Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs
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 expres...
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BMC
2023-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09414-1 |
| _version_ | 1797769669757632512 |
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| author | Chen Zhou Xinyan Cheng Fanming Meng Yongzhong Wang Wanyun Luo Enqin Zheng Gengyuan Cai Zhenfang Wu Zicong Li Linjun Hong |
| author_facet | Chen Zhou Xinyan Cheng Fanming Meng Yongzhong Wang Wanyun Luo Enqin Zheng Gengyuan Cai Zhenfang Wu Zicong Li Linjun Hong |
| author_sort | Chen Zhou |
| collection | DOAJ |
| description | 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. |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-12T21:12:20Z |
| publishDate | 2023-07-01 |
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| series | BMC Genomics |
| spelling | doaj.art-cd83b334d9f94fb6bcded5df4e99b9522023-07-30T11:08:45ZengBMCBMC Genomics1471-21642023-07-0124111910.1186/s12864-023-09414-1Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigsChen Zhou0Xinyan Cheng1Fanming Meng2Yongzhong Wang3Wanyun Luo4Enqin Zheng5Gengyuan Cai6Zhenfang Wu7Zicong Li8Linjun Hong9National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityGuangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural SciencesNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityNational Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural UniversityAbstract 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.https://doi.org/10.1186/s12864-023-09414-1CircRNAErhualianYorkshirePeri-ImplantationEndometriumEmbryo implantation |
| spellingShingle | Chen Zhou Xinyan Cheng Fanming Meng Yongzhong Wang Wanyun Luo Enqin Zheng Gengyuan Cai Zhenfang Wu Zicong Li Linjun Hong Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs BMC Genomics CircRNA Erhualian Yorkshire Peri-Implantation Endometrium Embryo implantation |
| title | Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs |
| title_full | Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs |
| title_fullStr | Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs |
| title_full_unstemmed | Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs |
| title_short | Identification and characterization of circRNAs in peri-implantation endometrium between Yorkshire and Erhualian pigs |
| title_sort | identification and characterization of circrnas in peri implantation endometrium between yorkshire and erhualian pigs |
| topic | CircRNA Erhualian Yorkshire Peri-Implantation Endometrium Embryo implantation |
| url | https://doi.org/10.1186/s12864-023-09414-1 |
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