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Wu G, Tian N, She F, Cao A, Wu W, Zheng S, Yang N. Characteristics analysis of Early Responsive to Dehydration genes in Arabidopsis thaliana ( AtERD). PLANT SIGNALING & BEHAVIOR 2023; 18:2105021. [PMID: 35916255 PMCID: PMC10730211 DOI: 10.1080/15592324.2022.2105021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Early Responsive to Dehydration (ERD) genes are rapidly induced in response to various biotic and abiotic stresses, such as bacteria, drought, light, temperature and high salt in Arabidopsis thaliana. Sixteen ERD of Arabidopsis thaliana (AtERD) genes have been previously identified. The lengths of the coding region of the genes are 504-2838 bp. They encode 137-745 amino acids. In this study, the AtERD genes structure and promoter are analyzed through bioinformatics, and a overall function is summarized and a systematic signal pathway involving AtERD genes is mapped. AtERD9, AtERD11 and AtERD13 have the GST domain. AtERD10 and AtERD14 have the Dehyd domain. The promoters regions contain 32 light responsive elements, 23 ABA responsive elements, 5 drought responsive elements, 5 meristem expression related elements and 132 core promoter elements. The study provides a theoretical guidance for subsequent studies of AtERD genes.
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Affiliation(s)
- Guofan Wu
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Nongfu Tian
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Fawen She
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Aohua Cao
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Wangze Wu
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Sheng Zheng
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Ning Yang
- Laboratory of the Research for Molecular Mechanism and Functional Genes of Plant Stress Adaptation, College of Life Sciences, Northwest Normal University, Lanzhou, China
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2
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Zhu HY, Kang XJ, Jin L, Zhang PY, Wu H, Tan T, Yu Y, Fan Y. Histone demethylase KDM4A overexpression improved the efficiency of corrected human tripronuclear zygote development. Mol Hum Reprod 2021; 27:6143036. [PMID: 33599278 PMCID: PMC7939728 DOI: 10.1093/molehr/gaab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/03/2021] [Indexed: 01/22/2023] Open
Abstract
Human zygotes are difficult to obtain for research because of limited resources and ethical debates. Corrected human tripronuclear (ch3PN) zygotes obtained by removal of the extra pronucleus from abnormally fertilized tripronuclear (3PN) zygotes are considered an alternative resource for basic scientific research. In the present study, eight-cell and blastocyst formation efficiency were significantly lower in both 3PN and ch3PN embryos than in normal fertilized (2PN) embryos, while histone H3 lysine 9 trimethylation (H3K9me3) levels were much higher. It was speculated that the aberrant H3K9me3 level detected in ch3PN embryos may be related to low developmental competence. Microinjection of 1000 ng/µl lysine-specific demethylase 4A (KDM4A) mRNA effectively reduced the H3K9me3 level and significantly increased the developmental competence of ch3PN embryos. The quality of ch3PN zygotes improved as the grading criteria, cell number and pluripotent expression significantly increased in response to KDM4A mRNA injection. Developmental genes related to zygotic genome activation (ZGA) were also upregulated. These results indicate that KDM4A activates the transcription of the ZGA program by enhancing the expression of related genes, promoting epigenetic modifications and regulating the developmental potential of ch3PN embryos. The present study will facilitate future studies of ch3PN embryos and could provide additional options for infertile couples.
