51
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Fang Y, Xia W, Cai W, Zhang X, Zhang J, Fu X, Li S, Fang X, Sun S, Wang Z, Zhang X, Zhu S, Li J. Effects of TLR4 overexpression on sperm quality, seminal plasma biomarkers, sperm DNA methylation and pregnancy rate in sheep. Theriogenology 2019; 142:368-375. [PMID: 31711688 DOI: 10.1016/j.theriogenology.2019.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/04/2019] [Accepted: 10/09/2019] [Indexed: 11/28/2022]
Abstract
Genetic modification provides a means to enhancing disease resistance in animals. In this study, the first generation of genetically modified (GM) sheep overexpressing TLR4 was produced by microinjection for better disease resistance. To compare semen characteristics including sperm quality, seminal plasma biochemical index, sperm DNA methylation and pregnancy rate of three-year old transgenic sheep with TLR4 overexpressed (toll like receptor 4, TLR4) and non-transgenic ram. Sixteen transgenic ram of F0 generation were produced by microinjection of the TLR4 plasmid into the pronucleus of fertilized ova. Seven transgenic sheep of F1 generation was produced by breeding F0 transgenic founders with non-transgenic sheep of the same breed. There were no significant differences between transgenic and control rams for all semen quality parameters, including semen volume, sperm concentration, sperm viability, and percentages of sperm with an intact plasma membrane, acrosomal integrity, and viable sperm with high mitochondrial membrane potential in both F0 and F1 generation. Furthermore, no significant differences were found for seminal plasma concentrations of zinc, neutral alpha-glucosidase, acid phosphatase or fructose, nor for levels of H19 and IGF2R methylation in sperm DNA. In addition, pregnancy rate was also similar between these two groups. In conclusion, there was no evidence that TLR4 overexpression altered the sperm quality, seminal plasma or sperm DNA of transgenic sheep.
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Affiliation(s)
- Yi Fang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130062, China
| | - Wei Xia
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Wentao Cai
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xiaosheng Zhang
- Animal Husbandry and Veterinary Research Institute of Tianjin, Tianjin, China
| | - Jinlong Zhang
- Animal Husbandry and Veterinary Research Institute of Tianjin, Tianjin, China
| | - Xiangwei Fu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Sa Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xiaohuan Fang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Shuchun Sun
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China; Research Center of Cattle and Sheep Embryo Engineering Technique of Hebei Province, Baoding, China
| | - Zhigang Wang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China; Research Center of Cattle and Sheep Embryo Engineering Technique of Hebei Province, Baoding, China
| | - Xiaolei Zhang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, China
| | - Shien Zhu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Junjie Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China; Research Center of Cattle and Sheep Embryo Engineering Technique of Hebei Province, Baoding, China.
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52
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Edgar JA. L-ascorbic acid and the evolution of multicellular eukaryotes. J Theor Biol 2019; 476:62-73. [DOI: 10.1016/j.jtbi.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/10/2019] [Accepted: 06/02/2019] [Indexed: 12/26/2022]
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Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation. Dev Cell 2019; 51:21-34.e5. [PMID: 31474564 DOI: 10.1016/j.devcel.2019.07.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/28/2019] [Accepted: 07/24/2019] [Indexed: 02/03/2023]
Abstract
Facultative heterochromatin forms and reorganizes in response to external stimuli. However, how the initial establishment of such a chromatin state is regulated in cell-cycle-arrested cells remains unexplored. Mouse gonocytes are arrested male germ cells, at which stage the genome-wide DNA methylome forms. Here, we discovered transiently accessible heterochromatin domains of several megabases in size in gonocytes and named them differentially accessible domains (DADs). Open DADs formed in gene desert and gene cluster regions, primarily at transposons, with the reprogramming of histone marks, suggesting DADs as facultative heterochromatin. De novo DNA methylation took place with two waves in gonocytes: the first region specific and the second genome-wide. DADs were resistant to the first wave and their opening preceded the second wave. In addition, the higher-order chromosome architecture was reorganized with less defined chromosome compartments in gonocytes. These findings suggest that multiple layers of chromatin reprogramming facilitate de novo DNA methylation.
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54
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Aging of spermatogonial stem cells by Jnk-mediated glycolysis activation. Proc Natl Acad Sci U S A 2019; 116:16404-16409. [PMID: 31358627 DOI: 10.1073/pnas.1904980116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Because spermatogonial stem cells (SSCs) are immortal by serial transplantation, SSC aging in intact testes is considered to be caused by a deteriorated microenvironment. Here, we report a cell-intrinsic mode of SSC aging by glycolysis activation. Using cultured SSCs, we found that aged SSCs proliferated more actively than young SSCs and showed enhanced glycolytic activity. Moreover, they remained euploid and exhibited stable androgenetic imprinting patterns with robust SSC activity despite having shortened telomeres. Aged SSCs showed increased Wnt7b expression, which was associated with decreased Polycomb complex 2 activity. Our results suggest that aberrant Wnt7b expression activated c-jun N-terminal kinase (JNK), which down-regulated mitochondria numbers by suppressing Ppargc1a Down-regulation of Ppargc1a probably decreased reactive oxygen species and enhanced glycolysis. Analyses of the Klotho-deficient aging mouse model and 2-y-old aged rats confirmed JNK hyperactivation and increased glycolysis. Therefore, not only microenvironment but also intrinsic activation of JNK-mediated glycolysis contributes to SSC aging.
