Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics
The fertility rate and litter size of female pigs are critically affected by the expression of estrus. The objective of this study was to elucidate the regulatory mechanisms of estrus expression by analyzing the differential expression of genes and long intergenic non-coding RNAs (lincRNA), as well...
| প্রধান লেখক: | , , , , , , , , , |
|---|---|
| বিন্যাস: | প্রবন্ধ |
| ভাষা: | English |
| প্রকাশিত: |
MDPI AG
2024-03-01
|
| মালা: | Animals |
| বিষয়গুলি: | |
| অনলাইন ব্যবহার করুন: | https://www.mdpi.com/2076-2615/14/5/791 |
| _version_ | 1827319865387515904 |
|---|---|
| author | Mingzheng Liu Jiahao Chen Chunlei Zhang Shuhan Liu Xiaohuan Chao Huan Yang Asim Muhammad Bo Zhou Weiping Ao Allan P. Schinckel |
| author_facet | Mingzheng Liu Jiahao Chen Chunlei Zhang Shuhan Liu Xiaohuan Chao Huan Yang Asim Muhammad Bo Zhou Weiping Ao Allan P. Schinckel |
| author_sort | Mingzheng Liu |
| collection | DOAJ |
| description | The fertility rate and litter size of female pigs are critically affected by the expression of estrus. The objective of this study was to elucidate the regulatory mechanisms of estrus expression by analyzing the differential expression of genes and long intergenic non-coding RNAs (lincRNA), as well as the utilization of alternative polyadenylation (APA) sites, in the vulva and vagina during the estrus and diestrus stages of Large White and indigenous Chinese Mi gilts. Our study revealed that the number of differentially expressed genes (DEG) in the vulva was less than that in the vagina, and the DEGs in the vulva were enriched in pathways such as “neural” pathways and steroid hormone responses, including the “Calcium signaling pathway” and “Oxytocin signaling pathway”. The DEGs in the vagina were enriched in the “Metabolic pathways” and “VEGF signaling pathway”. Furthermore, 27 and 21 differentially expressed lincRNAs (DEL), whose target genes were enriched in the “Endocrine resistance” pathway, were identified in the vulva and vagina, respectively. Additionally, we observed that 63 and 618 transcripts of the 3′-untranslated region (3′-UTR) were lengthened during estrus in the vulva and vagina, respectively. Interestingly, the genes undergoing APA events in the vulva exhibited species-specific enrichment in neural or steroid-related pathways, whereas those in the vagina were enriched in apoptosis or autophagy-related pathways. Further bioinformatic analysis of these lengthened 3′-UTRs revealed the presence of multiple miRNAs binding sites and cytoplasmic polyadenylation element (CPE) regulatory aspects. In particular, we identified more than 10 CPEs in the validated lengthened 3′-UTRs of the <i>NFIX</i>, <i>PCNX4</i>, <i>CEP162</i> and <i>ABHD2</i> genes using RT-qPCR. These findings demonstrated the involvement of APA and lincRNAs in the regulation of estrus expression in female pigs, providing new insights into the molecular mechanisms underlying estrus expression in pigs. |
| first_indexed | 2024-04-25T00:36:50Z |
| format | Article |
| id | doaj.art-bc4457993ffd4d96bc769a48a278325b |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-04-25T00:36:50Z |
| publishDate | 2024-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-bc4457993ffd4d96bc769a48a278325b2024-03-12T16:38:20ZengMDPI AGAnimals2076-26152024-03-0114579110.3390/ani14050791Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive TranscriptomicsMingzheng Liu0Jiahao Chen1Chunlei Zhang2Shuhan Liu3Xiaohuan Chao4Huan Yang5Asim Muhammad6Bo Zhou7Weiping Ao8Allan P. Schinckel9College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Tarim University, Alar 843300, ChinaDepartment of Animal Sciences, Purdue University, West Lafayette, IN 47907-2054, USAThe fertility rate and litter size of female pigs are critically affected by the expression of estrus. The objective of this study was to elucidate the regulatory mechanisms of estrus expression by analyzing the differential expression of genes and long intergenic non-coding RNAs (lincRNA), as well as the utilization of alternative polyadenylation (APA) sites, in the vulva and vagina during the estrus and diestrus stages of Large White and indigenous Chinese Mi gilts. Our study revealed that the number of differentially expressed genes (DEG) in the vulva was less than that in the vagina, and the DEGs in the vulva were enriched in pathways such as “neural” pathways and steroid hormone responses, including the “Calcium signaling pathway” and “Oxytocin signaling pathway”. The DEGs in the vagina were enriched in the “Metabolic pathways” and “VEGF signaling pathway”. Furthermore, 27 and 21 differentially expressed lincRNAs (DEL), whose target genes were enriched in the “Endocrine resistance” pathway, were identified in the vulva and vagina, respectively. Additionally, we observed that 63 and 618 transcripts of the 3′-untranslated region (3′-UTR) were lengthened during estrus in the vulva and vagina, respectively. Interestingly, the genes undergoing APA events in the vulva exhibited species-specific enrichment in neural or steroid-related pathways, whereas those in the vagina were enriched in apoptosis or autophagy-related pathways. Further bioinformatic analysis of these lengthened 3′-UTRs revealed the presence of multiple miRNAs binding sites and cytoplasmic polyadenylation element (CPE) regulatory aspects. In particular, we identified more than 10 CPEs in the validated lengthened 3′-UTRs of the <i>NFIX</i>, <i>PCNX4</i>, <i>CEP162</i> and <i>ABHD2</i> genes using RT-qPCR. These findings demonstrated the involvement of APA and lincRNAs in the regulation of estrus expression in female pigs, providing new insights into the molecular mechanisms underlying estrus expression in pigs.https://www.mdpi.com/2076-2615/14/5/791alternative polyadenylationestrusLncRNApigs |
| spellingShingle | Mingzheng Liu Jiahao Chen Chunlei Zhang Shuhan Liu Xiaohuan Chao Huan Yang Asim Muhammad Bo Zhou Weiping Ao Allan P. Schinckel Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics Animals alternative polyadenylation estrus LncRNA pigs |
| title | Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics |
| title_full | Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics |
| title_fullStr | Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics |
| title_full_unstemmed | Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics |
| title_short | Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics |
| title_sort | deciphering estrus expression in gilts the role of alternative polyadenylation and lincrnas in reproductive transcriptomics |
| topic | alternative polyadenylation estrus LncRNA pigs |
| url | https://www.mdpi.com/2076-2615/14/5/791 |
| work_keys_str_mv | AT mingzhengliu decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT jiahaochen decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT chunleizhang decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT shuhanliu decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT xiaohuanchao decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT huanyang decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT asimmuhammad decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT bozhou decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT weipingao decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics AT allanpschinckel decipheringestrusexpressioningiltstheroleofalternativepolyadenylationandlincrnasinreproductivetranscriptomics |