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Affiliation(s)
- Hai-Ying Zhu
- Department of Gynecology and Obstetrics, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, China
| | - Xiang-Jin Kang
- Department of Gynecology and Obstetrics, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, China
| | - Long Jin
- Department of Gynecology and Obstetrics, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, China
| | - Pu-Yao Zhang
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Han Wu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Tao Tan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Yang Yu
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Yong Fan
- Department of Gynecology and Obstetrics, Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, China
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3
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Sankar A, Lerdrup M, Manaf A, Johansen JV, Gonzalez JM, Borup R, Blanshard R, Klungland A, Hansen K, Andersen CY, Dahl JA, Helin K, Hoffmann ER. KDM4A regulates the maternal-to-zygotic transition by protecting broad H3K4me3 domains from H3K9me3 invasion in oocytes. Nat Cell Biol 2020; 22:380-388. [PMID: 32231309 PMCID: PMC7212036 DOI: 10.1038/s41556-020-0494-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 02/26/2020] [Indexed: 11/09/2022]
Abstract
The importance of germline-inherited post-translational histone modifications on priming early mammalian development is just emerging1-4. Histone H3 lysine 9 (H3K9) trimethylation is associated with heterochromatin and gene repression during cell-fate change5, whereas histone H3 lysine 4 (H3K4) trimethylation marks active gene promoters6. Mature oocytes are transcriptionally quiescent and possess remarkably broad domains of H3K4me3 (bdH3K4me3)1,2. It is unknown which factors contribute to the maintenance of the bdH3K4me3 landscape. Lysine-specific demethylase 4A (KDM4A) demethylates H3K9me3 at promoters marked by H3K4me3 in actively transcribing somatic cells7. Here, we report that KDM4A-mediated H3K9me3 demethylation at bdH3K4me3 in oocytes is crucial for normal pre-implantation development and zygotic genome activation after fertilization. The loss of KDM4A in oocytes causes aberrant H3K9me3 spreading over bdH3K4me3, resulting in insufficient transcriptional activation of genes, endogenous retroviral elements and chimeric transcripts initiated from long terminal repeats during zygotic genome activation. The catalytic activity of KDM4A is essential for normal epigenetic reprogramming and pre-implantation development. Hence, KDM4A plays a crucial role in preserving the maternal epigenome integrity required for proper zygotic genome activation and transfer of developmental control to the embryo.
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Affiliation(s)
- Aditya Sankar
- DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Biotech Research Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark.
| | - Mads Lerdrup
- DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adeel Manaf
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Norway
| | - Jens Vilstrup Johansen
- Biotech Research Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Javier Martin Gonzalez
- Transgenic Core Facility, Department of Experimental Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rehannah Borup
- DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robert Blanshard
- DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Klaus Hansen
- Biotech Research Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Yding Andersen
- Laboratory of Reproductive Biology, Section 5712, University Hospital of Copenhagen, Copenhagen, Denmark
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Norway.
| | - Kristian Helin
- Biotech Research Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark. .,Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Ogawa S, Yamada M, Nakamura A, Sugawara T, Nakamura A, Miyajima S, Harada Y, Ooka R, Okawa R, Miyauchi J, Tsumura H, Yoshimura Y, Miyado K, Akutsu H, Tanaka M, Umezawa A, Hamatani T. Zscan5b Deficiency Impairs DNA Damage Response and Causes Chromosomal Aberrations during Mitosis. Stem Cell Reports 2019; 12:1366-1379. [PMID: 31155506 PMCID: PMC6565874 DOI: 10.1016/j.stemcr.2019.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 01/01/2023] Open
Abstract
Zygotic genome activation (ZGA) begins after fertilization and is essential for establishing pluripotency and genome stability. However, it is unclear how ZGA genes prevent mitotic errors. Here we show that knockout of the ZGA gene Zscan5b, which encodes a SCAN domain with C2H2 zinc fingers, causes a high incidence of chromosomal abnormalities in embryonic stem cells (ESCs), and leads to the development of early-stage cancers. After irradiation, Zscan5b-deficient ESCs displayed significantly increased levels of γ-H2AX despite increased expression of the DNA repair genes Rad51l3 and Bard. Re-expression of Zscan5b reduced γ-H2AX content, implying a role for Zscan5b in DNA damage repair processes. A co-immunoprecipitation analysis showed that Zscan5b bound to the linker histone H1, suggesting that Zscan5b may protect chromosomal architecture. Our report demonstrates that the ZGA gene Zscan5b is involved in genomic integrity and acts to promote DNA damage repair and regulate chromatin dynamics during mitosis. Deficiency of zygotic genome activation gene Zscan5b causes chromosomal anomalies Zscan5b binds to linker histone H1 and protects chromosomal structure Irradiated Zscan5b-deficient ESCs show significantly increased DNA stress markers Zscan5b-deficient ESCs develop small choriocarcinomas and embryonal carcinomas
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Affiliation(s)
- Seiji Ogawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo 160-8582, Japan; Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Mitsutoshi Yamada
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Akihiro Nakamura
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Tohru Sugawara
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Akari Nakamura
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Shoko Miyajima
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Yuichirou Harada
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Reina Ooka
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo 160-8582, Japan
| | - Ryuichiro Okawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo 160-8582, Japan
| | - Jun Miyauchi
- Department of Central Laboratory, Saitama Municipal Hospital, 2460 Midori-ku, Saitama, Saitama-ken 336-8522, Japan
| | - Hideki Tsumura
- Division of Laboratory Animal Resources, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Yasunori Yoshimura
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kenji Miyado
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Hidenori Akutsu
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Mamoru Tanaka
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo 160-8582, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Toshio Hamatani
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo 160-8582, Japan.