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55
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Maezawa S, Yukawa M, Alavattam KG, Barski A, Namekawa SH. Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis. Nucleic Acids Res 2019; 46:593-608. [PMID: 29126117 PMCID: PMC5778473 DOI: 10.1093/nar/gkx1052] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022] Open
Abstract
During spermatogenesis, germ cells undergo massive cellular reconstruction and dynamic chromatin remodeling to facilitate highly diverse transcriptomes, which are required for the production of functional sperm. However, it remains unknown how germline chromatin is organized to promote the dynamic, complex transcriptomes of spermatogenesis. Here, using ATAC-seq, we establish the varied landscape of open chromatin during spermatogenesis. We identify the reorganization of accessible chromatin in intergenic and intronic regions during the mitosis-to-meiosis transition. During the transition, mitotic-type open chromatin is closed while the de novo formation of meiotic-type open chromatin takes place. Contrastingly, differentiation processes such as spermatogonial differentiation and the meiosis-to-postmeiosis transition involve chromatin closure without the de novo formation of accessible chromatin. In spermiogenesis, the germline-specific Polycomb protein SCML2 promotes the closure of open chromatin at autosomes for gene suppression. Paradoxically, we identify the massive de novo formation of accessible chromatin when the sex chromosomes undergo meiotic sex chromosome inactivation, and this is also mediated by SCML2. These results reveal meiotic sex chromosome inactivation as an active process for chromatin organization. Together, our results unravel the genome-wide, dynamic reorganization of open chromatin and reveal mechanisms that underlie diverse transcriptomes during spermatogenesis.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Masashi Yukawa
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
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56
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Oblette A, Rondeaux J, Dumont L, Delessard M, Saulnier J, Rives A, Rives N, Rondanino C. DNA methylation and histone post-translational modifications in the mouse germline following in-vitro maturation of fresh or cryopreserved prepubertal testicular tissue. Reprod Biomed Online 2019; 39:383-401. [PMID: 31315814 DOI: 10.1016/j.rbmo.2019.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/22/2019] [Accepted: 05/09/2019] [Indexed: 02/07/2023]
Abstract
RESEARCH QUESTION Do cryopreservation and in-vitro culture procedures affect the expression of DNA methyltransferases (DNMT) and histone-modifying enzymes, as well as the establishment of DNA methylation and histone post-translational modifications (PTM) in germ cells in prepubertal mouse testicular tissue? DESIGN This study investigated the expression of epigenetic modification enzymes, DNA methylation and histone PTM, and the spermatogenic progression after in-vitro maturation of fresh or cryopreserved mouse prepubertal testicular tissue. Fresh or cryopreserved testicular fragments from 6-7 days post-partum mice were cultured for 30 days in the presence of retinol with or without FSH. RESULTS The in-vitro maturation of fresh or cryopreserved tissue allowed the differentiation of spermatogonia into spermatozoa. Differences in the levels of transcripts encoding epigenetic modification enzymes (Dnmt1, Dnmt3a, Jarid1b, Src1, Sirt1, Hdac1) were found between 30-day tissue cultures and age-matched in-vivo controls. DNMT1/DNMT3a expression and the presence of 5-methylcytosine (5mC) were detected in spermatogonia and leptotene/zygotene spermatocytes in cultures. The relative 5mC fluorescence intensity was similar in spermatozoa produced in cultures of cryopreserved tissues or in vivo. H3K4me3, H3K9ac and H4K8ac were present in all germ cell types but differences in the proportion of germ cells containing these epigenetic marks were found after cultures. CONCLUSIONS Despite differences with the in-vivo situation, DNA methylation and histone methylation and acetylation occur in the mouse germline in in-vitro matured fresh or cryopreserved mouse prepubertal testicular tissue, and the expression of the enzymes catalysing these epigenetic modifications are maintained in vitro.
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Affiliation(s)
- Antoine Oblette
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Julie Rondeaux
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Ludovic Dumont
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Marion Delessard
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Justine Saulnier
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Aurélie Rives
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Nathalie Rives
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France
| | - Christine Rondanino
- Normandie University, UNIROUEN, EA 4308 'Gametogenesis and Gamete Quality', Rouen University Hospital, Department of Reproductive Biology-CECOS, Rouen F 76000, France.
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Fang L, Zhou Y, Liu S, Jiang J, Bickhart DM, Null DJ, Li B, Schroeder SG, Rosen BD, Cole JB, Van Tassell CP, Ma L, Liu GE. Integrating Signals from Sperm Methylome Analysis and Genome-Wide Association Study for a Better Understanding of Male Fertility in Cattle. EPIGENOMES 2019; 3:epigenomes3020010. [PMID: 34968233 PMCID: PMC8594688 DOI: 10.3390/epigenomes3020010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/03/2019] [Accepted: 05/11/2019] [Indexed: 01/18/2023] Open
Abstract
Decreased male fertility is a big concern in both human society and the livestock industry. Sperm DNA methylation is commonly believed to be associated with male fertility. However, due to the lack of accurate male fertility records (i.e., limited mating times), few studies have investigated the comprehensive impacts of sperm DNA methylation on male fertility in mammals. In this study, we generated 10 sperm DNA methylomes and performed a preliminary correlation analysis between signals from sperm DNA methylation and signals from large-scale (n = 27,214) genome-wide association studies (GWAS) of 35 complex traits (including 12 male fertility-related traits). We detected genomic regions, which experienced DNA methylation alterations in sperm and were associated with aging and extreme fertility phenotypes (e.g., sire-conception rate or SCR). In dynamic hypomethylated regions (HMRs) and partially methylated domains (PMDs), we found genes (e.g., HOX gene clusters and microRNAs) that were involved in the embryonic development. We demonstrated that genomic regions, which gained rather than lost methylations during aging, and in animals with low SCR were significantly and selectively enriched for GWAS signals of male fertility traits. Our study discovered 16 genes as the potential candidate markers for male fertility, including SAMD5 and PDE5A. Collectively, this initial effort supported a hypothesis that sperm DNA methylation may contribute to male fertility in cattle and revealed the usefulness of functional annotations in enhancing biological interpretation and genomic prediction for complex traits and diseases.
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Affiliation(s)
- Lingzhao Fang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Derek M. Bickhart
- Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53718, USA
| | - Daniel J. Null
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Bingjie Li
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
- Correspondence: (L.M.); (G.E.L.); Tel.: +1-301-405-1389 (L.M.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (G.E.L.)
