The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken

Liu, Zihao; Han, Shunshun; Shen, Xiaoxu; Wang, Yan; Cui, Can; He, Haorong; Chen, Yuqi; Zhao, Jing; Li, Diyan; Zhu, Qing; Yin, Huadong

doi:10.7150/ijbs.35073

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Int J Biol Sci 2019; 15(7):1404-1418. doi:10.7150/ijbs.35073 This issue Cite

Research Paper

The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken

Zihao Liu^*, Shunshun Han^*, Xiaoxu Shen^*, Yan Wang^*, Can Cui, Haorong He, Yuqi Chen, Jing Zhao, Diyan Li, Qing Zhu, Huadong Yin^✉

Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
^* These authors contributed equally to this work.

Citation:

Liu Z, Han S, Shen X, Wang Y, Cui C, He H, Chen Y, Zhao J, Li D, Zhu Q, Yin H. The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken. Int J Biol Sci 2019; 15(7):1404-1418. doi:10.7150/ijbs.35073. https://www.ijbs.com/v15p1404.htm

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Abstract

Scope: As DNA methylation is one of the key epigenetic mechanisms involved in embryonic muscle development, elucidating its relationship with non-coding RNAs and genes is essential for understanding early muscle development. The methylome profiles of pre-hatching chicken across multiple developmental stages remain incomplete although several related studies have been reported.

Methods: In this study, we performed single-base-resolution bisulfite sequencing together with RNA-seq of broilers and layers in different embryonic development points (E10, E13, E16 and E19) to explore the genetic basis of embryonic muscle development in chicken. The differential methylated regions and novel lncRNAs were identified for association analyses. Through genomic position and correlation analysis between DMRs and lncRNAs, the target lncRNAs were detected to participate in the embryonic muscle formation and the results were then verified in vitro experiments.

Results: Comparison of methylome profiles between two chicken lines revealed that lower methylation in broilers might contribute to muscle development in embryonic period. Differential methylated region analysis showed that the majority of differential methylated regions were hypo-DMRs for broilers. Differential methylated genes were significantly enriched in muscle development-related terms at E13 and E19. Furthermore, we identified a long non-coding RNA MyH1-AS that potentially regulated embryonic muscle development, proved by the regulatory network construction and further in vitro experiments.

Conclusion: Our study revealed an integrative landscape of middle- to late-stage of embryonic myogenesis in chicken, gave rise to a comprehensive understanding of epigenetic and transcriptional regulation in muscle development. Moreover, we provided a reliable data resource for further embryonic muscle development studies.

Keywords: DNA methylation, transcriptome, chicken, muscle development, embryonic

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APA

Liu, Z., Han, S., Shen, X., Wang, Y., Cui, C., He, H., Chen, Y., Zhao, J., Li, D., Zhu, Q., Yin, H. (2019). The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken. International Journal of Biological Sciences, 15(7), 1404-1418. https://doi.org/10.7150/ijbs.35073.

ACS

Liu, Z.; Han, S.; Shen, X.; Wang, Y.; Cui, C.; He, H.; Chen, Y.; Zhao, J.; Li, D.; Zhu, Q.; Yin, H. The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken. Int. J. Biol. Sci. 2019, 15 (7), 1404-1418. DOI: 10.7150/ijbs.35073.

NLM

CSE

Liu Z, Han S, Shen X, Wang Y, Cui C, He H, Chen Y, Zhao J, Li D, Zhu Q, Yin H. 2019. The landscape of DNA methylation associated with the transcriptomic network in layers and broilers generates insight into embryonic muscle development in chicken. Int J Biol Sci. 15(7):1404-1418.

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