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5
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de Carvalho-Siqueira GQ, Ananina G, de Souza BB, Borges MG, Ito MT, da Silva-Costa SM, de Farias Domingos I, Falcão DA, Lopes-Cendes I, Bezerra MAC, da Silva Araújo A, Lucena-Araújo AR, de Souza Gonçalves M, Saad STO, Costa FF, de Melo MB. Whole-exome sequencing indicates FLG2 variant associated with leg ulcers in Brazilian sickle cell anemia patients. Exp Biol Med (Maywood) 2019; 244:932-939. [PMID: 31079484 DOI: 10.1177/1535370219849592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although sickle cell anemia results from homozygosity for a single mutation at position 7 of the β-globin chain, the clinical aspects of this condition are very heterogeneous. Complications include leg ulcers, which have a negative impact on patients’ quality of life and are related to the severity of the disease. Nevertheless, the complex pathogenesis of this complication has yet to be elucidated. To identify novel genes associated with leg ulcers in sickle cell anemia, we performed whole-exome sequencing of extreme phenotypes in a sample of Brazilian sickle cell anemia patients and validated our findings in another sample. Our discovery cohort consisted of 40 unrelated sickle cell anemia patients selected based on extreme phenotypes: 20 patients without leg ulcers, aged from 40 to 61 years, and 20 with chronic leg ulcers. DNA was extracted from peripheral blood leukocytes and used for whole-exome sequencing. After the bioinformatics analysis, eight variants were selected for validation by Sanger sequencing and TaqMan® genotyping in 293 sickle cell anemia patients (153 without leg ulcers) from two different locations in Brazil. After the validation, Fisher’s exact test revealed a statistically significant difference in a stop codon variant (rs12568784 G/T) in the FLG2 gene between the GT and GG genotypes ( P = 0.035). We highlight the importance of rs12568784 in leg ulcer development as this variant of the FLG2 gene results in impairment of the skin barrier, predisposing the individual to inflammation and infection. Additionally, we suggest that the remaining seven variants and the genes in which they occur could be strong candidates for leg ulcers in sickle cell anemia. Impact statement To our knowledge, the present study is the first to use whole-exome sequencing based on extreme phenotypes to identify new candidate genes associated with leg ulcers in sickle cell anemia patients. There are few studies about this complication; the pathogenesis remains complex and has yet to be fully elucidated. We identified interesting associations in genes never related with this complication to our knowledge, especially the variant in the FLG2 gene. The knowledge of variants related with leg ulcer in sickle cell anemia may lead to a better comprehension of the disease’s etiology, allowing prevention and early treatment options in risk genotypes while improving quality of life for these patients.