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Correspondence: (L.M.); (G.E.L.); Tel.: +1-301-405-1389 (L.M.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (G.E.L.)
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Abstract
Germ cells undergo epigenome reprogramming for proper development of the next generation. The achievement of in vitro germ cell derivation from human and mouse pluripotent stem cells and further differentiation in a plane culture and in aggregation with gonadal somatic cells offers unprecedented opportunities for investigation of the germ cell development. Moreover, advances in low-input/single-cell genomics have enabled detailed investigation of epigenome dynamics during germ cell development. These technologies have advanced our knowledge of epigenome reprogramming during the specification and development of primordial germ cells, their sex differentiation, and gametogenesis. Key findings include details of chromatin remodeling and transcriptional regulation, progressive and comprehensive DNA demethylation, and tight links between DNA demethylation and histone marks during the development of primordial germ cells, acquisition of unique totipotent epigenome during oogenesis (e.g., broad H3K4me3 domains and low-level three-dimensional genomic organization), and unexpected organization of the sperm genome. Moreover, these studies suggest the importance of epigenome analyses for in-depth evaluations of in vitro gametogenesis.
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Affiliation(s)
- Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan.
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan; Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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59
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Research update and opportunity of non-hormonal male contraception: Histone demethylase KDM5B-based targeting. Pharmacol Res 2019; 141:1-20. [DOI: 10.1016/j.phrs.2018.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/29/2018] [Accepted: 12/09/2018] [Indexed: 12/28/2022]
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60
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Kawabata Y, Kamio A, Jincho Y, Sakashita A, Takashima T, Kobayashi H, Matsui Y, Kono T. Sex-specific histone modifications in mouse fetal and neonatal germ cells. Epigenomics 2019; 11:543-561. [PMID: 30667280 DOI: 10.2217/epi-2018-0193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIMS Epigenetic signatures of germline cells are dynamically reprogrammed to induce appropriate differentiation, development and sex specification. We investigated sex-specific epigenetic changes in mouse fetal germ cells (FGCs) and neonatal germ cells. MATERIALS & METHODS Six histone marks in mouse E13.5 FGCs and P1 neonatal germ cells were analyzed by chromatin immunoprecipitation and sequencing. These datasets were compared with transposase-accessible chromatin sites, DNA methylation and transcriptome. RESULTS Different patterns of each histone mark were detected in female and male FGCs, and H3K4me3/H3K27me3 bivalent marks were enriched in different chromosomal regions of female and male FGCs. CONCLUSION Our results suggest that histone modifications may affect FGC gene expression following DNA methylation erasure, contributing to the differentiation into female and male germ cells.
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Affiliation(s)
- Yukiko Kawabata
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Asuka Kamio
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan.,NODAI Genome Research Centre, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Yuko Jincho
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Akihiko Sakashita
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Tomoya Takashima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Centre, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Yasuhisa Matsui
- Cell Resource Centre for Biomedical Research, Institute of Development, Aging & Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
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Miki Y, Tsukamoto S, Minami N. How does the promoter of an oocyte-specific gene function in male germ cells? J Reprod Dev 2018; 64:463-468. [PMID: 30197401 PMCID: PMC6305850 DOI: 10.1262/jrd.2018-060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studying gene expression in germ cells is useful for elucidating mechanisms of transcriptional regulation, because different genes are activated in male and female germ cells. The promoter regions of an oocyte-specific gene, Oog1, have been characterized. Driving the expression of green fluorescent protein with these different promoter regions provided us with critical information on the regulation of gene expression. The 3.9 kb long promoter functions in both male and female germ cells in transgenic mice. What is the cause of this sexually dimorphic expression? There may be important factors within and perhaps also outside this 3.9 kb promoter region that are required to maintain proper sex-specific gene expression.
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Affiliation(s)
- Yuka Miki
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Satoshi Tsukamoto
- Laboratory Animal and Genome Sciences Section, National Institute for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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62
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Epigenetic Erosion in Adult Stem Cells: Drivers and Passengers of Aging. Cells 2018; 7:cells7120237. [PMID: 30501028 PMCID: PMC6316114 DOI: 10.3390/cells7120237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 02/06/2023] Open
Abstract
In complex organisms, stem cells are key for tissue maintenance and regeneration. Adult stem cells replenish continuously dividing tissues of the epithelial and connective types, whereas in non-growing muscle and nervous tissues, they are mainly activated upon injury or stress. In addition to replacing deteriorated cells, adult stem cells have to prevent their exhaustion by self-renewal. There is mounting evidence that both differentiation and self-renewal are impaired upon aging, leading to tissue degeneration and functional decline. Understanding the molecular pathways that become deregulate in old stem cells is crucial to counteract aging-associated tissue impairment. In this review, we focus on the epigenetic mechanisms governing the transition between quiescent and active states, as well as the decision between self-renewal and differentiation in three different stem cell types, i.e., spermatogonial stem cells, hematopoietic stem cells, and muscle stem cells. We discuss the epigenetic events that channel stem cell fate decisions, how this epigenetic regulation is altered with age, and how this can lead to tissue dysfunction and disease. Finally, we provide short prospects of strategies to preserve stem cell function and thus promote healthy aging.
