1
|
Du X, Liu Y, He X, Tao L, Fang M, Chu M. Identification and expression profile analysis of circRNAs associated with goat uterus with different fecundity during estrous cycle. BMC Genomics 2025; 26:349. [PMID: 40197288 PMCID: PMC11974169 DOI: 10.1186/s12864-025-11489-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Accepted: 03/13/2025] [Indexed: 04/10/2025] Open
Abstract
BACKGROUND The Yunshang Black Goat, a distinguished meat goat breed native to China, is renowned for its superior reproductive capabilities. Despite this, there is considerable phenotypic variability within the breed. During the reproductive cycle, the uterus plays a pivotal role, with its functions evolving in line with the different stages of the cycle. This study focuses on the uterine tissues, including both the endometrium and myometrium, of Yunshang Black Goats with high fecundity (HF) and low fecundity (LF) during the proliferative (FP) and secretory (LP) phases of the estrous cycle. By examining these tissues, we aim to elucidate the underlying molecular and physiological mechanisms of the observed differences in reproductive success. RESULTS High-throughput sequencing was conducted, followed by bioinformatics analysis to identify the expression profiles of circRNAs. A total of 7,445 circRNAs were identified through the integration of findings from find_circ and CIRI2 software. Comparative analyses between the FPLF vs. FPHF and LPLF vs. LPHF revealed 149 differentially expressed (DE) circRNAs (94 up-regulated and 55 down-regulated) and 276 DE circRNAs (56 up-regulated and 220 down-regulated), respectively. The enrichment analysis indicated that the primary pathways involved were the Sphingolipid signaling pathway, MAPK signaling pathway, and GnRH signaling pathway, all of which are closely associated with cellular growth and development. Additionally, several key candidate genes were identified, such as FGF2 and MBTPS1. We also predicted a total of 281 miRNA-circRNA binding pairs, encompassing 263 circRNAs and 60 miRNAs, and simultaneously, 14 coding circRNAs were anticipated. CONCLUSION Based on the analysis, we have established the expression profiles of circRNAs during the follicular and luteal phases, respectively. Furthermore, using various analytical methods and data from high- and low-yield experimental control groups over different periods, we have identified multiple circRNAs that affect the high reproductive capacity of goats. Through enrichment analysis of the host genes of these circRNAs, we have discovered several key candidate genes. These findings provide fundamental data for the study of the molecular mechanisms underlying the fecundity of goats and pave the way for future genetic improvement strategies.
Collapse
Affiliation(s)
- Xiaolong Du
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- Department of Animal Genetics and Breeding, Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, National Engineering Laboratory for Animal Breeding, MARA, China Agricultural University, Beijing, 100193, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Lin Tao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Meiying Fang
- Department of Animal Genetics and Breeding, Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, National Engineering Laboratory for Animal Breeding, MARA, China Agricultural University, Beijing, 100193, China.
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| |
Collapse
|
2
|
Sun Q, Li Y, Yang W, Feng W, Zhou J, Cao Y, Zhang B, Zhu Z, Han C. CircMYH9/miR-133a-3p/CXCR4 axis: a novel regulatory network in sperm fertilization and embryo development. MOLECULAR BIOMEDICINE 2024; 5:69. [PMID: 39671083 PMCID: PMC11645365 DOI: 10.1186/s43556-024-00236-5] [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: 05/16/2024] [Revised: 11/26/2024] [Accepted: 11/27/2024] [Indexed: 12/14/2024] Open
Abstract
This study aimed to investigate the influence of sperm miRNAs on fertilization rates (FR) in in vitro fertilization (IVF) and to explore potential regulatory mechanisms in sperm-mediated fertilization and embryo development. Through high-throughput sequencing, we identified differentially expressed miRNAs in sperm, with miR-133a-3p significantly upregulated in samples associated with low FR and available embryo rate (AER). Key regulatory circRNAs and mRNAs were further identified via the Starbase database, intersected with differentially expressed RNA, and analyzed through GO, KEGG, and PPI analyses. The circMYH9/miR-133a-3p/CXCR4 axis emerged as a critical regulatory network. In vitro assays using the GC-2 spd mouse spermatogenic cell line revealed that miR-133a-3p inhibited cell growth and proliferation while promoting apoptosis. circMYH9, acting as a competing endogenous RNA (ceRNA) for miR-133a-3p, modulated CXCR4 expression, enhancing GC-2 spd cell growth and inhibiting apoptosis through the miR-133a-3p/CXCR4 axis. In vivo experiments using a mouse model confirmed that circMYH9 overexpression increased IVF success rates and promoted embryo development via this axis. Mechanistically, miR-133a-3p suppresses sperm fertilization and embryo development by targeting the circMYH9/miR-133a-3p/CXCR4 axis. These findings suggest that this regulatory network could serve as a novel biomarker for assessing fertilization potential and embryo quality in clinical settings and as a potential therapeutic target to improve IVF outcomes and address infertility. This study provides valuable insights into the molecular mechanisms governing sperm function and early embryonic development.
