|
1
|
Ma L, Zhao X, Wang H, Chen Z, Zhang K, Xue J, Luo Y, Liu H, Jiang X, Wang J, Ma X, Mao F, Zhong Y, Liu Y, Deng R, Zhou Y, Wang C, Xie Y, Chen Y, Wang Q, Gao G. DNA Methylation Patterns and Transcriptomic Data Were Integrated to Investigate Candidate Genes Influencing Reproductive Traits in Ovarian Tissue from Sichuan White Geese. Int J Mol Sci 2025; 26:3408. [PMID: 40244255 PMCID: PMC11989590 DOI: 10.3390/ijms26073408] [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: 03/07/2025] [Revised: 04/02/2025] [Accepted: 04/03/2025] [Indexed: 04/18/2025] Open
Abstract
Ovarian tissue is critical for goose reproduction. This study aimed to investigate gene regulation by DNA methylation in relation to the reproductive traits of geese. We performed whole-genome bisulfite sequencing (WGBS) on ovarian tissues from Sichuan white geese (high-laying-rate group: HLRG, ♀ = 3; low-laying-rate group: LLRG, ♀ = 3) during the laying period. The results showed a higher level of hypermethylated differentially methylated regions (DMRs) in the HLRG, indicating a higher overall methylation level compared to the LLRG. In total, we identified 2831 DMRs and 733 differentially methylated genes (DMGs), including 363 genes with upregulated methylation. These DMGs were significantly enriched in pathways related to microtubule function (GO:0005874; GO:0000226), GnRH secretion, thyroid hormone signaling, ECM-receptor interaction, and PI3K-Akt signaling. Integration with RNA-seq data identified eight overlapping genes between DMGs and differentially expressed genes (DEGs), with five genes (CUL9, MEGF6, EML6, SYNE2, AK1BA) exhibiting a correlation between hypomethylation and high expression. EML6, in particular, emerged as a promising candidate, potentially regulating follicle growth and development in Sichuan white geese. Future studies should focus on further verifying the role of the EML6 gene. In conclusion, this study provides important insights into the regulatory mechanisms of DNA methylation influencing reproductive traits in geese, offering novel candidate markers for future goose breeding programs.
Collapse
Affiliation(s)
- Lin Ma
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Xianzhi Zhao
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Haiwei Wang
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Zhuping Chen
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Keshan Zhang
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Jiajia Xue
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Yi Luo
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Hanyu Liu
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin 150030, China; (H.L.); (X.J.)
| | - Xinshuai Jiang
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin 150030, China; (H.L.); (X.J.)
| | - Jiayue Wang
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China; (J.W.); (X.M.); (F.M.); (Y.Z.); (Y.L.); (R.D.); (Y.Z.)
| | - Xiaohui Ma
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China; (J.W.); (X.M.); (F.M.); (Y.Z.); (Y.L.); (R.D.); (Y.Z.)
| | - Fanglei Mao
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China; (J.W.); (X.M.); (F.M.); (Y.Z.); (Y.L.); (R.D.); (Y.Z.)
| | - Yuhan Zhong
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China; (J.W.); (X.M.); (F.M.); (Y.Z.); (Y.L.); (R.D.); (Y.Z.)
| | - Yueyang Liu
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China; (J.W.); (X.M.); (F.M.); (Y.Z.); (Y.L.); (R.D.); (Y.Z.)
| | - Rui Deng
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China; (J.W.); (X.M.); (F.M.); (Y.Z.); (Y.L.); (R.D.); (Y.Z.)
| | - Yanli Zhou
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China; (J.W.); (X.M.); (F.M.); (Y.Z.); (Y.L.); (R.D.); (Y.Z.)
| | - Chao Wang
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Youhui Xie
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Ying Chen
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Qigui Wang
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| | - Guangliang Gao
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Science, Chongqing 402460, China; (L.M.); (X.Z.); (H.W.); (Z.C.); (K.Z.); (J.X.); (Y.L.); (C.W.); (Y.X.); (Y.C.)
