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Liu M, Chen J, Zhang C, Liu S, Chao X, Yang H, Muhammad A, Zhou B, Ao W, Schinckel AP. Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics. Animals (Basel) 2024; 14:791. [PMID: 38473176 DOI: 10.3390/ani14050791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
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 NFIX, PCNX4, CEP162 and ABHD2 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.
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Affiliation(s)
- Mingzheng Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiahao Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunlei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuhan Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohuan Chao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Asim Muhammad
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiping Ao
- College of Animal Science and Technology, Tarim University, Alar 843300, China
| | - Allan P Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907-2054, USA
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Bharati J, Kumar S, Mohan NH, Chandra Das B, Devi SJ, Gupta VK. Ovarian follicle transcriptome dynamics reveals enrichment of immune system process during transition from small to large follicles in cyclic Indian Ghoongroo pigs. J Reprod Immunol 2023; 160:104164. [PMID: 37924675 DOI: 10.1016/j.jri.2023.104164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023]
Abstract
Ovarian follicular development is a critical determinant of reproductive performance in litter bearing species like pigs, wherein economic gains depend on litter size. The study aimed to gain insight into the differentially expressed genes (DEGs) and signalling pathways regulating follicular growth and maturation in Ghoongroo pigs. Transcriptome profiling of porcine small follicles (SF) and large follicles (LF) was conducted using NovaSeq600 sequencing platform and DEGs were identified using DESeq2 with threshold of Padj. < 0.05 and log2 fold change cut off 0.58 (LF vs. SF). Functional annotations and bioinformatics analysis of DEGs were performed to find out biological functions, signalling pathways and hub genes regulating follicular dynamics. Transcriptome analysis revealed 709 and 479 genes unique to SF and LF stages, respectively, and 11,993 co-expressed genes in both the groups. In total, 507 DEGs (284 upregulated and 223 downregulated) were identified, which encoded for diverse proteins including transcription factors (TFs). These DEGs were functionally linked to response to stimulus, lipid metabolic process, developmental process, extracellular matrix organisation along with the immune system process, indicating wide-ranging mechanisms associated with follicular transition. The enriched KEGG pathways in LF stage consisted of ovarian steroidogenesis, cholesterol and retinol metabolism, cell adhesion molecules, cytokine receptor interaction and immune signalling pathways, depicting intra-follicular control of varied ovarian function. The hub gene analysis revealed APOE, SCARB1, MMP9, CYP17A1, TYROBP as key regulators of follicular development. This study identified candidate genes and TFs providing steroidogenic advantage to LFs which makes them fit for selection into the ovulatory pool of follicles.
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Affiliation(s)
- Jaya Bharati
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India.
| | - Satish Kumar
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - N H Mohan
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Bikash Chandra Das
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Salam Jayachitra Devi
- Computer Applications and Information Technology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Vivek Kumar Gupta
- Director, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
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3
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Zhu Y, Ye J, Qin P, Yan X, Gong X, Li X, Liu Y, Li Y, Yu T, Zhang Y, Ling Y, Wang J, Cao H, Fang F. Analysis of serum reproductive hormones and ovarian genes in pubertal female goats. J Ovarian Res 2023; 16:69. [PMID: 37024956 PMCID: PMC10080748 DOI: 10.1186/s13048-023-01150-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/29/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Age at puberty is an important factor affecting goat fertility, with endocrine and genetic factors playing a crucial role in the onset of puberty. To better understand the relationship between endocrine and genetic factors and mechanisms underlying puberty onset in goats, reproductive hormone levels were analyzed by ELISA and ultraperformance liquid chromatography-multiple reaction monitoring-multistage/mass spectrometry and RNA sequencing was performed to analyze ovarian genes. RESULTS Serum follicle stimulating hormone, luteinizing hormone, estradiol, 11-deoxycortisol, 11-deoxycorticosterone, corticosterone, cortisone, and cortisol levels were found to be higher but progesterone were lower in pubertal goats as compared to those in prepubertal goats (P < 0.05). A total of 18,139 genes were identified in cDNA libraries, and 75 differentially expressed genes (DEGs) were identified (|log2 fold change|≥ 1, P ≤ 0.05), of which 32 were significantly up- and 43 were down-regulated in pubertal goats. Gene ontology enrichment analyses indicated that DEGs were mainly involved in "metabolic process," "signaling," "reproduction," and "growth." Further, DEGs were significantly enriched in 91 Kyoto Encyclopedia of Genes and Genomes pathways, including estrogen signaling pathway, steroid hormone biosynthesis, and cAMP signaling pathway. Bioinformatics analysis showed that PRLR and THBS1 were highly expressed in pubertal ovaries, and ZP3, ZP4, and ASTL showed low expression, suggesting their involvement in follicular development and lutealization. CONCLUSIONS To summarize, serum hormone changes and ovarian DEGs expression were investigated in our study. Further studies are warranted to comprehensively explore the functions of DEGs in goat puberty.
