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Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods

文献类型： 外文期刊

作者： Lei, Qiuxia 1 ; Hu, Xin 1 ; Han, Haixia 1 ; Wang, Jie 1 ; Liu, Wei 1 ; Zhou, Yan 1 ; Cao, Dingguo 1 ; Li, Fuwei 1 ; Liu, Jie 1 ;

作者机构： 1.Shandong Acad Agr Sci, Poultry Inst, Jinan 250023, Peoples R China

2.Poultry Breeding Engn Technol Ctr Shandong Prov, Jinan 250023, Peoples R China

3.Chinese Acad Agr Sci, Inst Anim Sci, Beijing 100193, Peoples R China

4.Univ Liege, Gembloux Agro Bio Tech, Mol & Cellular Biol, B-5030 Gembloux, Belgium

关键词： Circular RNA; ceRNA; Chicken; Breast muscle; Development

期刊名称：BMC GENOMICS （ 影响因子：4.547； 五年影响因子：4.931 ）

ISSN： 1471-2164

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCI

摘要： 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.

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