| |
Collapse
|
|
2
|
Zhang C, Yang L, Zhang H, Wu F, Zhang Y, Zhang K, Wu C, Li R, Dong M, Zhao S, Song H. TAF1 is needed for the proliferation and maturation of thyroid follicle cells via Notch signaling. Am J Physiol Endocrinol Metab 2024; 326:E832-E841. [PMID: 38656129 DOI: 10.1152/ajpendo.00403.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Thyroid dysgenesis (TD) is the common pathogenic mechanism of congenital hypothyroidism (CH). In addition, known pathogenic genes are limited to those that are directly involved in thyroid development. To identify additional candidate pathogenetic genes, we performed forward genetic screening for TD in zebrafish, followed by positional cloning. The candidate gene was confirmed in vitro using the Nthy-ori 3.1 cell line and in vivo using a zebrafish model organism. We obtained a novel zebrafish line with thyroid dysgenesis and identified the candidate pathogenetic mutation TATA-box binding protein associated Factor 1 (taf1) by positional cloning. Further molecular studies revealed that taf1 was needed for the proliferation of thyroid follicular cells by binding to the NOTCH1 promoter region. Knockdown of TAF1 impaired the proliferation and maturation of thyroid cells, thereby leading to thyroid dysplasia. This study showed that TAF1 promoted Notch signaling and that this association played a pivotal role in thyroid development.NEW & NOTEWORTHY In our study, we obtained a novel zebrafish line with thyroid dysgenesis (TD) and identified the candidate pathogenetic mutation TATA-box binding protein associated Factor 1 (taf1). Further researches revealed that taf1 was required for thyroid follicular cells by binding to the NOTCH1 promoter region. Our findings revealed a novel role of TAF1 in thyroid morphogenesis.
Collapse
Affiliation(s)
- Caoxu Zhang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Liu Yang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Haiyang Zhang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Fengyao Wu
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Yue Zhang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Kaiwen Zhang
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Chenyang Wu
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Rui Li
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Mei Dong
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Shuangxia Zhao
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Huaidong Song
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| |
Collapse
|
|
3
|
Orlova SY, Ruzina MN, Emelianova OR, Sergeev AA, Chikurova EA, Orlov AM, Mugue NS. In Search of a Target Gene for a Desirable Phenotype in Aquaculture: Genome Editing of Cyprinidae and Salmonidae Species. Genes (Basel) 2024; 15:726. [PMID: 38927661 PMCID: PMC11202958 DOI: 10.3390/genes15060726] [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: 04/24/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Aquaculture supplies the world food market with a significant amount of valuable protein. Highly productive aquaculture fishes can be derived by utilizing genome-editing methods, and the main problem is to choose a target gene to obtain the desirable phenotype. This paper presents a review of the studies of genome editing for genes controlling body development, growth, pigmentation and sex determination in five key aquaculture Salmonidae and Cyprinidae species, such as rainbow trout (Onchorhynchus mykiss), Atlantic salmon (Salmo salar), common carp (Cyprinus carpio), goldfish (Carassius auratus), Gibel carp (Carassius gibelio) and the model fish zebrafish (Danio rerio). Among the genes studied, the most applicable for aquaculture are mstnba, pomc, and acvr2, the knockout of which leads to enhanced muscle growth; runx2b, mutants of which do not form bones in myoseptae; lepr, whose lack of function makes fish fast-growing; fads2, Δ6abc/5Mt, and Δ6bcMt, affecting the composition of fatty acids in fish meat; dnd mettl3, and wnt4a, mutants of which are sterile; and disease-susceptibility genes prmt7, gab3, gcJAM-A, and cxcr3.2. Schemes for obtaining common carp populations consisting of only large females are promising for use in aquaculture. The immobilized and uncolored zebrafish line is of interest for laboratory use.
Collapse
Affiliation(s)
- Svetlana Yu. Orlova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Maria N. Ruzina
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Olga R. Emelianova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Alexey A. Sergeev
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Evgeniya A. Chikurova
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
| | - Alexei M. Orlov
- Laboratory of Oceanic Ichthyofauna, Shirshov Institute of Oceanology, Russian Academy of Sciences, 117218 Moscow, Russia
- Laboratory of Behavior of Lower Vertebrates, Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia
- Department of Ichthyology, Dagestan State University, 367000 Makhachkala, Russia
| | - Nikolai S. Mugue
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, 105187 Moscow, Russia; (S.Y.O.)
- Laboratory of Genome Evolution and Speciation, Institute of Developmental Biology Russian Academy of Sciences, 117808 Moscow, Russia
| |
Collapse
|
|
4
|
Rath MF. Homeobox gene-encoded transcription factors in development and mature circadian function of the rodent pineal gland. J Pineal Res 2024; 76:e12950. [PMID: 38558122 DOI: 10.1111/jpi.12950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/15/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
Homeobox genes encode transcription factors that are widely known to control developmental processes. This is also the case in the pineal gland, a neuroendocrine brain structure devoted to nighttime synthesis of the hormone melatonin. Thus, in accordance with high prenatal gene expression, knockout studies have identified a specific set of homeobox genes that are essential for development of the pineal gland. However, as a special feature of the pineal gland, homeobox gene expression persists into adulthood, and gene product abundance exhibits 24 h circadian rhythms. Recent lines of evidence show that some homeobox genes even control expression of enzymes catalyzing melatonin synthesis. We here review current knowledge of homeobox genes in the rodent pineal gland and suggest a model for dual functions of homeobox gene-encoded transcription factors in developmental and circadian mature neuroendocrine function.
Collapse
Affiliation(s)
- Martin F Rath
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|