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63
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Zhou Y, Connor EE, Bickhart DM, Li C, Baldwin RL, Schroeder SG, Rosen BD, Yang L, Van Tassell CP, Liu GE. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. Gigascience 2018; 7:4965117. [PMID: 29635292 PMCID: PMC5928411 DOI: 10.1093/gigascience/giy039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown. Results Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in somatic cells and identified meiosis-related genes such asKIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. In addition to the common HMRs around gene promoters, which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated in sperm and could affect the promoter structures by introducing new regulatory elements. Conclusions Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Erin E Connor
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Derek M Bickhart
- The Cell Wall Utilization and Biology Laboratory, US Department of Agriculture, Agriculture Research Service, Madison, WI, 53706, USA
| | - Congjun Li
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
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Ferreira M, Verbinnen I, Fardilha M, Van Eynde A, Bollen M. The deletion of the protein phosphatase 1 regulator NIPP1 in testis causes hyperphosphorylation and degradation of the histone methyltransferase EZH2. J Biol Chem 2018; 293:18031-18039. [PMID: 30305391 DOI: 10.1074/jbc.ac118.005577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/25/2018] [Indexed: 12/15/2022] Open
Abstract
Germ cell proliferation is epigenetically controlled, mainly through DNA methylation and histone modifications. However, the pivotal epigenetic regulators of germ cell self-renewal and differentiation in postnatal testis are still poorly defined. The histone methyltransferase enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of Polycomb repressive complex 2, represses target genes through trimethylation of histone H3 at Lys-27 (H3K27me3), and interacts (in)directly with both protein phosphatase 1 (PP1) and nuclear inhibitor of PP1 (NIPP1). Here, we report that postnatal, testis-specific ablation of NIPP1 in mice results in loss of EZH2 and reduces H3K27me3 levels. Mechanistically, the NIPP1 deletion abrogated PP1-mediated EZH2 dephosphorylation at two cyclin-dependent kinase sites (Thr-345/487), thereby generating hyperphosphorylated EZH2, which is a substrate for proteolytic degradation. Accordingly, alanine mutation of these residues prolonged the half-life of EZH2 in male germ cells. Our study discloses a key role for the PP1:NIPP1 holoenzyme in stabilizing EZH2 and maintaining the H3K27me3 mark on genes that are important for germ cell development and spermatogenesis.
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Affiliation(s)
- Mónica Ferreira
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and; Institute for Research in Biomedicine (iBiMED), Health Sciences Department, University of Aveiro, 3810 Aveiro, Portugal
| | - Iris Verbinnen
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and
| | - Margarida Fardilha
- Institute for Research in Biomedicine (iBiMED), Health Sciences Department, University of Aveiro, 3810 Aveiro, Portugal
| | - Aleyde Van Eynde
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and.
| | - Mathieu Bollen
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and.
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65
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Watanabe T, Cui X, Yuan Z, Qi H, Lin H. MIWI2 targets RNAs transcribed from piRNA-dependent regions to drive DNA methylation in mouse prospermatogonia. EMBO J 2018; 37:e95329. [PMID: 30108053 PMCID: PMC6138435 DOI: 10.15252/embj.201695329] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022] Open
Abstract
Argonaute/Piwi proteins can regulate gene expression via RNA degradation and translational regulation using small RNAs as guides. They also promote the establishment of suppressive epigenetic marks on repeat sequences in diverse organisms. In mice, the nuclear Piwi protein MIWI2 and Piwi-interacting RNAs (piRNAs) are required for DNA methylation of retrotransposon sequences and some other sequences. However, its underlying molecular mechanisms remain unclear. Here, we show that piRNA-dependent regions are transcribed at the stage when piRNA-mediated DNA methylation takes place. MIWI2 specifically interacts with RNAs from these regions. In addition, we generated mice with deletion of a retrotransposon sequence either in a representative piRNA-dependent region or in a piRNA cluster. Both deleted regions were required for the establishment of DNA methylation of the piRNA-dependent region, indicating that piRNAs determine the target specificity of MIWI2-mediated DNA methylation. Our results indicate that MIWI2 affects the chromatin state through base-pairing between piRNAs and nascent RNAs, as observed in other organisms possessing small RNA-mediated epigenetic regulation.
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Affiliation(s)
- Toshiaki Watanabe
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiekui Cui
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Zhongyu Yuan
- Zhiyuan College, Shanghai Jiaotong University, Shanghai, China
| | - Hongying Qi
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
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66
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Lecluze E, Jégou B, Rolland AD, Chalmel F. New transcriptomic tools to understand testis development and functions. Mol Cell Endocrinol 2018; 468:47-59. [PMID: 29501799 DOI: 10.1016/j.mce.2018.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 12/16/2022]
Abstract
The testis plays a central role in the male reproductive system - secreting several hormones including male steroids and producing male gametes. A complex and coordinated molecular program is required for the proper differentiation of testicular cell types and maintenance of their functions in adulthood. The testicular transcriptome displays the highest levels of complexity and specificity across all tissues in a wide range of species. Many studies have used high-throughput sequencing technologies to define the molecular dynamics and regulatory networks in the testis as well as to identify novel genes or gene isoforms expressed in this organ. This review intends to highlight the complementarity of these transcriptomic studies and to show how the use of different sequencing protocols contribute to improve our global understanding of testicular biology.
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Affiliation(s)
- Estelle Lecluze
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France.
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67
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Sisakhtnezhad S. In silico analysis of single‐cell RNA sequencing data from 3 and 7 days old mouse spermatogonial stem cells to identify their differentially expressed genes and transcriptional regulators. J Cell Biochem 2018; 119:7556-7569. [DOI: 10.1002/jcb.27066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
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68
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Sakashita A, Yeh YHV, Namekawa SH, Lin SP. Epigenomic and single-cell profiling of human spermatogonial stem cells. Stem Cell Investig 2018; 5:11. [PMID: 29782571 PMCID: PMC5945786 DOI: 10.21037/sci.2018.04.04] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 04/09/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Akihiko Sakashita
- Division of Reproductive Sciences, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Yu-Han V. Yeh
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Satoshi H. Namekawa
- Division of Reproductive Sciences, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University/Academia Sinica, Taipei, Taiwan
- Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
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69
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Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline. Proc Natl Acad Sci U S A 2018; 115:4957-4962. [PMID: 29686098 DOI: 10.1073/pnas.1804512115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Repressive H3K27me3 and active H3K4me2/3 together form bivalent chromatin domains, molecular hallmarks of developmental potential. In the male germline, these domains are thought to persist into sperm to establish totipotency in the next generation. However, it remains unknown how H3K27me3 is established on specific targets in the male germline. Here, we demonstrate that a germline-specific Polycomb protein, SCML2, binds to H3K4me2/3-rich hypomethylated promoters in undifferentiated spermatogonia to facilitate H3K27me3. Thus, SCML2 establishes bivalent domains in the male germline of mice. SCML2 regulates two major classes of bivalent domains: Class I domains are established on developmental regulator genes that are silent throughout spermatogenesis, while class II domains are established on somatic genes silenced during late spermatogenesis. We propose that SCML2-dependent H3K27me3 in the male germline prepares the expression of developmental regulator and somatic genes in embryonic development.
