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Current JZ, Chaney HL, Zhang M, Dugan EM, Chimino GL, Yao J. Characterization of bovine long non-coding RNAs, OOSNCR1, OOSNCR2 and OOSNCR3, and their roles in oocyte maturation and early embryonic development. Reprod Biol 2024; 24:100915. [PMID: 38936296 DOI: 10.1016/j.repbio.2024.100915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/29/2024]
Abstract
In mammals, early embryogenesis relies heavily on the regulation of maternal transcripts including protein-coding and non-coding RNAs stored in oocytes. In this study, the expression of three bovine oocyte expressed long non-coding RNAs (lncRNAs), OOSNCR1, OOSNCR2, and OOSNCR3, was characterized in somatic tissues, the ovarian follicle, and throughout early embryonic development. Moreover, the functional requirement of each transcript during oocyte maturation and early embryonic development was investigated using a siRNA-mediated knockdown approach. Tissue distribution analysis revealed that OOSNCR1, OOSNCR2 and OOSNCR3 are predominantly expressed in fetal ovaries. Follicular cell expression analysis revealed that these lncRNAs are highly expressed in the oocytes, with minor expression detected in the cumulus cells (CCs) and mural granulosa cells (mGCs). The expression for all three genes was highest during oocyte maturation, decreased at fertilization, and ceased altogether by the 16-cell stage. Knockdown of OOSNCR1, OOSNCR2 and OOSNCR3 in immature oocytes was achieved by microinjection of the cumulus-enclosed germinal vesicle (GV) oocytes with siRNAs targeting these lncRNAs. Knockdown of OOSNCR1, OOSNCR2 and OOSNCR3 did not affect cumulus expansion, but oocyte survival at 12 h post-insemination was significantly reduced. In addition, knockdown of OOSNCR1, OOSNCR2 and OOSNCR3 in immature oocytes resulted in a decreased rate of blastocyst development, and reduced expression of genes associated with oocyte competency such as nucleoplasmin 2 (NPM2), growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15), and JY-1 in MII oocytes. The data herein suggest a functional requirement of OOSNCR1, OOSNCR2, and OOSNCR3 during bovine oocyte maturation and early embryogenesis.
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Affiliation(s)
- Jaelyn Z Current
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Heather L Chaney
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Mingxiang Zhang
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Emily M Dugan
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Gianna L Chimino
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States
| | - Jianbo Yao
- Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, United States.
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Zhang H, Liu Z, Wang J, Zeng T, Ai X, Wu K. An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs. Int J Mol Sci 2023; 24:14812. [PMID: 37834260 PMCID: PMC10573446 DOI: 10.3390/ijms241914812] [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: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Meishan pigs are a well-known indigenous pig breed in China characterized by a high fertility. Notably, the number of endometrial grands is significantly higher in Meishan pigs than Duroc pigs. The characteristics of the endometrial tissue are related to litter size. Therefore, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-sequencing (RNA-seq) to analyze the mechanisms underlying the differences in fecundity between the breeds. We detected the key transcription factors, including Double homeobox (Dux), Ladybird-like homeobox gene 2 (LBX2), and LIM homeobox 8 (Lhx8), with potentially pivotal roles in the regulation of the genes related to endometrial development. We identified the differentially expressed genes between the breeds, including SOX17, ANXA4, DLX3, DMRT1, FLNB, IRF6, CBFA2T2, TFCP2L1, EFNA5, SLIT2, and CYFIP2, with roles in epithelial cell differentiation, fertility, and ovulation. Interestingly, ANXA4, CBFA2T2, and TFCP2L1, which were upregulated in the Meishan pigs in the RNA-seq analysis, were identified again by the integration of the ATAC-seq and RNA-seq data. Moreover, we identified genes in the cancer or immune pathways, FoxO signaling, Wnt signaling, and phospholipase D signaling pathways. These ATAC-seq and RNA-seq analyses revealed the accessible chromatin and potential mechanisms underlying the differences in the endometrial tissues between the two types of pigs.
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Affiliation(s)
| | | | | | | | | | - Keliang Wu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.Z.); (Z.L.); (J.W.); (T.Z.); (X.A.)
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Zhao L, Li Q, Kuang Y, Xu P, Sun X, Meng Q, Wang W, Zeng Y, Chen B, Fu J, Dong J, Zhu J, Luo Y, Gu H, Li C, Li C, Wu L, Mao X, Fan H, Liu R, Zhang Z, Li Q, Du J, He L, Jin L, Wang L, Sang Q. Heterozygous loss-of-function variants in LHX8 cause female infertility characterized by oocyte maturation arrest. Genet Med 2022; 24:2274-2284. [PMID: 36029299 DOI: 10.1016/j.gim.2022.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022] Open
Abstract
PURPOSE The genetic causes of oocyte maturation arrest leading to female infertility are largely unknown, and no population-based genetic analysis has been applied in cohorts of patients with infertility. We aimed to identify novel pathogenic genes causing oocyte maturation arrest by using a gene-based burden test. METHODS Through comparison of exome sequencing data from 716 females with infertility characterized by oocyte maturation arrest and 3539 controls, we performed a gene-based burden test and identified a novel pathogenic gene LHX8. Splicing event was evaluated using a minigene assay, expression of LHX8 protein was assessed in HeLa cells, and nuclear subcellular localization was determined in both HeLa cells and mouse oocytes. RESULTS A total of 5 heterozygous loss-of-function LHX8 variants were identified from 6 independent families (c.389+1G>T, c.412C>T [p.Arg138∗], c.282C>A [p.Cys94∗]; c.257dup [p.Tyr86∗]; and c.180del, [p.Ser61Profs∗30]). All the identified variants in LHX8 produced truncated LHX8 protein and resulted in loss of LHX8 nuclear localization in both HeLa cells and mouse oocytes. CONCLUSION By combining genetic evidence and functional evaluations, we identified a novel pathogenic gene LHX8 and established the causative relationship between LHX8 haploinsufficiency and female infertility characterized by oocyte maturation arrest.
