Integration Analysis of circRNA-miRNA-mRNA and Identification of Critical Networks in Valgus-Varus Deformity (Gallus gallus)

Jianzeng Li; Yanchao Ma; Chunxia Cai; Lujie Zhang; Xinxin Liu; Ruirui Jiang; Donghua Li; Zhuanjian Li; Xiangtao Kang; Yadong Tian; Ruili Han

doi:10.3390/genes14030622

Integration Analysis of circRNA-miRNA-mRNA and Identification of Critical Networks in Valgus-Varus Deformity (Gallus gallus)

Genes (Basel). 2023 Mar 1;14(3):622. doi: 10.3390/genes14030622.

Authors

Jianzeng Li^{1

2}, Yanchao Ma^{1

2}, Chunxia Cai^{1

2}, Lujie Zhang^{1

2}, Xinxin Liu^{1

2}, Ruirui Jiang^{1

2}, Donghua Li^{1

2}, Zhuanjian Li^{1

2}, Xiangtao Kang^{1

2}, Yadong Tian^{1

2}, Ruili Han^{1

2}

Affiliations

¹ College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.
² Key Research Project of the Shennong Laboratory, Zhengzhou 450002, China.

Abstract

Valgus-valgus deformity (VVD) is a common leg deformity in broilers with inward or outward deviation of the tibiotarsus and tarsometatarsus. The competing endogenous RNA (ceRNA) network plays an essential role in the study of leg disease. However, its role in the etiology and pathogenesis of VVD remains unclear. Here, based on case (VVD) and control (normal) group design, we performed analyses of differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs) and differentially expressed mRNAs (DEmRNAs). Transcriptome data derived 86 DEcircRNAs, 13 DEmiRNAs and 410 DEmRNAs. Functional analysis showed that DEmRNAs were significantly enriched in cell cycle, apoptosis, ECM-receptor interaction, FoxO signaling pathway and protein processing synthesis. DEcirc/miRNA-associated DEmRNAs were associated with skeletal and muscle growth and development pathways, including mTOR, Wnt, and VEGF signaling pathways. Subsequently, a circRNA-miRNA-mRNA regulatory network was constructed based on the ceRNA hypothesis, including 8 circRNAs, 6 miRNAs, and 31 mRNAs, which were significantly enriched in the skeletal developmental pathway. Finally, two key mRNAs (CDC20 and CTNNB1) and their regulatory axes were screened by the PPI network and cytohubba. The expression levels of CDC20 and CTNNB1 in cartilage and seven other tissues were also quantified by qPCR. In conclusion, we analyzed the functions of DEmRNA, DEcircRNA and DEmiRNA and constructed the hub ceRNA regulatory axis, and obtained two hub genes, CDC20 and CTNNB1. The study more deeply explored the etiology and pathogenesis of VVD and lays the foundation for further study of the role of the ceRNA network on skeletal development.

Keywords: RNA-seq; broiler; competing endogenous RNA; skeletal development; valgus-varus deformity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bird Diseases* / genetics
Bone Diseases / genetics
Bone Diseases / veterinary
Cartilage / metabolism
Chickens
Gene Regulatory Networks*
Hindlimb*
Male
MicroRNAs / genetics
RNA, Circular / genetics
RNA, Messenger / genetics

Substances

RNA, Circular
RNA, Messenger
MicroRNAs

Grants and funding

This study was supported by the Natural Science Foundation of Henan Province (no. 222300420458); Scientific Studio of Zhongyuan Scholars (no. 30601985); Natural Science Foundation of Henan Province Youth Project (no. 202300410203); Zhongyuan Science and Technology Innovation Leading Scientist Project (214200510003), and Program for Innovative Research Team (in Science and Technology) in University of Henan Province (21IRTSTHN022).