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Affiliation(s)
- Yanyun Zhu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Jing Ye
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Ping Qin
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Xu Yan
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Xinbao Gong
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Xiaoqian Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Ya Liu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yunsheng Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Tong Yu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yunhai Zhang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yinghui Ling
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Juhua Wang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Hongguo Cao
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Fugui Fang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China.
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China.
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Bao Y, Li X, El-Samahy MA, Yang H, Wang Z, Yang F, Yao X, Wang F. Exploration the role of INHBA in Hu sheep granulosa cells using RNA-Seq. Theriogenology 2023; 197:198-208. [PMID: 36525859 DOI: 10.1016/j.theriogenology.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 11/26/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Activin/inhibin is an important factor for the fecundity of Hu sheep, and it is involved in follicular development in ovaries. Inhibin subunit beta A (INHBA) participates in the synthesis of activin A and inhibin A. In this study, we also noted a positive correlation between INHBA level and the secretion of both activin A and inhibin A in culture medium. Nevertheless, both knockdown and overexpression of INHBA downregulated the expression of Inhibin Subunit Alpha (INHA). Based on RNA-Sequencing, we further examined the effect and molecular mechanism of INHBA knockdown in GCs on mRNA expression. A total of 1,687 differentially expressed genes (DEGs) were identified (Fold change ≥ 2; False-discovory-rates (FDR) ≤ 0.01), of which 602 genes were upregulated and 1,087 genes were downregulated in the INHBA interference group compared with the control groups. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the regulation of cell cycle, protein serine/threonine kinase activity, and actin cytoskeleton reorganization. Moreover, DEGs were significantly enriched in 40 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including P53, progesterone-mediated oocyte maturation, and PI3K-AKT signaling pathways. We also noted a positive correlation between INHBA level and many PI3K/Akt/mTOR pathway-related genes at the gene or/and protein expression. Overall, this study may contribute to a better understanding of the roles of INHBA on GCs of prolific sheep, as well as the molecular effect of low INHBA expression on GCs, clarifying some reproductive failures.
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Affiliation(s)
- Yongjin Bao
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodan Li
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
| | - M A El-Samahy
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China; Animal Production Research Institute, ARC, Ministry of Agriculture, Giza, Egypt
| | - Hua Yang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhibo Wang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fan Yang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaolei Yao
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, 210095, China.
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Du Z, D’Alessandro E, Asare E, Zheng Y, Wang M, Chen C, Wang X, Song C. Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes. Genes (Basel) 2022; 13:genes13081359. [PMID: 36011270 PMCID: PMC9407582 DOI: 10.3390/genes13081359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
Retrotransposons account for more than one-third of the pig reference genome. On account of the genome variability in different breeds, structural variation (SV) caused by retrotranspos-on-generated deletion or insertion (indel) may have a function in the genome. Litter size is one of the most important reproductive traits and significantly impacts profitability in terms of pig production. We used the method of bioinformatics, genetics, and molecular biology to make an analysis among different pig genomes. Predicted 100 SVs were annotated as retrotransposon indel in 20 genes related to reproductive performance. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE indel, and eight RIPs were generated by the ERV indel. We selected 12 RIPs to make the second round PCR detection in 24 individuals among nine pig breeds. The PCR detection results revealed that the RIP-A1CF-4 insertion in the breed of Bama, Large White, and Meishan only had the homozygous genotype but low to moderately polymorphisms were present in other breeds. We found that RIP-CWH43-9, RIP-IDO2-9, RIP-PRLR-6, RIP-VMP1-12, and RIP-OPN-1 had a rich polymorphism in the breed of Large White pigs. The statistical analysis revealed that RIP-CWH43-9 had a SINE insertion profitable to the reproductive traits of TNB and NBA but was significantly affected (p < 0.01) and (p < 0.05) in the reproductive traits of litter birthweight (LW) in Large White. On the other hand, the SINE insertion in IDO2-9 may be a disadvantage to the reproductive traits of LW, which was significantly affected (p < 0.05) in Large White. These two RIPs are significant in pig genome research and could be useful molecular markers in the breeding system.
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Affiliation(s)
- Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, University of Messina, Via Palatucci snc, 98168 Messina, Italy;
| | - Emmanuel Asare
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Mengli Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (E.A.); (Y.Z.); (M.W.); (C.C.); (X.W.)