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Affiliation(s)
- Lin Zhao
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China; NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Shanghai, China
| | - Qun Li
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China; Human Phenome Institute, Fudan University, Shanghai, China
| | - Yanping Kuang
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Peng Xu
- Hainan Jinghua Hejing Hospital for Reproductive Medicine, Haikou, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Qingxia Meng
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Wenjing Wang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Yang Zeng
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Biaobang Chen
- NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Shanghai, China
| | - Jing Fu
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jie Dong
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Jiawei Zhu
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yuxi Luo
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Hao Gu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Caihong Li
- Shenyang Jinghua Hospital, Liaoning, China
| | - Chunyi Li
- Shenyang Jinghua Hospital, Liaoning, China
| | - Ling Wu
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyan Mao
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Huizhen Fan
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Ruyi Liu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Zhihua Zhang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Qiaoli Li
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Jing Du
- NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Shanghai, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Lei Wang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.
| | - Qing Sang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.
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Chantepie L, Bodin L, Sarry J, Woloszyn F, Plisson-Petit F, Ruesche J, Drouilhet L, Fabre S. Genome-Wide Identification of a Regulatory Mutation in BMP15 Controlling Prolificacy in Sheep. Front Genet 2020; 11:585. [PMID: 32636872 PMCID: PMC7317000 DOI: 10.3389/fgene.2020.00585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/14/2020] [Indexed: 12/30/2022] Open
Abstract
The search for the genetic determinism of prolificacy variability in sheep has evidenced several major mutations in genes playing a crucial role in the control of ovulation rate. In the Noire du Velay (NV) sheep population, a recent genetic study has evidenced the segregation of such a mutation named FecL L . However, based on litter size (LS) records of FecL L non-carrier ewes, the segregation of a second prolificacy major mutation was suspected in this population. In order to identify this mutation, we have combined a case/control genome-wide association study with ovine 50k SNP chip genotyping, whole genome sequencing, and functional analyses. A new single nucleotide polymorphism (OARX:50977717T > A, NC_019484) located on the X chromosome upstream of the BMP15 gene was evidenced to be highly associated with the prolificacy variability (P = 1.93E-11). The variant allele was called FecX N and shown to segregate also in the Blanche du Massif Central (BMC) sheep population. In both NV and BMC, the FecX N allele frequency was estimated close to 0.10, and its effect on LS was estimated at +0.20 lamb per lambing at the heterozygous state. Homozygous FecX N carrier ewes were fertile with increased prolificacy in contrast to numerous mutations affecting BMP15. At the molecular level, FecX N was shown to decrease BMP15 promoter activity and supposed to impact BMP15 expression in the oocyte. This regulatory action was proposed as the causal mechanism for the FecX N mutation to control ovulation rate and prolificacy in sheep.
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Affiliation(s)
| | | | | | | | | | | | | | - Stéphane Fabre
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
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Saleh AA, Hammoud MH, Dabour NA, Hafez EE, Sharaby MA. BMPR-1B, BMP-15 and GDF-9 genes structure and their relationship with litter size in six sheep breeds reared in Egypt. BMC Res Notes 2020; 13:215. [PMID: 32299511 PMCID: PMC7160958 DOI: 10.1186/s13104-020-05047-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/28/2020] [Indexed: 01/11/2023] Open
Abstract
Objective The aim of this work was to investigate three different mutations; Fec-B, FecXG, Fec-GH at three candidate genes; Bone morphogenetic protein receptor IB, Bone morphogenetic protein 15 and Growth Differentiation Factor 9, respectively, in six sheep breeds reared in Egypt namely; Rahmani, Barki, Rahmani X Barki cross, Awassi, Awassi X Suffolk cross, and Ossimi and their association with litter size. Results Genomic DNA of 132 sheep was investigated for the Fec-B, FecXG, and Fec-GH mutations by Restriction Fragment Length Polymorphism, Single-Stranded Conformation Polymorphism and DNA sequencing. The results revealed that all breeds did not carry Fec-B mutation. On the other side, the mutations of FecXG, and Fec-GH were detected in Rahmani, and Rahmani X Barki cross which is associated with the high twinning rate/litter size of Rahmani (1.28) and Rahmani X Barki cross (1.22). While, the average litter size for other breeds had almost a constant values rate over six parities, ranging between 1.00 and 1.04.
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Affiliation(s)
- Ahmed A Saleh
- College of Animal Science and Technology, Southwest University, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Beibei, 400716, Chongqing, People's Republic of China. .,Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria, Egypt.
| | - M H Hammoud
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria, Egypt
| | - Nasraa A Dabour
- Dairy Science and Technology Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria, Egypt
| | - E E Hafez
- Plant Protection and Bio-molecular diagnosis Department, Arid Lands Cultivation Research Institute (ALCRI), The City of Scientific Research and Technology Applications, Alexandria, Egypt
| | - Mahmoud A Sharaby
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria, Egypt
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