Collapse
Affiliation(s)
- Qian Sun
- Suzhou Medical College, Soochow University, Suzhou, 215123, China
- Department of Gynecology, The First Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang, 222061, China
| | - Yanyu Li
- Suzhou Medical College, Soochow University, Suzhou, 215123, China
- Clinical Medicine Postgraduate Workstation, Soochow University, Xuzhou, 221009, China
- Department of Gynecology, Xuzhou Central Hospital, No. 199, South Jiefang Road, Quanshan District, Xuzhou, 221009, China
| | - Wen Yang
- Department of Gynecology, The First Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang, 222061, China
| | - Wen Feng
- Department of Gynecology, The First Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang, 222061, China
| | - Jiayun Zhou
- Department of Gynecology, Xuzhou Central Hospital, No. 199, South Jiefang Road, Quanshan District, Xuzhou, 221009, China
| | - Yijuan Cao
- Department of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou, 221009, China
| | - Bei Zhang
- Suzhou Medical College, Soochow University, Suzhou, 215123, China.
- Clinical Medicine Postgraduate Workstation, Soochow University, Xuzhou, 221009, China.
- Department of Gynecology, Xuzhou Central Hospital, No. 199, South Jiefang Road, Quanshan District, Xuzhou, 221009, China.
| | - Zuobin Zhu
- Xuzhou Engineering Research Center of Medical Genetics and Transformation, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, 221004, China.
| | - Conghui Han
- Clinical Medicine Postgraduate Workstation, Soochow University, Xuzhou, 221009, China.
- Department of Urology, Xuzhou Central Hospital, Xuzhou, 221009, China.
- Department of Urology, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, 221009, China.
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
- Department of Urology, Heilongjiang Provincial Hospital, Harbin, 150006, China.
| |
Collapse
|
3
|
Liu J, Feng G, Guo C, Li Z, Liu D, Liu G, Zou X, Sun B, Guo Y, Deng M, Li Y. Identification of functional circRNAs regulating ovarian follicle development in goats. BMC Genomics 2024; 25:893. [PMID: 39342142 PMCID: PMC11439210 DOI: 10.1186/s12864-024-10834-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024] Open
Abstract
BARKGROUND Circular RNAs (circRNAs) play important regulatory roles in a variety of biological processes in mammals. Multiple birth-traits in goats are affected by several factors, but the expression and function of circRNAs in follicular development of goats are not clear. In this study, we aimed to investigate the possible regulatory mechanisms of circRNA and collected five groups of large follicles (Follicle diameter > 6 mm) and small follicles (1 mm < Follicle diameter < 3 mm) from Leizhou goats in estrus for RNA sequencing. RESULTS RNA sequencing showed that 152 circRNAs were differentially expressed in small and large follicles. Among them, 101 circRNAs were up-regulated in large follicles and 51 circRNAs were up-regulated in small follicles. GO and KEGG enrichment analyses showed that parental genes of the differential circRNAs were significantly enriched in important pathways, such as ovarian steroidogenesis, GnRH signaling pathway, animal autophagy and oxytocin signalling pathway. BioSignal analysis revealed that 152 differentially expressed circRNAs could target 91 differential miRNAs including miR-101 family (chi-miR-101-3p, chi-miR-101-5p), miR-202 family (chi-miR-202-5p, chi-miR-202-3p),60 circRNAs with translation potential. Based on the predicted sequencing results, the ceRNA networks chicirc_008762/chi-miR-338-3p/ARHGAP18 and chicirc_040444/chi-miR-338-3p/STAR were constructed in this study. Importantly, the new gene circCFAP20DC was first discovered in goats. The EDU assay and flow cytometry results indicated that circCFAP20DC enhanced the proliferation of follicular granulosa cells(GCs). Real-time quantitative PCR and western blotting assays showed that circCFAP20DC activated the Retinoblastoma(RB) pathway and promoted the progression of granulosa cells from G1 to S phase. CONCLUSION Differential circRNAs in goat size follicles may have important biological functions for follicular development. The novel gene circCFAP20DC activates the RB pathway, promoting the progression of GCs from G1 to S phase. This, in turn, enhances the proliferation of follicular GCs in goats.