- Correspondence:
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Gao Q, Chu Q, Liu M, Gao S, Xu Q, Zhou B. Functional variants in the promoter region of sulfotransferase 1C1 gene associated with estrogen degradation in gilts. Anim Sci J 2022; 93:e13738. [PMID: 35665986 DOI: 10.1111/asj.13738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 11/28/2022]
Abstract
Chinese indigenous Mi gilts have clearer estrus expression than European Large White gilts, and sulfotransferase 1C1 (SULT1C1) gene was differentially expressed between them. To investigate the differential expression mechanism of porcine SULT1C1 gene, we cloned its promoter region and predicted its activity. Six deletion expression vectors (P1, P2, P3, P4, P5, and P6) for the promoter of SULT1C1 gene were constructed. Vector P3 (-1084/+261) had the highest expression activity, whereas vector P4 (-642/+261) showed a reduced in promoter activity, which suggests that the core promoter region of SULT1C1 gene is located between -1084 bp and -642 bp. Two single nucleotide polymorphisms (SNPs), c. - 994 G > A (rs345070974) and c. - 946 G > A (rs337902009) were found in Mi and Large White gilts between -1100 and -661 bp, and the expression vectors with four haplotypes (GG, AA, GA, and AG) of two SNPs were constructed. The relative luciferase activity of vector with haplotype GG was the greatest among four vectors. These indicate that c. - 994 G > A and c. - 946 G > A are key mutations for promoter activity of SULT1C1 gene. Porcine SULT1C1 promoter with -994 G allele and -946 G allele significantly improved the gene expression level. It could be involved in different estrus expression between Large White and Mi gilts.
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Affiliation(s)
- Qinxue Gao
- Jiangsu Agri‐animal Husbandry Vocational College Taizhou China
| | - Qingpo Chu
- College of Animal Science and Technology Nanjing Agricultural University Nanjing China
| | - Mingzheng Liu
- College of Animal Science and Technology Nanjing Agricultural University Nanjing China
| | - Siyuan Gao
- College of Animal Science and Technology Nanjing Agricultural University Nanjing China
| | - Qinglei Xu
- College of Animal Science and Technology Nanjing Agricultural University Nanjing China
| | - Bo Zhou
- College of Animal Science and Technology Nanjing Agricultural University Nanjing China
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Liu M, Xu Q, Zhao J, Guo Y, Zhang C, Chao X, Cheng M, Schinckel AP, Zhou B. Comprehensive Transcriptome Analysis of Follicles from Two Stages of the Estrus Cycle of Two Breeds Reveals the Roles of Long Intergenic Non-Coding RNAs in Gilts. BIOLOGY 2022; 11:biology11050716. [PMID: 35625443 PMCID: PMC9138455 DOI: 10.3390/biology11050716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022]
Abstract
Simple Summary This study provides new perspectives about the roles of lincRNAs in the estrus expression of gilts, which is correlated with ovarian steroid hormone and follicular development. Follicular tissues from two stages of the estrus cycle of Large White and Mi gilts were used for RNA-seq. Some genes and lincRNAs related to estrus expression in pigs were discovered. PPI and ceRNA networks related to the estrus expression were constructed. These results suggest that the estrus expression may be affected by lincRNAs and their target genes. Abstract Visible and long-lasting estrus expression of gilts and sows effectively sends a mating signal. To reveal the roles of Long Intergenic Non-coding RNAs (lincRNAs) in estrus expression, RNA-seq was used to investigate the lincRNAs expression of follicular tissues from Large White gilts at diestrus (LD) and estrus (LE), and Chinese Mi gilts at diestrus (MD) and estrus (ME). Seventy-three differentially expressed lincRNAs (DELs) were found in all comparisons (LE vs. ME, LD vs. LE, and MD vs. ME comparisons). Eleven lincRNAs were differentially expressed in both LD vs. LE and MD vs. ME comparisons. Fifteen DELs were mapped onto the pig corpus luteum number Quantitative Trait Loci (QTL) fragments. A protein–protein interaction (PPI) network that involved estrus expression using 20 DEGs was then constructed. Interestingly, three predicted target DEGs (PTGs) (CYP19A1 of MSTRG.10910, CDK1 of MSTRG.10910 and MSTRG.23984, SCARB1 of MSTRG.1559) were observed in the PPI network. A competitive endogenous RNA (ceRNA) network including three lincRNAs, five miRNAs, and five genes was constructed. Our study provides new insight into the lincRNAs associated with estrus expression and follicular development in gilts.
