Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs

Chen Zhou; Xinyan Cheng; Fanming Meng; Yongzhong Wang; Wanyun Luo; Enqin Zheng; Gengyuan Cai; Zhenfang Wu; Zicong Li; Linjun Hong

doi:10.1186/s12864-023-09414-1

Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs

BMC Genomics. 2023 Jul 24;24(1):412. doi: 10.1186/s12864-023-09414-1.

Authors

Chen Zhou^#^{1

2}, Xinyan Cheng^#^{1

2}, Fanming Meng^{3

4}, Yongzhong Wang^{1

2}, Wanyun Luo^{1

2}, Enqin Zheng^{1

2

4

5}, Gengyuan Cai^{1

2

4

5}, Zhenfang Wu^{1

2

4

5}, Zicong Li^{6

7

8

9}, Linjun Hong^{10

11

12

13}

Affiliations

¹ National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
² Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
³ Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
⁴ State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China.
⁵ Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China.
⁶ National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China. lizicong@scau.edu.cn.
⁷ Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China. lizicong@scau.edu.cn.
⁸ State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China. lizicong@scau.edu.cn.
⁹ Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China. lizicong@scau.edu.cn.
¹⁰ National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China. linjun.hong@scau.edu.cn.
¹¹ Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China. linjun.hong@scau.edu.cn.
¹² State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, 510640, China. linjun.hong@scau.edu.cn.
¹³ Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, China. linjun.hong@scau.edu.cn.

^# Contributed equally.

Abstract

Background: One of the most critical periods for the loss of pig embryos is the 12th day of gestation when implantation begins. Recent studies have shown that non-coding RNAs (ncRNAs) play important regulatory roles during pregnancy. Circular RNAs (circRNAs) are a kind of ubiquitously expressed ncRNAs that can directly regulate the binding proteins or regulate the expression of target genes by adsorbing micro RNAs (miRNA).

Results: We used the Illumina Novaseq6,000 technology to analyze the circRNA expression profile in the endometrium of three Erhualian (EH12) and three Yorkshire (YK12) pigs on day 12 of gestation. Overall, a total of 22,108 circRNAs were identified. Of these, 4051 circRNAs were specific to EH12 and 5889 circRNAs were specific to YK12, indicating a high level of breed specificity. Further analysis showed that there were 641 significant differentially expressed circRNAs (SDEcircRNAs) in EH12 compared with YK12 (FDR < 0.05). Functional enrichment of differential circRNA host genes revealed many pathways and genes associated with reproduction and regulation of embryo development. Network analysis of circRNA-miRNA interactions further supported the idea that circRNAs act as sponges for miRNAs to regulate gene expression. The prediction of differential circRNA binding proteins further explored the potential regulatory pathways of circRNAs. Analysis of SDEcircRNAs suggested a possible reason for the difference in embryo survival between the two breeds at the peri-implantation stage.

Conclusions: Together, these data suggest that circRNAs are abundantly expressed in the endometrium during the peri-implantation period in pigs and are important regulators of related genes. The results of this study will help to further understand the differences in molecular pathways between the two breeds during the critical implantation period of pregnancy, and will help to provide insight into the molecular mechanisms that contribute to the establishment of pregnancy and embryo loss in pigs.

Keywords: CircRNA; Embryo implantation; Endometrium; Erhualian; Peri-Implantation; Yorkshire.

MeSH terms

Animals
Embryo Implantation / genetics
Endometrium / metabolism
Female
Gene Expression Profiling / methods
Gene Regulatory Networks
MicroRNAs* / genetics
MicroRNAs* / metabolism
Pregnancy
RNA, Circular* / genetics
RNA, Circular* / metabolism
Reproduction
Swine / genetics

Substances

RNA, Circular
MicroRNAs

Abstract

MeSH terms

Substances

Grants and funding