kb upstream and downstream) and functionally enriched in several pathways related to skeletal muscle development that have been extensively studied, indicating that these genes may be in cis-regulatory relationships. In addition, Pearson’s correlation coefficients demonstrated that 990 lncRNAs and 7436 mRNAs were possibly in trans-regulatory relationships. These co-expressed mRNAs were enriched in various developmentally-related biological processes, such as myocyte proliferation and differentiation, myoblast differentiation, and myoblast fusion. The number of transcripts (906 lncRNAs and 4422 mRNAs) differentially expressed across various stages declined with the progression of differentiation. Then, 4422 differentially expressed genes were assigned to four clusters according to K-means analysis. Genes in the K1 cluster likely play important roles in myoblast proliferation and those in the K4 cluster were likely associated with the initiation of myoblast differentiation, while genes in the K2 and K3 clusters were likely related to myoblast fusion. This study provides a catalog of chicken lncRNAs and mRNAs for further experimental investigations and facilitates a better understanding of skeletal muscle development. View Full-Text
Keywords: RNA sequencing; lncRNA; mRNA; myoblasts; chicken RNA sequencing; lncRNA; mRNA; myoblasts; chicken

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Li, T.; Zhang, G.; Wu, P.; Duan, L.; Li, G.; Liu, Q.; Wang, J. Dissection of Myogenic Differentiation Signatures in Chickens by RNA-Seq Analysis. Genes 2018, 9, 34.

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