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Affiliation(s)
- Mingzheng Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Qinglei Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Jing Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Yanli Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Chunlei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Xiaohuan Chao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Meng Cheng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Allan P. Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907-2054, USA;
| | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
- Correspondence:
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8
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Park Y, Park YB, Lim SW, Lim B, Kim JM. Time Series Ovarian Transcriptome Analyses of the Porcine Estrous Cycle Reveals Gene Expression Changes during Steroid Metabolism and Corpus Luteum Development. Animals (Basel) 2022; 12:ani12030376. [PMID: 35158699 PMCID: PMC8833361 DOI: 10.3390/ani12030376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The estrous cycle, which is divided into follicular and luteal phases based on ovulation, is influenced by reproductive hormones which affect reproduction and cause changes in the reproductive system of the pig. As the main reproductive organ, the ovary is involved in ovulation and changes in the corpus luteum. We aimed to identify dynamic changes in gene expression through differentially expressed gene profiling and to provide a comprehensive understanding of the molecular mechanisms that occur in the pig ovary during the estrous cycle. The transcriptome analysis revealed that the dynamic change in gene expression was more activated in the luteal phase than in the follicular phase. Functional analysis revealed that the metestrus and diestrus periods are important in preparation for pregnancy or the next estrous cycle after ovulation. Abstract The porcine estrous cycle is influenced by reproductive hormones, which affect porcine reproduction and result in physiological changes in the reproductive organs. The ovary is involved in ovulation, luteinization, corpus luteum development, and luteolysis. Here, we aimed to provide a comprehensive understanding of the gene expression patterns in porcine ovarian transcriptomes during the estrous cycle through differentially expressed genes profiling and description of molecular mechanisms. The transcriptomes of porcine ovary were obtained during the estrous cycle at three-day intervals from day 0 to day 18 using RNA-seq. At seven time points of the estrous cycle, 4414 DEG were identified; these were classified into three clusters according to their expression patterns. During the late metestrus and diestrus periods, the expression in cluster 1 increased rapidly, and steroid biosynthesis was significant in the pathway. Cluster 2 gene expression patterns represented the cytokine–cytokine receptor interaction in significant pathways. In cluster 3, the hedgehog signaling pathway was selected as the significant pathway. Our study exhibited dynamic gene expression changes with these three different patterns of cluster 1, 2, and 3. The results helped identify the functions and related significant genes especially during the late metestrus and diestrus periods in the estrous cycle.
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Changes in Transcriptomic Profiles in Different Reproductive Periods in Yaks. BIOLOGY 2021; 10:biology10121229. [PMID: 34943144 PMCID: PMC8698885 DOI: 10.3390/biology10121229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/21/2022]
Abstract
Simple Summary The molecular regulation mechanism of yak ovarian activity has attracted extensive attention. This study investigated the global gene expression profiles in different reproductive stages (anestrus, estrus, and pregnancy) by RNA-seq technology. Enrichment analysis revealed that DEGs were involved in the process of follicular growth, ovulation, and hormone metabolism. This study explored the regulation mechanism of the yak ovary in the reproductive cycle and laid a theoretical foundation for further understanding the reproductive characteristics of yak. Abstract Yak reproductive characteristics have received extensive attention, though the molecular regulation mechanism of its ovarian activity remains to be explored. Therefore, this study initially conducted a comparative analysis of yak ovarian activities in anestrus, estrus, and pregnancy regarding their morphology and histology, followed by implementing RNA sequencing (RNA-seq) technology to detect the overall gene expression and biological mechanism in different reproductive stages. H&E staining showed that there were more growing follicles and mature follicles in ovarian tissue sections during estrus than ovarian tissues during non-estrus. The RNA-seq analysis of yak ovary tissues in three periods showed that DEGs related to follicular development and hormone metabolism were screened in the three comparison groups, such as COL1A2, NR4A1, THBS2, PTGS2, SCARB1, STAR, and WNT2B. Bioinformatics analysis showed that these DEGs are involved in ion binding, cell development, metabolic processes, enriched in ECM–receptor interactions, steroid biosynthesis, together with aldosterone generation/discharge and Wnt/PI3K-Akt signaling pathways. In addition, we speculate alternate splice development events to have important role/s in regulating ovarian functional genomic expression profiles. These results provide essential knowledge aimed at scrutinizing pivotal biomarkers for yak ovarian activity, together with paving the way for enhancing researchers’ focus on improving yak reproductive performance.
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Ran X, Hu F, Mao N, Ruan Y, Yi F, Niu X, Huang S, Li S, You L, Zhang F, Tang L, Wang J, Liu J. Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs. Porcine Health Manag 2021; 7:52. [PMID: 34470660 PMCID: PMC8411529 DOI: 10.1186/s40813-021-00226-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although lots of quantitative trait loci (QTLs) and genes present roles in litter size of some breeds, the information might not make it clear for the huge diversity of reproductive capability in pig breeds. To elucidate the inherent mechanisms of heterogeneity of reproductive capability in litter size of Xiang pig, we performed transcriptome analysis for the expression profile in ovaries using RNA-seq method. RESULTS We identified 1,419 up-regulated and 1,376 down-regulated genes in Xiang pigs with large litter size. Among them, 1,010 differentially expressed genes (DEGs) were differently spliced between two groups with large or small litter sizes. Based on GO and KEGG analysis, numerous members of genes were gathered in ovarian steroidogenesis, steroid biosynthesis, oocyte maturation and reproduction processes. CONCLUSIONS Combined with gene biological function, twelve genes were found out that might be related with the reproductive capability of Xiang pig, of which, eleven genes were recognized as hub genes. These genes may play a role in promoting litter size by elevating steroid and peptide hormones supply through the ovary and facilitating the processes of ovulation and in vivo fertilization.