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Affiliation(s)
| | - Galina Ananina
- 1 Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Campinas, SP 13083-875, Brazil
| | - Bruno Batista de Souza
- 1 Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Campinas, SP 13083-875, Brazil
| | - Murilo Guimarães Borges
- 2 Department of Medical Genetics and Genome Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, SP 13083-887, Brazil
| | - Mirta Tomie Ito
- 1 Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Campinas, SP 13083-875, Brazil
| | - Sueli Matilde da Silva-Costa
- 1 Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Campinas, SP 13083-875, Brazil
| | - Igor de Farias Domingos
- 3 Genetics Postgraduate Program, Federal University of Pernambuco, Recife, PE 50670-901, Brazil
| | - Diego Arruda Falcão
- 3 Genetics Postgraduate Program, Federal University of Pernambuco, Recife, PE 50670-901, Brazil
| | - Iscia Lopes-Cendes
- 2 Department of Medical Genetics and Genome Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, SP 13083-887, Brazil
| | | | | | | | | | | | | | - Mônica Barbosa de Melo
- 1 Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Campinas, SP 13083-875, Brazil
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6
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Suzuki S, Minami N. CHD1 Controls Cell Lineage Specification Through Zygotic Genome Activation. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2018; 229:15-30. [PMID: 29177762 DOI: 10.1007/978-3-319-63187-5_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In mammals, the processes spanning from fertilization to the generation of a new organism are very complex and are controlled by multiple genes. Life begins with the encounter of eggs and spermatozoa, in which gene expression is inactive prior to fertilization. After several cell divisions, cells arise that are specialized in implantation, a developmental process unique to mammals. Cells involved in the establishment and maintenance of implantation differentiate from totipotent embryos, and the remaining cells generate the embryo proper. Although this process of differentiation, termed cell lineage specification, is supported by various gene expression networks, many components have yet to be identified. Moreover, despite extensive research it remains unclear which genes are controlled by each of the factors involved. Although it has become clear that epigenetic factors regulate gene expression, elucidation of the underlying mechanisms remains challenging. In this chapter, we propose that the chromatin remodeling factor CHD1, together with epigenetic factors, is involved in a subset of gene expression networks involved in processes spanning from zygotic genome activation to cell lineage specification.
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Affiliation(s)
- Shinnosuke Suzuki
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8052, Japan.
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7
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Wang Y, Ding X, Tan Z, Ning C, Xing K, Yang T, Pan Y, Sun D, Wang C. Genome-Wide Association Study of Piglet Uniformity and Farrowing Interval. Front Genet 2017; 8:194. [PMID: 29234349 PMCID: PMC5712316 DOI: 10.3389/fgene.2017.00194] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 11/15/2017] [Indexed: 02/04/2023] Open
Abstract
Piglet uniformity (PU) and farrowing interval (FI) are important reproductive traits related to production and economic profits in the pig industry. However, the genetic architecture of the longitudinal trends of reproductive traits still remains elusive. Herein, we performed a genome-wide association study (GWAS) to detect potential genetic variation and candidate genes underlying the phenotypic records at different parities for PU and FI in a population of 884 Large White pigs. In total, 12 significant SNPs were detected on SSC1, 3, 4, 9, and 14, which collectively explained 1–1.79% of the phenotypic variance for PU from parity 1 to 4, and 2.58–4.11% for FI at different stages. Of these, seven SNPs were located within 16 QTL regions related to swine reproductive traits. One QTL region was associated with birth body weight (related to PU) and contained the peak SNP MARC0040730, and another was associated with plasma FSH concentration (related to FI) and contained the SNP MARC0031325. Finally, some positional candidate genes for PU and FI were identified because of their roles in prenatal skeletal muscle development, fetal energy substrate, pre-implantation, and the expression of mammary gland epithelium. Identification of novel variants and candidate genes will greatly advance our understanding of the genetic mechanisms of PU and FI, and suggest a specific opportunity for improving marker assisted selection or genomic selection in pigs.