Collapse
Affiliation(s)
- Jie Liu
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Guanghang Feng
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Conghui Guo
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihan Li
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Dewu Liu
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Guangbin Liu
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Xian Zou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Baoli Sun
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yongqing Guo
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Deng
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yaokun Li
- Herbivore Laboratory, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
- National Joint Engineering Research Center, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Key Laboratory of Agricultural Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
4
|
Zhang H, Ye H, Zhou H, Liu Y, Xie F, Wang Q, Yin Z, Zhang X. RNA-Seq Analysis Revealed circRNAs Associated with Resveratrol-Induced Apoptosis of Porcine Ovarian Granulosa Cells. Cells 2024; 13:1571. [PMID: 39329754 PMCID: PMC11429535 DOI: 10.3390/cells13181571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/13/2024] [Accepted: 09/17/2024] [Indexed: 09/28/2024] Open
Abstract
Circular RNAs (circRNAs) are a class of circular non-coding RNAs that play essential roles in the intricate and dynamic networks governing cell growth, development, and apoptosis. Resveratrol (RSV), a non-flavonoid polyphenol, is known to participate in follicular development and ovulation. In our previous research, we established a model using porcine ovarian granulosa cells (POGCs) treated with resveratrol, which confirmed its regulatory effects on long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) within these cells. However, the influence of resveratrol on circRNA expression has not been thoroughly investigated. To explore how resveratrol affects circRNA levels in POGCs, we designed an experiment with three groups: a control group (CON, n = 3, 0 μM RSV), a low-dose RSV group (LOW, n = 3, 50 μM RSV), and a high-dose RSV group (HIGH, n = 3, 100 μM RSV) for circRNA sequencing. We identified a total of 10,045 candidate circRNAs from POGCs treated with different concentrations of resveratrol (0, 50, and 100 μM). Differential expression analysis indicated that 96 circRNAs were significantly altered in the LOW vs. CON group, while 109 circRNAs showed significant changes in the HIGH vs. CON group. These circRNAs were notably enriched in biological processes associated with cell metabolism, apoptosis, and oxidative stress. Functional enrichment analysis of the host genes revealed their involvement in critical signaling pathways, including mTOR, AMPK, and apoptosis pathways. Additionally, we identified potential miRNA sponge candidates among the differentially expressed circRNAs, particularly novel_circ_0012954 and novel_circ_0004762, which exhibited strong connectivity within miRNA-target networks. Our findings provide valuable insights into the regulatory mechanisms of circRNAs in the context of resveratrol-induced apoptosis in POGCs, highlighting their potential as innovative therapeutic targets in reproductive biology.
Collapse
Affiliation(s)
- Huibin Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (H.Z.); (H.Y.); (H.Z.); (Y.L.); (F.X.); (Q.W.)
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Haibo Ye
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (H.Z.); (H.Y.); (H.Z.); (Y.L.); (F.X.); (Q.W.)
| | - Hanyu Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (H.Z.); (H.Y.); (H.Z.); (Y.L.); (F.X.); (Q.W.)
| | - Yangguang Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (H.Z.); (H.Y.); (H.Z.); (Y.L.); (F.X.); (Q.W.)
| | - Fan Xie
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (H.Z.); (H.Y.); (H.Z.); (Y.L.); (F.X.); (Q.W.)
| | - Qianqian Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (H.Z.); (H.Y.); (H.Z.); (Y.L.); (F.X.); (Q.W.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (H.Z.); (H.Y.); (H.Z.); (Y.L.); (F.X.); (Q.W.)