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Affiliation(s)
- Xueqin Ran
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fengbin Hu
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Ning Mao
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Yiqi Ruan
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fanli Yi
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Xi Niu
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Shihui Huang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Sheng Li
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Longjiang You
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Fuping Zhang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Liangting Tang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China
| | - Jiafu Wang
- College of Animal Science, Institute of Agro-Bioengineering and Key Laboratory of Plant Resource Conservative and Germplam Innovation in Mountainous Region (Ministry of Education), Guizhou University, 550025, Guiyang, China.
| | - Jianfeng Liu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
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11
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Whole Transcriptome Analysis: Implication to Estrous Cycle Regulation. BIOLOGY 2021; 10:biology10060464. [PMID: 34070240 PMCID: PMC8225199 DOI: 10.3390/biology10060464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023]
Abstract
Simple Summary The databases of mRNA and non-coding-RNAs (miRNA, circRNA, lncRNA) in the ovary of Xinong Sannen goat were reported in this study. The differential expression of mRNA and non-coding RNAs were analyzed, and the comprehensive analysis of the four databases provided RNA networks that regulate estrous cycle, which is essential to improve reproduction. Abstract Estrous cycle is one of the placental mammal characteristics after sexual maturity, including estrus stage (ES) and diestrus stage (DS). Estrous cycle is important in female physiology and its disorder may lead to diseases, such as polycystic ovary syndrome, ovarian carcinoma, anxiety, and epilepsy. In the latest years, effects of non-coding RNAs and messenger RNA (mRNA) on estrous cycle have started to arouse much concern, however, a whole transcriptome analysis among non-coding RNAs and mRNA has not been reported. Here, we report a whole transcriptome analysis of goat ovary in estrus and diestrus periods. Estrus synchronization was conducted to induce the estrus phase and on day 32, the goats shifted into the diestrus stage. The ovary RNA of estrus and diestrus stages was respectively collected to perform RNA-sequencing. Then, the circular RNA (circRNA), microRNA (miRNA), long non-coding RNA (lncRNA), and mRNA databases of goat ovary were acquired, and the differential expressions between estrus and diestrus stages were screened to construct circRNA-miRNA-mRNA/lncRNA and lncRNA-miRNA/mRNA networks, thus providing potential pathways that are involved in the regulation of estrous cycle. Differentially expressed mRNAs, such as MMP9, TIMP1, 3BHSD, and PTGIS, and differentially expressed miRNAs that play key roles in the regulation of estrous cycle, such as miR-21-3p, miR-202-3p, and miR-223-3p, were extracted from the network. Our data provided the miRNA, circRNA, lncRNA, and mRNA databases of goat ovary and each differentially expressed profile between ES and DS. Networks among differentially expressed miRNAs, circRNAs, lncRNAs, and mRNAs were constructed to provide valuable resources for the study of estrous cycle and related diseases.
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Bao X, Song Y, Li T, Zhang S, Huang L, Zhang S, Cao J, Liu X, Zhang J. Comparative Transcriptome Profiling of Ovary Tissue between Black Muscovy Duck and White Muscovy Duck with High- and Low-Egg Production. Genes (Basel) 2020; 12:57. [PMID: 33396489 PMCID: PMC7824526 DOI: 10.3390/genes12010057] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022] Open
Abstract
The egg-laying rate is an important indicator for evaluating fertility of poultry. In order to better understand the laying mechanism of Muscovy ducks, gene expression profiles and pathways of ovarian tissues in high- and low-laying black (BH and BL) and white Muscovy ducks (WH and WL) during the peak production period were performed by using RNA-seq. The total number of reads produced for each ovarian sample ranged from 44,344,070 to 47,963,328. A total of 113, 619 and 87 differentially expressed genes (DEGs) were identified in BH-vs-WH, BL-vs-BH and BL-vs-WL, respectively. Among them, 54, 356 and 49 genes were up regulated and 59, 263 and 38 genes were down regulated. In addition, there were only 10 up-regulated genes in WL-vs-WH. In the comparison of DEGs in black and white Muscovy ducks, two co-expressed DEG genes were detected between BH-vs-WH and BL-vs-WL and seven DEGs were co-expressed between BL-vs-BH and WL-vs-WH. The RNA-Seq data were confirmed to be reliable by qPCR. Numerous DEGs known to be involved in ovarian development were identified, including TGFβ2, NGFR, CEBPD, CPEB2, POSTN, SMOC1, FGF18, EFNA5 and SDC4. Gene Ontology (GO) annotations indicated that DEGs related to ovarian development were mainly enriched in biological processes of "circadian sleep/wake cycle process," "negative regulation of transforming growth factor-β secretion," "positive regulation of calcium ion transport" in BH-vs-WH and "cell surface receptor signaling pathway," "Notch signaling pathway" and "calcium ion transport" in BL-vs-BH. Besides, "steroid biosynthetic process," "granulosa cell development" and "egg coat formation" were mainly enriched in BL-vs-WL and "reproduction," "MAPK cascade" and "mitotic cell cycle" were mainly enriched in WL-vs-WH. KEGG pathway analysis showed that the PI3K-Akt signaling pathway and ovarian steroidogenesis were the most enriched in Muscovy duck ovary transcriptome data. This work highlights potential genes and pathways that may affect ovarian development in Muscovy duck.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jianqin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (X.B.); (Y.S.); (T.L.); (S.Z.); (L.H.); (S.Z.); (J.C.); (X.L.)