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Affiliation(s)
- Yuan Wang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhen Tan
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Xing
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ting Yang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yongjie Pan
- Beijing Shunxin Agriculture Co., Ltd., Beijing, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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8
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Chung YG, Matoba S, Liu Y, Eum JH, Lu F, Jiang W, Lee JE, Sepilian V, Cha KY, Lee DR, Zhang Y. Histone Demethylase Expression Enhances Human Somatic Cell Nuclear Transfer Efficiency and Promotes Derivation of Pluripotent Stem Cells. Cell Stem Cell 2015; 17:758-766. [DOI: 10.1016/j.stem.2015.10.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/04/2015] [Accepted: 10/03/2015] [Indexed: 01/02/2023]
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9
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Suzuki S, Nozawa Y, Tsukamoto S, Kaneko T, Manabe I, Imai H, Minami N. CHD1 acts via the Hmgpi pathway to regulate mouse early embryogenesis. Development 2015; 142:2375-84. [PMID: 26092847 DOI: 10.1242/dev.120493] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 05/14/2015] [Indexed: 11/20/2022]
Abstract
The protein CHD1 is a member of the family of ATPase-dependent chromatin remodeling factors. CHD1, which recognizes trimethylated histone H3 lysine 4, has been implicated in transcriptional activation in organisms ranging from yeast to humans. It is required for pre-mRNA maturation, maintenance of mouse embryonic stem cell pluripotency and rapid growth of the mouse epiblast. However, the function(s) of CHD1 in mouse preimplantation embryos has not yet been examined. Here, we show that loss of CHD1 function led to embryonic lethality after implantation. In mouse embryos in which Chd1 was targeted by siRNA microinjection, the expression of the key regulators of cell fate specification Pou5f1 (also known as Oct4), Nanog and Cdx2 was dramatically decreased, starting at mid-preimplantation gene activation (MGA). Moreover, expression of Hmgpi and Klf5, which regulate Pou5f1, Nanog and Cdx2, was also significantly suppressed at zygotic gene activation (ZGA). Suppression of Hmgpi expression in Chd1-knockdown embryos continued until the blastocyst stage, whereas suppression of Klf5 expression was relieved by the morula stage. Next, we rescued HMGPI expression via Hmgpi mRNA microinjection in Chd1-knockdown embryos. Consequently, Pou5f1, Nanog and Cdx2 expression was restored at MGA and live offspring were recovered. These findings indicate that CHD1 plays important roles in mouse early embryogenesis via activation of Hmgpi at ZGA.
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Affiliation(s)
- Shinnosuke Suzuki
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nozawa
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Satoshi Tsukamoto
- Laboratory of Animal and Genome Sciences Section, National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Takehito Kaneko
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Ichiro Manabe
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hiroshi Imai
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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10
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Suzuki S, Nozawa Y, Tsukamoto S, Kaneko T, Imai H, Minami N. Histone methyltransferase Smyd3 regulates early embryonic lineage commitment in mice. Reproduction 2015; 150:21-30. [PMID: 25918436 DOI: 10.1530/rep-15-0019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/24/2015] [Indexed: 01/21/2023]
Abstract
SET and MYND domain-containing protein 3 (Smyd3) is a histone H3 lysine 4 (H3K4) di- and tri-methyltransferase that forms a transcriptional complex with RNA polymerase II and activates the transcription of oncogenes and cell cycle genes in human cancer cells. However, the study of Smyd3 in mammalian early embryonic development has not yet been addressed. In the present study, we investigated the expression pattern of Smyd3 in mouse preimplantation embryos and the effects of RNA interference (RNAi)-mediated Smyd3 repression on the development of mouse embryos. We showed that Smyd3 mRNA levels increased after the two-cell stage, peaked at the four-cell stage, and gradually decreased thereafter. Moreover, in two-cell to eight-cell embryos, SMYD3 staining was more intense in the nuclei than it was in the cytoplasm. In Smyd3-knockdown embryos, the percentage of inner cell mass (ICM)-derived colony formation and trophectoderm (TE)-derived cell attachment were significantly decreased, which resulted in a reduction in the number of viable offspring. Furthermore, the expression of Oct4 and Cdx2 during mid-preimplantation gene activation was significantly decreased in Smyd3-knockdown embryos. In addition, the transcription levels of ICM and epiblast markers, such as Oct4, Nanog, and Sox2, the transcription levels of primitive endoderm markers, such as Gata6, and the transcription levels of TE markers, such as Cdx2 and Eomes, were significantly decreased in Smyd3-knockdown blastocysts. These findings indicate that SMYD3 plays an important role in early embryonic lineage commitment and peri-implantation development through the activation of lineage-specific genes.
