Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods.
[en] BACKGROUND: The growth and development of skeletal muscle are regulated by protein-coding genes and non-coding RNA. Circular RNA (circRNA) is a type of non-coding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. To better understand the regulatory mechanism of circRNAs during the development of muscle in chicken, we performed RNA-seq with linear RNA depletion for chicken breast muscle in 12 (E 12) and17 (E 17) day embryos, and 1 (D 1), 14 (D 14), 56 (D 56), and 98 (D 98) days post-hatch.
RESULTS: We identified 5755 differentially expressed (DE)-circRNAs during muscle development. We profiled the expression of DE-circRNAs and mRNAs (identified in our previous study) at up to six time points during chicken muscle development and uncovered a significant profile (profile 16) for circRNA upregulation during aging in muscle tissues. To investigate competing endogenous RNA (ceRNA) regulation in muscle and identify muscle-related circRNAs, we constructed a circRNA-miRNA-mRNA regulatory network using the circRNAs and mRNAs from profile 16 and miRNAs identified in our previous study, which included 361 miRNAs, 68 circRNAs, 599 mRNAs, and 31,063 interacting pairs. Functional annotation showed that upregulated circRNAs might contribute to glycolysis/gluconeogenesis, biosynthesis of amino acids, pyruvate metabolism, carbon metabolism, glycogen and sucrose metabolism through the ceRNA network, and thus affected postnatal muscle development by regulating muscle protein deposition. Of them, circRNA225 and circRNA226 from the same host gene might be key circRNAs that could regulate muscle development by interacting with seven common miRNAs and 207 mRNAs. Our experiments also demonstrated that there were interactions among circRNA225, gga-miR-1306-5p, and heat shock protein alpha 8 (HSPA8).
CONCLUSIONS: Our results suggest that adequate supply of nutrients such as energy and protein after hatching may be a key factor in ensuring chicken yield, and provide several candidate circRNAs for future studies concerning ceRNA regulation during chicken muscle development.
Disciplines :
Genetics & genetic processes Animal production & animal husbandry
Author, co-author :
Lei, Qiuxia; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China ; Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, 250023, China
Hu, Xin ; Université de Liège - ULiège > TERRA Research Centre ; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China ; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
Han, Haixia; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China
Wang, Jie; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China
Liu, Wei; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China
Zhou, Yan; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China
Cao, Dingguo; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China
Li, Fuwei; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China
Liu, Jie; Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, 250023, China. jqsyzslj@163.com ; Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, 250023, China. jqsyzslj@163.com
Language :
English
Title :
Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods.
Agricultural Breed Project of Shandong Province Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences
Funding text :
We thank International Science Editing (http://www.internationalscienceediting.com) for editing this manuscript.This research was funded by the Natural Science Foundation of Shandong province (ZR2019BC077), the Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences (CXGC2021A13). China Agriculture Research System of MOF and MARA (CARS-41). Agricultural Breed Project of Shandong Province(2020LZGC013). Shandong Provincial Natural Science Foundation (ZR2020MC169); Collection, Protection and Accurate Identification of Livestock Germplasm Resources (2019LZGC019); China Agriculture Research System of MOF and MARA(CARS-40); Major Scientific and Technological Innovation Project (MSTIP): the Research and Demonstration on Key Technologies of Precision Breeding and Management of Laying Hens(2019JZZY020611).
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