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13
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Gao S, Tao R, Tong X, Xu Q, Zhao J, Guo Y, Schinckel AP, Zhou B. Identification of Functional Single Nucleotide Polymorphisms in Porcine HSD17B14 Gene Associated with Estrus Behavior Difference between Large White and Mi Gilts. Biomolecules 2020; 10:biom10111545. [PMID: 33198360 PMCID: PMC7697482 DOI: 10.3390/biom10111545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 11/16/2022] Open
Abstract
Steroid hormone levels are associated with estrous behavior, which affects timely mating and reproductive efficiency in pigs. 17β-hydroxysteroid dehydrogenase type 14 (HSD17B14) modulates steroid synthesis and metabolism. To identify the functional single nucleotide polymorphisms (SNPs) in the porcine HSD17B14 gene, ear tissues from Large White and Mi gilts were collected to extract genomic DNA. Variable lengths of truncated promoter of HSD17B14 gene were used to determine the promoter activity by a dual luciferase reporter system. The vector HSD17B14Phe or HSD17B14Val was transfected into porcine granulosa cells (GCs). The core promoter region was identified between -72bp and -218bp. Six of seven SNPs had significant differences of allele frequency between Large White and Mi gilts. The plasmids with the wild genotype AA of rs329427898 maintained a smaller fraction of promoter activity compared with the plasmids with the mutant genotype GG, while the plasmids with wild the genotype TT of rs319864566 had a greater promoter activity than the plasmids with the mutant genotype CC. A missense mutation (Phe73Val) caused changes in the structural dynamics and function of the HSD17B14 protein. The highly expressed HSD17B14Val degraded less estradiol into estrone, while the relatively lowly expressed HSD17B14Phe degraded more estradiol into estrone, suggesting the protein activity of HSD17B14Phe was greater than that of HSD17B14Val. Moreover, the HSD17B14Phe group has a greater apoptosis rate of porcine GCs. The HSD17B14 gene could been used as a candidate molecular marker for estrus behavior in pigs.
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Affiliation(s)
- Siyuan Gao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (S.G.); (R.T.); (X.T.); (Q.X.); (J.Z.); (Y.G.)
| | - Ruixin Tao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (S.G.); (R.T.); (X.T.); (Q.X.); (J.Z.); (Y.G.)
| | - Xian Tong
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (S.G.); (R.T.); (X.T.); (Q.X.); (J.Z.); (Y.G.)
| | - Qinglei Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (S.G.); (R.T.); (X.T.); (Q.X.); (J.Z.); (Y.G.)
| | - Jing Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (S.G.); (R.T.); (X.T.); (Q.X.); (J.Z.); (Y.G.)
| | - Yanli Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (S.G.); (R.T.); (X.T.); (Q.X.); (J.Z.); (Y.G.)
| | - Allan P. Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907-2054, USA;
| | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (S.G.); (R.T.); (X.T.); (Q.X.); (J.Z.); (Y.G.)