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Affiliation(s)
- Shinnosuke Suzuki
- Laboratory of Reproductive BiologyGraduate School of Agriculture, Kyoto University, Kyoto 606-8052, JapanLaboratory of Animal and Genome Sciences SectionNational Institute of Radiological Sciences, Chiba 263-8555, JapanGraduate School of MedicineInstitute of Laboratory Animals, Kyoto University, Kyoto 606-8501, Japan
| | - Yusuke Nozawa
- Laboratory of Reproductive BiologyGraduate School of Agriculture, Kyoto University, Kyoto 606-8052, JapanLaboratory of Animal and Genome Sciences SectionNational Institute of Radiological Sciences, Chiba 263-8555, JapanGraduate School of MedicineInstitute of Laboratory Animals, Kyoto University, Kyoto 606-8501, Japan
| | - Satoshi Tsukamoto
- Laboratory of Reproductive BiologyGraduate School of Agriculture, Kyoto University, Kyoto 606-8052, JapanLaboratory of Animal and Genome Sciences SectionNational Institute of Radiological Sciences, Chiba 263-8555, JapanGraduate School of MedicineInstitute of Laboratory Animals, Kyoto University, Kyoto 606-8501, Japan
| | - Takehito Kaneko
- Laboratory of Reproductive BiologyGraduate School of Agriculture, Kyoto University, Kyoto 606-8052, JapanLaboratory of Animal and Genome Sciences SectionNational Institute of Radiological Sciences, Chiba 263-8555, JapanGraduate School of MedicineInstitute of Laboratory Animals, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroshi Imai
- Laboratory of Reproductive BiologyGraduate School of Agriculture, Kyoto University, Kyoto 606-8052, JapanLaboratory of Animal and Genome Sciences SectionNational Institute of Radiological Sciences, Chiba 263-8555, JapanGraduate School of MedicineInstitute of Laboratory Animals, Kyoto University, Kyoto 606-8501, Japan
| | - Naojiro Minami
- Laboratory of Reproductive BiologyGraduate School of Agriculture, Kyoto University, Kyoto 606-8052, JapanLaboratory of Animal and Genome Sciences SectionNational Institute of Radiological Sciences, Chiba 263-8555, JapanGraduate School of MedicineInstitute of Laboratory Animals, Kyoto University, Kyoto 606-8501, Japan
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Fine mapping of genome activation in bovine embryos by RNA sequencing. Proc Natl Acad Sci U S A 2014; 111:4139-44. [PMID: 24591639 DOI: 10.1073/pnas.1321569111] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During maternal-to-embryonic transition control of embryonic development gradually switches from maternal RNAs and proteins stored in the oocyte to gene products generated after embryonic genome activation (EGA). Detailed insight into the onset of embryonic transcription is obscured by the presence of maternal transcripts. Using the bovine model system, we established by RNA sequencing a comprehensive catalogue of transcripts in germinal vesicle and metaphase II oocytes, and in embryos at the four-cell, eight-cell, 16-cell, and blastocyst stages. These were produced by in vitro fertilization of Bos taurus taurus oocytes with sperm from a Bos taurus indicus bull to facilitate parent-specific transcriptome analysis. Transcripts from 12.4 to 13.7 × 10(3) different genes were detected in the various developmental stages. EGA was analyzed by (i) detection of embryonic transcripts, which are not present in oocytes; (ii) detection of transcripts from the paternal allele; and (iii) detection of primary transcripts with intronic sequences. These strategies revealed (i) 220, (ii) 937, and (iii) 6,848 genes to be activated from the four-cell to the blastocyst stage. The largest proportion of gene activation [i.e., (i) 59%, (ii) 42%, and (iii) 58%] was found in eight-cell embryos, indicating major EGA at this stage. Gene ontology analysis of genes activated at the four-cell stage identified categories related to RNA processing, translation, and transport, consistent with preparation for major EGA. Our study provides the largest transcriptome data set of bovine oocyte maturation and early embryonic development and detailed insight into the timing of embryonic activation of specific genes.