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China; (H.Z.); (H.Y.); (H.Z.); (Y.L.); (F.X.); (Q.W.)
| |
Collapse
|
5
|
Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Transcriptome Analysis Reveals Differentially Expressed circRNAs Associated with Fecundity in Small-Tail Han Sheep Thyroid with Different FecB Genotypes. Animals (Basel) 2023; 14:105. [PMID: 38200837 PMCID: PMC10777913 DOI: 10.3390/ani14010105] [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: 10/07/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Litter size is an economically important trait in sheep, and it is a complex trait controlled by multiple genes in multiple organs. Among them, the regulation of lamb number trait by the thyroid gland is a very important part. However, the molecular mechanisms of the thyroid gland in sheep reproduction remain unclear. Here, RNA-seq was used to detect transcriptome expression patterns in the thyroid gland between follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) STH sheep, respectively, and to identify differentially expressed circRNAs (DECs) associated with reproduction. Bioinformatic analysis of the source genes of these DECs revealed that they can be enriched in multiple signaling pathways involved in the reproductive process of animals. We found that the source genes of these DECs, such as GNAQ, VEGFC, MAPK1, STAT1, and HSD17B7, may play important roles in the reproductive process of animals. To better understand the function of these DECs, we constructed circRNA-miRNA co-expression networks. Dual luciferase reporter assays suggested that a ceRNA regulatory mechanism between circ_0003259-oar-miR-133-TXLNA and circ_0012128-oar-miR-370-3p-FGFR1 may hold. All of these DEC expression profiles in the thyroid gland provide a novel resource for elucidating the regulatory mechanisms underlying STH sheep prolificacy.
Collapse
Affiliation(s)
- Cheng Chang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| |
Collapse
|
6
|
Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Thyroid Transcriptomics Revealed the Reproductive Regulation of miRNA in the Follicular and Luteal Phases in Small-Tail Han Sheep with Different FecB Genotypes. Genes (Basel) 2023; 14:2024. [PMID: 38002966 PMCID: PMC10671830 DOI: 10.3390/genes14112024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
MicroRNA (miRNA) is a type of endogenous short-stranded ncRNA that influences many biological processes such as animal growth, development and metabolism. The thyroid gland is an important endocrine gland in sheep, and an increasing number of studies have shown that the thyroid gland plays an important role in animal reproduction, but the molecular mechanisms of the thyroid gland in sheep reproduction are poorly understood. In this study, RNA-seq was used to detect transcriptome expression patterns in the thyroid gland between the follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) small-tail Han (STH) sheep, respectively, and to identify differentially expressed miRNAs (DEMs) associated with reproduction. Bioinformatic analysis of the target genes of these DEMs revealed that they can be enriched in multiple GO terms associated with the reproductive process in animals and in the KEGG signaling pathway. The miRNA-mRNA coexpression network revealed that oar-miR-133 and oar-miR-370-3p may play an important role in sheep reproduction. The results of the dual-luciferase reporter assay suggest a possible targeting relationship between novel-51 and TARBP2. These results provided a novel resource for elucidating regulatory mechanisms underlying STH sheep prolificacy.
Collapse
Affiliation(s)
- Cheng Chang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| |
Collapse
|
7
|
Li C, Zhou M, He X, Di R, Zhang Z, Ren C, Liu Q, Chu M. Comparative proteomics of ovaries elucidated the potential targets related to ovine prolificacy. Front Vet Sci 2023; 10:1096762. [PMID: 37675075 PMCID: PMC10477366 DOI: 10.3389/fvets.2023.1096762] [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: 11/12/2022] [Accepted: 08/02/2023] [Indexed: 09/08/2023] Open
Abstract
Small Tail Han (STH) sheep, a unique Chinese breed, is recognized for its early maturity, year-round estrus, and prolificacy. However, the molecular mechanism of its high prolificacy has not been fully elucidated. The Proteomics approach is feasible and effective to reveal the proteins involved in the complex physiological processes of any organism. Given this, we performed the protein expression profiling of ovarian tissues during the luteal phase using polytocous STH sheep (litter size ≥2, three consecutive lambings) and monotocous STH sheep (litter size =1, three consecutive lambings) (PL vs. ML), and the follicular phase using polytocous STH sheep (litter size ≥2, three consecutive lambings) and monotocous STH sheep (litter size =1, three consecutive lambings) (PF vs. MF), respectively. Parallel Reaction Monitoring (PRM) was conducted to validate the differentially abundant proteins (DAPs). The tandem mass tag (TMT) quantitative proteomic results showed that a total of 5,237 proteins were identified, of which 49 and 44 showed differential abundance in the PL vs. ML and PF vs. MF groups, respectively. Enrichments analyses indicated that the DAPs including TIA1 cytotoxic granule-associated RNA-binding protein-like 1 (TIAL1), nicotinamide phosphoribosyltransferase (NAMPT), and cellular retinoic acid-binding protein 1 (CRABP1) were enriched at the luteal phase, while TIAL1, inhibin beta-a-subunit (A2ICA4), and W5PG55 were enriched at the follicular phase, potentially mediating reproductive processes in polytocous ewes. Furthermore, six DAPs were verified using PRM, confirming the accuracy of the TMT data acquired in this study. Together, our work expanded the database of indigenous sheep breeds and provided new ovarian candidate molecular targets, which will help in the study of the genetic mechanisms of ovine prolificacy.