- Correspondence: ; Tel.: +86-025-84395362
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14
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Di Lollo V, Canciello A, Orsini M, Bernabò N, Ancora M, Di Federico M, Curini V, Mattioli M, Russo V, Mauro A, Cammà C, Barboni B. Transcriptomic and computational analysis identified LPA metabolism, KLHL14 and KCNE3 as novel regulators of Epithelial-Mesenchymal Transition. Sci Rep 2020; 10:4180. [PMID: 32144311 PMCID: PMC7060278 DOI: 10.1038/s41598-020-61017-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/17/2020] [Indexed: 12/15/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a complex biological program between physiology and pathology. Here, amniotic epithelial cells (AEC) were used as in vitro model of transiently inducible EMT in order to evaluate the transcriptional insights underlying this process. Therefore, RNA-seq was used to identify the differentially expressed genes and enrichment analyses were carried out to assess the intracellular pathways involved. As a result, molecules exclusively expressed in AEC that experienced EMT (GSTA1-1 and GSTM3) or when this process is inhibited (KLHL14 and KCNE3) were identified. Lastly, the network theory was used to obtain a computational model able to recognize putative controller genes involved in the induction and in the prevention of EMT. The results suggested an opposite role of lysophosphatidic acid (LPA) synthesis and degradation enzymes in the regulation of EMT process. In conclusion, these molecules may represent novel EMT regulators and also targets for developing new therapeutic strategies.
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Affiliation(s)
- V Di Lollo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy. .,Molecular biology and genomic Unit, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy.
| | - A Canciello
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy.
| | - M Orsini
- Molecular biology and genomic Unit, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - N Bernabò
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - M Ancora
- Molecular biology and genomic Unit, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - M Di Federico
- Molecular biology and genomic Unit, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - V Curini
- Molecular biology and genomic Unit, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - M Mattioli
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - V Russo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - A Mauro
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - C Cammà
- Molecular biology and genomic Unit, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - B Barboni
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
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15
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Li X, Li C, Xu Y, Yao R, Li H, Ni W, Quan R, Zhang M, Liu L, Yu S, Ullah Y, Hu R, Li Y, Guo T, Wang X, Hu S. Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus. Funct Integr Genomics 2020; 20:563-573. [PMID: 32114660 DOI: 10.1007/s10142-020-00735-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/17/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022]
Abstract
Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes such as growth, development, and reproduction of animals. Here, we used RNA-seq technology to study the expression profile of lncRNAs in the anterior pituitary of sheep during estrus and anestrus. In this study, we identified a total of 995 lncRNAs, of which 335 lncRNAs were differentially expressed in two states (including 38 up-regulated and 297 down-regulated lncRNAs). RT-qPCR verified the expression levels of several lncRNAs. Target predictive analysis revealed that these lncRNAs can act in cis or trans and regulate the expression of genes involved in the regulation of sheep estrus. Target gene enrichment analysis of differentially expressed lncRNAs indicates that these lncRNAs can regulate sheep estrus by regulating hormone metabolism and energy metabolism. Through our research, we provide the expression profile of lncRNAs in the pituitary of sheep, which provides a valuable resource for further understanding of the genetic regulation of seasonal estrus in sheep from the perspective of lncRNAs.
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Affiliation(s)
- Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.,College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yaseen Ullah
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yaxin Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Tao Guo
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Xiaokui Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.
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16
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Srikanth K, Park W, Lim D, Lee KT, Jang GW, Choi BH, Ka H, Park JE, Kim JM. Serial gene co-expression network approach to mine biological meanings from integrated transcriptomes of the porcine endometrium during estrous cycle. Funct Integr Genomics 2019; 20:117-131. [PMID: 31396752 DOI: 10.1007/s10142-019-00703-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 07/03/2019] [Accepted: 07/22/2019] [Indexed: 01/22/2023]
Abstract
The estrous cycle is a complex process regulated by several hormones. To understand the dynamic changes in gene expression that takes place in the swine endometrium during the estrous cycle relative to the day of estrus onset, we performed RNA-sequencing analysis on days 0, 3, 6, 9, 12, 15, and 18, resulting in the identification of 4495 differentially expressed genes (DEGs; Q ≤ 0.05 and |log2FC| ≥ 1) at various phases in the estrous cycle. These DEGs were integrated into multiple gene co-expression networks based on different fold changes and correlation coefficient (R2) thresholds and a suitable network, which included 899 genes (|log2FC| ≥ 2 and R2 ≥ 0.99), was identified for downstream analyses based on the biological relevance of the Gene Ontology (GO) terms enriched. The genes in this network were partitioned into 6 clusters based on the expression pattern. Several GO terms including cell cycle, apoptosis, hormone signaling, and lipid biosynthetic process were found to be enriched. Furthermore, we found 15 significant KEGG pathways, including cell adhesion molecules, cytokine-cytokine receptor signaling, steroid biosynthesis, and estrogen signaling pathways. We identified several genes and GO terms to be stage-specific. Moreover, the identified genes and pathways extend our understanding of porcine endometrial regulation during estrous cycle and will serve as a good resource for future studies.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Kyung Tai Lee
- Animal Genetics and Breeding Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Gul Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Bong Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Hakhyun Ka
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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Li X, Li C, Wei J, Ni W, Xu Y, Yao R, Zhang M, Li H, Liu L, Dang H, Hazi W, Hu S. Comprehensive Expression Profiling Analysis of Pituitary Indicates that circRNA Participates in the Regulation of Sheep Estrus. Genes (Basel) 2019; 10:genes10020090. [PMID: 30696117 PMCID: PMC6409929 DOI: 10.3390/genes10020090] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 01/01/2023] Open
Abstract
The pituitary gland is the most important endocrine organ that mainly regulates animal estrus by controlling the hormones synthesis. There is a significant difference between the estrus state and anestrus state of sheep pituitary system. Here, we studied the circular RNA (circRNA) expression profiles of the anterior pituitary of estrus and anestrus sheep using RNA-seq technology. Through this study, we identified a total of 12,468 circRNAs and 9231 differentially expressed circRNAs in the estrus and anestrus pituitary system of sheep. We analyzed some differentially expressed circRNAs by reverse transcription quantitative-PCR (RT-qPCR), and some circRNAs were demonstrated using RNase-R+ resistance experiments. CircRNAs involving the regulation of estrus-related terms and pathways are enriched by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. In addition, we also predicted partial microRNA-circRNA interaction network for circRNAs that regulate sheep estrus. Overall, this study explored a potential substantial role played by circRNAs involved in pituitary regulation on sheep estrus and proposed new questions for further study.