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70
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Gaysinskaya V, Miller BF, De Luca C, van der Heijden GW, Hansen KD, Bortvin A. Transient reduction of DNA methylation at the onset of meiosis in male mice. Epigenetics Chromatin 2018; 11:15. [PMID: 29618374 PMCID: PMC5883305 DOI: 10.1186/s13072-018-0186-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 01/12/2023] Open
Abstract
Background Meiosis is a specialized germ cell cycle that generates haploid gametes. In the initial stage of meiosis, meiotic prophase I (MPI), homologous chromosomes pair and recombine. Extensive changes in chromatin in MPI raise an important question concerning the contribution of epigenetic mechanisms such as DNA methylation to meiosis. Interestingly, previous studies concluded that in male mice, genome-wide DNA methylation patters are set in place prior to meiosis and remain constant subsequently. However, no prior studies examined DNA methylation during MPI in a systematic manner necessitating its further investigation. Results In this study, we used genome-wide bisulfite sequencing to determine DNA methylation of adult mouse spermatocytes at all MPI substages, spermatogonia and haploid sperm. This analysis uncovered transient reduction of DNA methylation (TRDM) of spermatocyte genomes. The genome-wide scope of TRDM, its onset in the meiotic S phase and presence of hemimethylated DNA in MPI are all consistent with a DNA replication-dependent DNA demethylation. Following DNA replication, spermatocytes regain DNA methylation gradually but unevenly, suggesting that key MPI events occur in the context of hemimethylated genome. TRDM also uncovers the prior deficit of DNA methylation of LINE-1 retrotransposons in spermatogonia resulting in their full demethylation during TRDM and likely contributing to the observed mRNA and protein expression of some LINE-1 elements in early MPI. Conclusions Our results suggest that contrary to the prevailing view, chromosomes exhibit dynamic changes in DNA methylation in MPI. We propose that TRDM facilitates meiotic prophase processes and gamete quality control. Electronic supplementary material The online version of this article (10.1186/s13072-018-0186-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valeriya Gaysinskaya
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Brendan F Miller
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chiara De Luca
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Godfried W van der Heijden
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA.
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Weyrich A, Jeschek M, Schrapers KT, Lenz D, Chung TH, Rübensam K, Yasar S, Schneemann M, Ortmann S, Jewgenow K, Fickel J. Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy011. [PMID: 29992049 PMCID: PMC6031029 DOI: 10.1093/eep/dvy011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/19/2018] [Accepted: 04/06/2018] [Indexed: 05/14/2023]
Abstract
Epigenetic modifications, of which DNA methylation is the most stable, are a mechanism conveying environmental information to subsequent generations via parental germ lines. The paternal contribution to adaptive processes in the offspring might be crucial, but has been widely neglected in comparison to the maternal one. To address the paternal impact on the offspring's adaptability to changes in diet composition, we investigated if low protein diet (LPD) in F0 males caused epigenetic alterations in their subsequently sired sons. We therefore fed F0 male Wild guinea pigs with a diet lowered in protein content (LPD) and investigated DNA methylation in sons sired before and after their father's LPD treatment in both, liver and testis tissues. Our results point to a 'heritable epigenetic response' of the sons to the fathers' dietary change. Because we detected methylation changes also in the testis tissue, they are likely to be transmitted to the F2 generation. Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming ('metabolic shift'). Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change.
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Affiliation(s)
- A Weyrich
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
| | - M Jeschek
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Koenigin-Luise-Street 6-8, 14195 Berlin, Germany
| | - K T Schrapers
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
| | - D Lenz
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
| | - T H Chung
- Zymoresearch, EpiQuest, 17062 Murphy Avenue, Irvine, CA 92614, USA
| | - K Rübensam
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
| | - S Yasar
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
| | - M Schneemann
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
| | - S Ortmann
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
| | - K Jewgenow
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
| | - J Fickel
- Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Street 17, D-10315 Berlin, Germany
- Institute for Biochemistry and Biology, Potsdam University, Karl-Liebknecht-Street 24-25, 14476 Potsdam, Germany
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Transcriptome analysis provides insights into xylogenesis formation in Moso bamboo (Phyllostachys edulis) shoot. Sci Rep 2018; 8:3951. [PMID: 29500441 PMCID: PMC5834459 DOI: 10.1038/s41598-018-21766-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 02/07/2018] [Indexed: 01/21/2023] Open
Abstract
Maturation-related changes in cell wall composition and the molecular mechanisms underlying cell wall changes were investigated from the apical, middle and basal segments in moso bamboo shoot (MBS). With maturation extent from apical to basal regions in MBS, lignin and cellulose content increased, whereas heteroxylan exhibited a decreasing trend. Activities of phenylalanine amonnialyase (PAL), cinnamyl alcohol dehydrogenase (CAD) and cinnamate-4-hydroxylase (C4H), which are involved in lignin biosynthesis, increased rapidly from the apex to the base sections. The comparative transcriptomic analysis was carried out to identify some key genes involved in secondary cell walls (SCW) formation underlying the cell wall compositions changes including 63, 8, 18, and 31 functional unigenes encoding biosynthesis of lignin, cellulose, xylan and NAC-MYB-based transcription factors, respectively. Genes related to secondary cell wall formation and lignin biosynthesis had higher expression levels in the middle and basal segments compared to those in the apical segments. Furthermore, the expression profile of PePAL gene showed positive relationships with cellulose-related gene PeCESA4, xylan-related genes PeIRX9 and PeIRX10. Our results indicated that lignification occurred in the more mature middle and basal segments in MBS at harvest while lignification of MBS were correlated with higher expression levels of PeCESA4, PeIRX9 and PeIRX10 genes.