Collapse
Affiliation(s)
- Chunyan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Yunnan Provincial Engineering Laboratory of Animal Genetic Resource Conservation and Germplasm Enhancement, Yunnan Academy of Animal Husbandry and Veterinary Sciences, Kunming, China
| | - Mei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Chunhuan Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Qiuyue Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
8
|
Yousuf S, Malik WA, Feng H, Liu T, Xie L, Miao X. Genome wide identification and characterization of fertility associated novel CircRNAs as ceRNA reveal their regulatory roles in sheep fecundity. J Ovarian Res 2023; 16:115. [PMID: 37340323 DOI: 10.1186/s13048-023-01178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/29/2023] [Indexed: 06/22/2023] Open
Abstract
Reproductive traits play a vital role in determining the production efficiency of sheep. Maximizing the production is of paramount importance for breeders worldwide due to the growing population. Circular RNAs (circRNAs) act as miRNA sponges by absorbing miRNA activity through miRNA response elements (MREs) and participate in ceRNA regulatory networks (ceRNETs) to regulate mRNA expression. Despite of extensive research on role of circRNAs as miRNA sponges in various species, their specific regulatory roles and mechanism in sheep ovarian tissue are still not well understood. In this study, we performed whole genome sequencing of circRNAs, miRNA and mRNA employing bioinformatic techniques on ovine tissues of two contrasting sheep breeds "Small tail Han (X_LC) and Dolang sheep (D_LC)", which results into identification of 9,878 circRNAs with a total length of 23,522,667 nt and an average length of 2,381.32 nt. Among them, 44 differentially expressed circRNAs (DECs) were identified. Moreover, correlation between miRNA-mRNA and lncRNA-miRNA provided us with to prediction of miRNA binding sites on nine differentially expressed circRNAs and 165 differentially expressed mRNAs using miRanda. miRNA-mRNA and lncRNA-miRNA pairs with negative correlation were selected to determine the ceRNA score along with positively correlated pairs from lncRNA and mRNA network. Integration of ceRNA score and positively correlated pairs exhibit a significant ternary relationship among circRNAs-miRNA-mRNA demonestrated by ceRNA, comprising of 50 regulatory pairs sharring common nodes and predicted potential differentially expressed circRNAs-miRNAs-mRNAs regulatory axis. Based on functional enrichment analysis shortlisted key ceRNA regulatory pairs associated with reproduction including circRNA_3257-novel579_mature-EPHA3, circRNA_8396-novel130_mature-LOC101102473, circRNA_4140- novel34_mature > novel661_mature-KCNK9, and circRNA_8312-novel339_mature-LOC101110545. Furthermore, expression profiling, functional enrichments and qRT-PCR analysis of key target genes infer their implication in reproduction and metabolism. ceRNA target mRNAs evolutionary trajectories, expression profiling, functional enrichments, subcellular localizations following genomic organizations will provide new insights underlying molecular mechanisms of reproduction, and establish a solid foundation for future research. Graphical abstract summarizing the scheme of study.