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Affiliation(s)
- Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Junchang Wei
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Hanli Dang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China.
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.
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Tang LT, Ran XQ, Mao N, Zhang FP, Niu X, Ruan YQ, Yi FL, Li S, Wang JF. Analysis of alternative splicing events by RNA sequencing in the ovaries of Xiang pig at estrous and diestrous. Theriogenology 2018; 119:60-68. [PMID: 29982137 DOI: 10.1016/j.theriogenology.2018.06.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 06/16/2018] [Accepted: 06/24/2018] [Indexed: 12/30/2022]
Abstract
Alternative splicing (AS) is an important mechanism for controlling gene expression, which regulates multiple biological processes in higher organisms. Chinese indigenous Xiang pig has distinctive biological characteristics, such as small size, early sexual maturity, lower litter size and not very clear exhibition of estrous behaviors. To further understand how AS responds to estrous cycles in Xiang pig, the genome-wide analysis of AS events was performed by RNA-seq method in Xiang pig ovaries at diestrous and estrous. Using ASprofile program, we analyzed twelve basic AS events in Xiang pig ovaries and identified 68,775 AS events in 15,142 genes from diestrous ovaries and 69,493 AS events in 15,291 genes from the estrous ovaries with average 4.54 splicing events. 94.4-95.5% of expressed genes underwent alternative splicing in this tissues. The frequencies of AS events were similar to each other at diestrous and estrous. Transcription start site (TSS) was the predominant type of AS events, followed by transcription terminal site (TTS), and skipped exon (SKIP). The remaining type of AS events, e.g., intron retention (IR) and alternative exon ends (AE), showed the lower frequencies. Further comparison analysis of gene expression indicated that 4,433 genes had at least one splice variant differentially expressed during estrous, whereas only 2,382 of them were differentially expressed at gene level. Numerous genes involved in gonad development and hormone metabolism were differentially regulated through AS. Twelve genes with different types of alternatively splicing were validated by using RT-PCR method. The GO annotation and KEGG pathway analysis clearly revealed that a lot of DEGs (differentially expressed genes) and DSGs (differentially spliced genes) were involved in follicular development and ovarian steroid biosynthesis. A large number of DSGs, although not differentially expressed, were enriched in circadian rhythm and several signaling pathways. These pathways potentially regulated the female animal reproductive function in gene and/or AS level. Our results suggested that alternative splicing play an essential role in regulation of gene expression in female pigs during estrous. Numerous genes involved in gonad development, hormone metabolism, circadian rhythm were differentially regulated through alternative splicing.
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Affiliation(s)
- Liang-Ting Tang
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China
| | - Xue-Qin Ran
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China.
| | - Ning Mao
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China
| | - Fu-Ping Zhang
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China
| | - Xi Niu
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China
| | - Yi-Qi Ruan
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China
| | - Fan-Li Yi
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China
| | - Sheng Li
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China
| | - Jia-Fu Wang
- Institute of Agro-Bioengineering / College of Animal Science, Guizhou University, Guiyang, China; Tongren University, Tongren, China.
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19
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Yang S, Zhou X, Pei Y, Wang H, He K, Zhao A. Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9150723. [PMID: 29662904 PMCID: PMC5832140 DOI: 10.1155/2018/9150723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/29/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022]
Abstract
Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P ≤ 0.05, |log2 Ratio| ≥ 1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.
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Affiliation(s)
- Songbai Yang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Xiaolong Zhou
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Yue Pei
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Han Wang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Ke He
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Ayong Zhao
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
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