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73
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Rea M, Gripshover T, Fondufe-Mittendorf Y. Selective inhibition of CTCF binding by iAs directs TET-mediated reprogramming of 5-hydroxymethylation patterns in iAs-transformed cells. Toxicol Appl Pharmacol 2018; 338:124-133. [PMID: 29175454 PMCID: PMC5738917 DOI: 10.1016/j.taap.2017.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022]
Abstract
Methylation at cytosine (5mC) is a fundamental epigenetic DNA modification recently associated with iAs-mediated carcinogenesis. In contrast, the role of 5-hydroxymethylcytosine (5hmC), the oxidation product of 5mC in iAs-mediated carcinogenesis is unknown. Here we assess the hydroxymethylome in iAs-transformed cells, showing that dynamic modulation of hydroxymethylated DNA is associated with specific transcriptional networks. Moreover, this pathologic iAs-mediated carcinogenesis is characterized by a shift toward a higher hydroxymethylation pattern genome-wide. At specific promoters, hydroxymethylation correlated with increased gene expression. Furthermore, this increase in hydroxymethylation occurs concurrently with an upregulation of ten-eleven translocation (TET) enzymes that oxidize 5-methylcytosine (5mC) in DNA. To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. Further analyses suggest that this distal site acts as an enhancer, thus high CTCF occupancy at the enhancer region of TET1 and TET2 possibly drives their high expression in iAs-transformed cells. These results have major implications in understanding the impact of differential CTCF binding, genome architecture and its consequences in iAs-mediated pathogenesis.
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Affiliation(s)
- Matthew Rea
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Tyler Gripshover
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA; Eastern Kentucky University, Richmond, KY 40475, USA
| | - Yvonne Fondufe-Mittendorf
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA.
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74
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Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nat Genet 2017; 50:130-137. [PMID: 29255257 DOI: 10.1038/s41588-017-0008-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/10/2017] [Indexed: 01/21/2023]
Abstract
DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.
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Nagaoka SI, Saitou M. Reconstitution of Female Germ Cell Fate Determination and Meiotic Initiation in Mammals. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:213-222. [PMID: 29208639 DOI: 10.1101/sqb.2017.82.033803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Meiosis is a fundamental process that underpins sexual reproduction. In mammals, the execution of meiosis is tightly integrated within the complex processes of oogenesis and spermatogenesis, and elucidation of the molecular mechanisms regulating meiotic initiation remains challenging. We have recently developed in vitro culture strategies to induce mouse pluripotent stem cells into germ cells, which successfully contribute to both oogenesis and spermatogenesis and to fertile offspring. The culture strategies faithfully recapitulate transcriptional and epigenetic dynamics as well as signaling principles for germ cell specification, proliferation, and female sex determination/meiotic induction, providing a valuable platform for studies to illuminate the molecular mechanisms underlying such critical processes. Here, we review mammalian gametogenesis with a focus on the implementation of meiosis and, based on our recent studies, discuss new insights into the mechanisms for meiotic initiation and germ cell sex determination in mice.
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Affiliation(s)
- So I Nagaoka
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Center for iPS Cell Research and Application, Kyoto University, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
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76
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Maenohara S, Unoki M, Toh H, Ohishi H, Sharif J, Koseki H, Sasaki H. Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos. PLoS Genet 2017; 13:e1007042. [PMID: 28976982 PMCID: PMC5643148 DOI: 10.1371/journal.pgen.1007042] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/16/2017] [Accepted: 09/22/2017] [Indexed: 01/05/2023] Open
Abstract
The methylation of cytosine at CG sites in the mammalian genome is dynamically reprogrammed during gametogenesis and preimplantation development. It was previously shown that oocyte-derived DNMT1 (a maintenance methyltransferase) is essential for maintaining and propagating CG methylation at imprinting control regions in preimplantation embryos. In mammalian somatic cells, hemimethylated-CG-binding protein UHRF1 plays a critical role in maintaining CG methylation by recruiting DNMT1 to hemimethylated CG sites. However, the role of UHRF1 in oogenesis and preimplantation development is unknown. In the present study, we show that UHRF1 is mainly, but not exclusively, localized in the cytoplasm of oocytes and preimplantation embryos. However, smaller amounts of UHRF1 existed in the nucleus, consistent with the expected role in DNA methylation. We then generated oocyte-specific Uhrf1 knockout (KO) mice and found that, although oogenesis was itself unaffected, a large proportion of the embryos derived from the KO oocytes died before reaching the blastocyst stage (a maternal effect). Whole genome bisulfite sequencing revealed that blastocysts derived from KO oocytes have a greatly reduced level of CG methylation, suggesting that maternal UHRF1 is essential for maintaining CG methylation, particularly at the imprinting control regions, in preimplantation embryos. Surprisingly, UHRF1 was also found to contribute to de novo CG and non-CG methylation during oocyte growth: in Uhrf1 KO oocytes, transcriptionally-inactive regions gained less methylation, while actively transcribed regions, including the imprinting control regions, were unaffected or only slightly affected. We also found that de novo methylation was defective during the late stage of oocyte growth. To the best of our knowledge, this is the first study to demonstrate the role of UHRF1 in de novo DNA methylation in vivo. Our study reveals multiple functions of UHRF1 during the global epigenetic reprogramming of oocytes and early embryos. The methylation of cytosine at CG sites in the mammalian genome is an epigenetic modification that is important for cell differentiation and embryonic development. During oocyte growth, the actively transcribed regions gain both CG and non-CG methylation. However, after fertilization, such methylation is globally erased, except for certain gene control regions and a subset of retrotransposons that retain CG methylation. We examined the role of UHRF1, a protein essential for the maintenance of CG methylation in somatic cells, in oocytes and preimplantation embryos by generating oocyte-specific Uhrf1 gene knockout mice. We found that oocyte-derived maternal UHRF1 protein was important for nuclear localization of DNMT1 (a maintenance DNA methyltransferase) and for CG maintenance methylation, particularly at the imprinting control regions, in preimplantation embryos. Unexpectedly, we found that the gain in CG and non-CG methylation in oocytes was also affected by Uhrf1 knockout in certain genomic regions. To the best of our knowledge, this is the first study to demonstrate a role of UHRF1 in de novo DNA methylation in vivo. Our study reveals multiple functions of UHRF1 during the global epigenetic reprogramming of oocytes and preimplantation embryos.