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Wang L, Cao J, Ji P, Zhang D, Ma L, Dym M, Yu Z, Feng L. Oocyte-like cells induced from mouse spermatogonial stem cells. Cell Biosci 2012; 2:27. [PMID: 22863141 PMCID: PMC3505744 DOI: 10.1186/2045-3701-2-27] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 07/16/2012] [Indexed: 02/07/2023] Open
Abstract
Background During normal development primordial germ cells (PGCs) derived from the epiblast are the precursors of spermatogonia and oogonia. In culture, PGCs can be induced to dedifferentiate to pluripotent embryonic germ (EG) cells in the presence of various growth factors. Several recent studies have now demonstrated that spermatogonial stem cells (SSCs) can also revert back to pluripotency as embryonic stem (ES)-like cells under certain culture conditions. However, the potential dedifferentiation of SSCs into PGCs or the potential generation of oocytes from SSCs has not been demonstrated before. Results We report that mouse male SSCs can be converted into oocyte-like cells in culture. These SSCs-derived oocytes (SSC-Oocs) were similar in size to normal mouse mature oocytes. They expressed oocyte-specific markers and gave rise to embryos through parthenogenesis. Interestingly, the Y- and X-linked testis-specific genes in these SSC-Oocs were significantly down-regulated or turned off, while oocyte-specific X-linked genes were activated. The gene expression profile appeared to switch to that of the oocyte across the X chromosome. Furthermore, these oocyte-like cells lost paternal imprinting but acquired maternal imprinting. Conclusions Our data demonstrate that SSCs might maintain the potential to be reprogrammed into oocytes with corresponding epigenetic reversals. This study provides not only further evidence for the remarkable plasticity of SSCs but also a potential system for dissecting molecular and epigenetic regulations in germ cell fate determination and imprinting establishment during gametogenesis.
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Affiliation(s)
- Lu Wang
- Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 Chongqing S, Road, Shanghai, 200025, China.
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Nishi M, Akutsu H, Masui S, Kondo A, Nagashima Y, Kimura H, Perrem K, Shigeri Y, Toyoda M, Okayama A, Hirano H, Umezawa A, Yamamoto N, Lee SW, Ryo A. A distinct role for Pin1 in the induction and maintenance of pluripotency. J Biol Chem 2011; 286:11593-603. [PMID: 21296877 DOI: 10.1074/jbc.m110.187989] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The prominent characteristics of pluripotent stem cells are their unique capacity to self-renew and pluripotency. Although pluripotent stem cell proliferation is maintained by specific intracellular phosphorylation signaling events, it has not been well characterized how the resulting phosphorylated proteins are subsequently regulated. We here report that the peptidylprolyl isomerase Pin1 is indispensable for the self-renewal and maintenance of pluripotent stem cells via the regulation of phosphorylated Oct4 and other substrates. Pin1 expression was found to be up-regulated upon the induction of induced pluripotent stem (iPS) cells, and the forced expression of Pin1 with defined reprogramming factors was observed to further enhance the frequency of iPS cell generation. The inhibition of Pin1 activity significantly suppressed colony formation and induced the aberrant differentiation of human iPS cells as well as murine ES cells. We further found that Pin1 interacts with the phosphorylated Ser(12)-Pro motif of Oct4 and that this in turn facilitates the stability and transcriptional activity functions of Oct4. Our current findings thus uncover an atypical role for Pin1 as a putative regulator of the induction and maintenance of pluripotency via the control of phosphorylation signaling. These data suggest that the manipulation of Pin1 function could be a potential strategy for the stable induction and proliferation of human iPS cells.
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Affiliation(s)
- Mayuko Nishi
- Department of Microbiology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Japan
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