Genome-wide analysis of circular RNA-mediated ceRNA regulation in porcine skeletal muscle development

被引:5
作者
Yun, Jiale [1 ]
Huang, Xiaoyu [1 ]
Liu, Chang [1 ]
Shi, Mingyue [1 ]
Li, Wenxia [1 ]
Niu, Jin [1 ]
Cai, Chunbo [1 ]
Yang, Yang [1 ]
Gao, Pengfei [1 ]
Guo, Xiaohong [1 ]
Li, Bugao [1 ]
Lu, Chang [1 ]
Cao, Guoqing [1 ]
机构
[1] Shanxi Agr Univ, Coll Anim Sci, Taigu 030801, Peoples R China
基金
中国国家自然科学基金;
关键词
Pig; Skeletal muscle; RNA-seq; circRNA; ceRNA; EXPRESSION; DIFFERENTIATION; MYOD; PROLIFERATION; MYOGENIN; ORGANS; CELLS; PAX3;
D O I
10.1186/s12864-023-09284-7
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
BackgroundAs a diverse and abundant class of endogenous RNAs, circular RNAs (circRNAs) participate in various biological processes including cell proliferation and apoptosis. Nevertheless, few researchers have investigated the role of circRNAs in muscle development in cultivated pigs.ResultsIn this study, we used RNA-seq to construct circRNA expression profiles in skeletal muscle of Jinfen White pigs at the age of 1, 90, and 180 days. Among the 16,990 identified circRNAs, 584 circRNAs were differentially expressed. Moreover, the enrichment analysis of DE circRNA host genes showed that they were mainly involved in muscle contraction, muscle organ development and muscle system processes, as well as AMPK and cAMP-related signal pathways. We also constructed a circRNA-miRNA-mRNA co-expression network to find key circRNAs which many involved in the regulation of porcine skeletal muscle development through the competitive endogenous RNA (ceRNA) mechanism. It is noteworthy that circ_0018595/miR-1343/PGM1 axis may play a regulatory role in the development of porcine skeletal muscle.ConclusionsThis study identified the circRNAs and present the circRNA expression profile in the development of pigs, revealed that DE circRNA host genes participate in different cell fates and enriched the porcine ceRNA network. Thus, this work will become a valuable resource for further in-depth study of the regulatory mechanism of circRNA in the development of porcine skeletal muscle.
引用
收藏
页数:14
相关论文
共 76 条
[1]   Circular RNAs: analysis, expression and potential functions [J].
Barrett, Steven P. ;
Salzman, Julia .
DEVELOPMENT, 2016, 143 (11) :1838-1847
[2]   Control of muscle formation by the fusogenic micropeptide myomixer [J].
Bi, Pengpeng ;
Ramirez-Martinez, Andres ;
Li, Hui ;
Cannavino, Jessica ;
McAnally, John R. ;
Shelton, John M. ;
Sanchez-Ortiz, Efrain ;
Bassel-Duby, Rhonda ;
Olson, Eric N. .
SCIENCE, 2017, 356 (6335) :323-327
[3]   Genetic and epigenetic control of skeletal muscle development [J].
Brand-Saberi, B .
ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER, 2005, 187 (03) :199-207
[4]   The role of Pax genes in the development of tissues and organs:: Pax3 and Pax7 regulate muscle progenitor cell functions [J].
Buckingham, Margaret ;
Relaix, Frederic .
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, 2007, 23 :645-673
[5]   circPTPN4 regulates myogenesis via the miR-499-3p/NAMPT axis [J].
Cai, Bolin ;
Ma, Manting ;
Zhou, Zhen ;
Kong, Shaofen ;
Zhang, Jing ;
Zhang, Xiquan ;
Nie, Qinghua .
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY, 2022, 13 (01)
[6]   Circular RNA circHIPK3 Promotes the Proliferation and Differentiation of Chicken Myoblast Cells by Sponging miR-30a-3p [J].
Chen, Biao ;
Yu, Jiao ;
Guo, Lijin ;
Byers, Mary Shannon ;
Wang, Zhijun ;
Chen, Xiaolan ;
Xu, Haiping ;
Nie, Qinghua .
CELLS, 2019, 8 (02)
[7]   Transcriptome analysis of differentially expressed circRNAs miRNAs and mRNAs during the challenge of coccidiosis [J].
Chen, Xiaolan ;
Wang, Zhijun ;
Chen, Yangfeng ;
Akinci, Ibrahim ;
Luo, Wei ;
Xu, Yibin ;
Jebessa, Endashaw ;
Blake, Damer ;
Sparks, Nick ;
Hanotte, Olivier ;
Nie, Qinghua .
FRONTIERS IN IMMUNOLOGY, 2022, 13
[8]   A Novel Circular RNA Generated by FGFR2 Gene Promotes Myoblast Proliferation and Differentiation by Sponging miR-133a-5p and miR-29b-1-5p [J].
Chen, Xiaolan ;
Ouyang, Hongjia ;
Wang, Zhijun ;
Chen, Biao ;
Nie, Qinghua .
CELLS, 2018, 7 (11)
[9]   The mmu_circRNA_37492/hsa_circ_0012138 function as potential ceRNA to attenuate obstructive renal fibrosis [J].
Cheng, Xu ;
Ai, Kai ;
Yi, Lei ;
Liu, Wentao ;
Li, Yijian ;
Wang, Yinhuai ;
Zhang, Dongshan .
CELL DEATH & DISEASE, 2022, 13 (03)
[10]   Identification of Potential circRNA-microRNA-mRNA Regulatory Network in Skeletal Muscle [J].
Das, Arundhati ;
Shyamal, Sharmishtha ;
Sinha, Tanvi ;
Mishra, Smruti Sambhav ;
Panda, Amaresh C. .
FRONTIERS IN MOLECULAR BIOSCIENCES, 2021, 8