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Affiliation(s)
- Shoji Maenohara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- * E-mail: (HS); (MU)
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Jafar Sharif
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
- * E-mail: (HS); (MU)
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Miyauchi H, Ohta H, Nagaoka S, Nakaki F, Sasaki K, Hayashi K, Yabuta Y, Nakamura T, Yamamoto T, Saitou M. Bone morphogenetic protein and retinoic acid synergistically specify female germ-cell fate in mice. EMBO J 2017; 36:3100-3119. [PMID: 28928204 DOI: 10.15252/embj.201796875] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/29/2022] Open
Abstract
The mechanism for sex determination in mammalian germ cells remains unclear. Here, we reconstitute the female sex determination in mouse germ cells in vitro under a defined condition without the use of gonadal somatic cells. We show that retinoic acid (RA) and its key effector, STRA8, are not sufficient to induce the female germ-cell fate. In contrast, bone morphogenetic protein (BMP) and RA synergistically induce primordial germ cells (PGCs)/PGC-like cells (PGCLCs) derived from embryonic stem cells (ESCs) into fetal primary oocytes. The induction is characterized by entry into the meiotic prophase, occurs synchronously and recapitulates cytological and transcriptome progression in vivo faithfully. Importantly, the female germ-cell induction necessitates a proper cellular competence-most typically, DNA demethylation of relevant genes-which is observed in appropriately propagated PGCs/PGCLCs, but not in PGCs/PGCLCs immediately after induction. This provides an explanation for the differential function of BMP signaling between PGC specification and female germ-cell induction. Our findings represent a framework for a comprehensive delineation of the sex-determination pathway in mammalian germ cells, including humans.
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Affiliation(s)
- Hidetaka Miyauchi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,JST, ERATO, Kyoto, Japan
| | - Hiroshi Ohta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,JST, ERATO, Kyoto, Japan
| | - So Nagaoka
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,JST, ERATO, Kyoto, Japan
| | - Fumio Nakaki
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,JST, ERATO, Kyoto, Japan
| | - Kotaro Sasaki
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,JST, ERATO, Kyoto, Japan
| | - Katsuhiko Hayashi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,JST, PRESTO, Fukuoka, Japan.,Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yukihiro Yabuta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,JST, ERATO, Kyoto, Japan
| | - Tomonori Nakamura
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,JST, ERATO, Kyoto, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.,AMED-CREST, AMED, Tokyo, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan .,JST, ERATO, Kyoto, Japan.,Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
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78
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Cornet D, Cohen M, Clement A, Amar E, Fournols L, Clement P, Neveux P, Ménézo Y. Association between the MTHFR-C677T isoform and structure of sperm DNA. J Assist Reprod Genet 2017; 34:1283-1288. [PMID: 28842818 DOI: 10.1007/s10815-017-1015-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/01/2017] [Indexed: 10/19/2022] Open
Abstract
PURPOSE The aim of this study is to evaluate whether the MTHFR contribution to male decreased fertility can be attributable to anomalies in sperm nucleus DNA structure in relation to defective methylation. METHODS The presence of MTHFR C677T, contributing at most for male infertility, was determined from a venous blood sample, using real-time polymerase chain reaction (PCR). Sperm DNA fragmentation (SDF) and sperm nucleus decondensation index (SDI) measurements were performed using acridine orange and flow cytometry. SDF and SDI of men MTHFR C677T heterozygous or homozygous were compared to a general population of hypo-fertile patients RESULTS: SDF is not increased either in homozygous or heterozygous carriers of MTHFR C677T. In contrast, SDI is increased with a higher incidence in homozygous (p = 0.0006) than in heterozygous (p = 0.029) patients when compared with the control population. Using a critical threshold of 20% for either SDI or SDF assayed with our technique, the percentage of patients with results higher than this value is not significant with respect to fragmentation (0.128), but is significantly increased for decondensation (0.0003). CONCLUSIONS Defective methylation linked to MTHFR may contribute to sperm pathogenesis via increased SDI. After DNA structure analysis, especially SDI, treatment with 5-methyl tetrahydrofolate (MTHF), the metabolite downstream from the action of MTHFR, should be recommended as a therapeutic approach. Patients with a high SDI should be tested for MTHFR isoforms as part of a healthcare policy.
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Affiliation(s)
| | | | - Arthur Clement
- Laboratoire Clement, Avenue d'Eylau, 75016, Paris, France
| | - Edouard Amar
- American Hospital, 92200, Neuilly sur Seine, France
| | | | | | - Paul Neveux
- Centre Hospitalo Univesitaire d'Angers, 49000, Angers, France
| | - Yves Ménézo
- Laboratoire Clement, Avenue d'Eylau, 75016, Paris, France. .,American Hospital, 92200, Neuilly sur Seine, France. .,Centre Hospitalo Univesitaire d'Angers, 49000, Angers, France. .,London Fertility Associates, Harley St, London, UK.