Collapse
Affiliation(s)
- Salsabeel Yousuf
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Waqar Afzal Malik
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hui Feng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tianyi Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lingli Xie
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangyang Miao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
9
|
Zhang J, Wang C, Jia C, Zhang Y, Qing X, Zhang Y, Liu J, Xu S, Pan Z. The Role of Circular RNAs in the Physiology and Pathology of the Mammalian Ovary. Int J Mol Sci 2022; 23:15204. [PMID: 36499522 PMCID: PMC9737273 DOI: 10.3390/ijms232315204] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Circular RNAs (circRNAs) are an abundant class of endogenous non-coding RNAs (ncRNAs) generated from exonic, intronic, or untranslated regions of protein-coding genes or intergenic regions. The diverse, stable, and specific expression patterns of circRNAs and their possible functions through cis/trans regulation and protein-coding mechanisms make circRNA a research hotspot in various biological and pathological processes. It also shows practical value as biomarkers, diagnostic indicators, and therapeutic targets. This review summarized the characteristics, classification, biogenesis and elimination, detection and confirmation, and functions of circRNAs. We focused on research advances circRNAs in the mammalian ovary under conditions including ovarian cancer, polycystic ovarian syndrome (PCOS), and maternal aging, as well as during reproductive status, including ovarian follicle development and atresia. The roles of circRNAs in high reproductive traits in domestic animals were also summarized. Finally, we outlined some obstructive factors and prospects to work with circRNA, aiming to provide insights into the functional research interests of circRNAs in the reproduction and gynecology areas.
Collapse
Affiliation(s)
- Jinbi Zhang
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing 211169, China
| | - Caixia Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Jia
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yi Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Qing
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuge Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingge Liu
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing 211169, China
| | - Shiyong Xu
- College of Animal Science and Food Engineering, Jinling Institute of Technology, Nanjing 211169, China
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
10
|
Sun Z, Hong Q, Liu Y, He X, Di R, Wang X, Ren C, Zhang Z, Chu M. Characterization of circular RNA profiles of oviduct reveal the potential mechanism in prolificacy trait of goat in the estrus cycle. Front Physiol 2022; 13:990691. [PMID: 36187784 PMCID: PMC9521424 DOI: 10.3389/fphys.2022.990691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/24/2022] [Indexed: 12/29/2022] Open
Abstract
The mammalian oviduct is functionally highly diverse during the estrus cycle. It provides a suitable milieu for oocyte maturation, sperm capacitation, fertilization, early embryo development and transportation. While there have been many studies of molecular mechanisms on the kidding number of goats, a systematic analysis by which the underlying circular RNAs (circRNAs) changes in the oviduct related to prolificacy traits is lacking. Herein, we present a comprehensive circRNA atlas of the oviduct among high- and low-fecundity goats in the follicular phase (FH vs. FL), luteal phase (LH vs. LL), and estrus cycle (FH vs. LH; FL vs. LL) to unravel their potential regulatory mechanisms in improving kidding number. We generated RNA sequencing data, and identified 4,078 circRNAs from twenty sampled Yunshang black goats. Many of these circRNAs are exon-derived and differentially expressed between each comparison group. Subsequently, eight differentially expressed (DE) circRNAs were validated by RT‒qPCR, which was consistent with the RNA-seq data. GO and KEGG enrichment analyses suggested that numerous host genes of DE circRNAs were involved in the hormone secretion, gamete production, fertilization, and embryo development processes. The competing endogenous RNA (ceRNA) interaction network analysis revealed that 2,673 circRNA–miRNA–mRNA axes (including 15 DE circRNAs, 14 miRNAs, and 1,699 mRNAs) were formed, and several target genes derived from the ceRNA network were associated with oviduct functions and reproduction, including SMAD1, BMPR1B, IGF1, REV1, and BMP2K. Furthermore, miR-15a-5p, miR-181b-5p, miR-23b-5p, miR-204-3p, and miR-145-5p might play important roles in reproduction. Finally, a novel circRNA, circIQCG, was identified as potentially involved in embryo development. Overall, our study provides a resource of circRNAs to understand the oviductal function and its connection to prolificacy trait of goats in the differentiation estrus cycle.
Collapse
Affiliation(s)
- Zhipeng Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunhuan Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- *Correspondence: Zijun Zhang, ; Mingxing Chu,
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Zijun Zhang, ; Mingxing Chu,
| |
Collapse
|
11
|
Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data. Animals (Basel) 2022; 12:ani12182365. [PMID: 36139225 PMCID: PMC9495118 DOI: 10.3390/ani12182365] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.
Collapse
|