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79
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Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X. Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta. Nucleic Acids Res 2017; 45:2503-2515. [PMID: 28158710 PMCID: PMC5389525 DOI: 10.1093/nar/gkx057] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/21/2017] [Indexed: 12/22/2022] Open
Abstract
Activator protein 1 (AP-1) is a transcription factor that recognizes two versions of a 7-base pair response element, either 5΄-TGAGTCA-3΄ or 5΄-MGAGTCA-3΄ (where M = 5-methylcytosine). These two elements share the feature that 5-methylcytosine and thymine both have a methyl group in the same position, 5-carbon of the pyrimidine, so each of them has two methyl groups at nucleotide positions 1 and 5 from the 5΄ end, resulting in four methyl groups symmetrically positioned in duplex DNA. Epstein-Barr Virus Zta is a key transcriptional regulator of the viral lytic cycle that is homologous to AP-1. Zta recognizes several methylated Zta-response elements, including meZRE1 (5΄-TGAGMCA-3΄) and meZRE2 (5΄-TGAGMGA-3΄), where a methylated cytosine occupies one of the inner thymine residues corresponding to the AP-1 element, resulting in the four spatially equivalent methyl groups. Here, we study how AP-1 and Zta recognize these methyl groups within their cognate response elements. These methyl groups are in van der Waals contact with a conserved di-alanine in AP-1 dimer (Ala265 and Ala266 in Jun), or with the corresponding Zta residues Ala185 and Ser186 (via its side chain carbon Cβ atom). Furthermore, the two ZRE elements differ at base pair 6 (C:G versus G:C), forming a pseudo-symmetric sequence (meZRE1) or an asymmetric sequence (meZRE2). In vitro DNA binding assays suggest that Zta has high affinity for all four sequences examined, whereas AP-1 has considerably reduced affinity for the asymmetric sequence (meZRE2). We ascribe this difference to Zta Ser186 (a unique residue for Zta) whose side chain hydroxyl oxygen atom interacts with the two half sites differently, whereas the corresponding Ala266 of AP-1 Jun protein lacks such flexibility. Our analyses demonstrate a novel mechanism of 5mC/T recognition in a methylation-dependent, spatial and sequence-specific approach by basic leucine-zipper transcriptional factors.
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Affiliation(s)
- Samuel Hong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Molecular and Systems Pharmacology graduate program, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - John R Horton
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samuel H Speck
- Department of Microbiology & Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Emory Vaccine Center, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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80
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Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice. PLoS Genet 2017; 13:e1006926. [PMID: 28749988 PMCID: PMC5549759 DOI: 10.1371/journal.pgen.1006926] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 08/08/2017] [Accepted: 07/15/2017] [Indexed: 12/13/2022] Open
Abstract
Mammalian genomes harbor millions of retrotransposon copies, some of which are transpositionally active. In mouse prospermatogonia, PIWI-interacting small RNAs (piRNAs) combat retrotransposon activity to maintain the genomic integrity. The piRNA system destroys retrotransposon-derived RNAs and guides de novo DNA methylation at some retrotransposon promoters. However, it remains unclear whether DNA methylation contributes to retrotransposon silencing in prospermatogonia. We have performed comprehensive studies of DNA methylation and polyA(+) RNAs (transcriptome) in developing male germ cells from Pld6/Mitopld and Dnmt3l knockout mice, which are defective in piRNA biogenesis and de novo DNA methylation, respectively. The Dnmt3l mutation greatly reduced DNA methylation levels at most retrotransposons, but its impact on their RNA abundance was limited in prospermatogonia. In Pld6 mutant germ cells, although only a few retrotransposons exhibited reduced DNA methylation, many showed increased expression at the RNA level. More detailed analysis of RNA sequencing, nascent RNA quantification, profiling of cleaved RNA ends, and the results obtained from double knockout mice suggest that PLD6 works mainly at the posttranscriptional level. The increase in retrotransposon expression was larger in Pld6 mutants than it was in Dnmt3l mutants, suggesting that RNA degradation by the piRNA system plays a more important role than does DNA methylation in prospermatogonia. However, DNA methylation had a long-term effect: hypomethylation caused by the Pld6 or Dnmt3l mutation resulted in increased retrotransposon expression in meiotic spermatocytes. Thus, posttranscriptional silencing plays an important role in the early stage of germ cell development, then transcriptional silencing becomes important in later stages. In addition, intergenic and intronic retrotransposon sequences, in particular those containing the antisense L1 promoters, drove ectopic expression of nearby genes in both mutant spermatocytes, suggesting that retrotransposon silencing is important for the maintenance of not only genomic integrity but also transcriptomic integrity. Retrotransposons are a class of transposable elements, of which mobility has mutagenic potential. Therefore, it is important to regulate the expression of retrotransposons for maintaining the genomic integrity. In male germ cells, DNA methylation and the piRNA system are thought to play roles in retrotransposon silencing. However, genome-wide DNA methylation is once erased (in primordial germ cells) and reestablished (in prospermatogonia) during development. In prospermatogonia, piRNAs guide de novo DNA methylation at some retrotransposons. To clarify the contribution of DNA methylation and the piRNA system to retrotransposon silencing in the course of male germ cell development, we analyzed DNA methylation and RNA expression in Dnmt3l and Pld6 knockout mice, which are defective in de novo DNA methylation and piRNA biogenesis, respectively. Our results reveal that, in prospermatogonia, the piRNA system works mainly at the posttranscriptional level, and plays a more important role than does DNA methylation in retrotransposon silencing. However, DNA methylation becomes much more important in later stages when germ cells enter meiosis (in spermatocytes). We also found that hypomethylated retrotransposons can drive ectopic expression of nearby genes; therefore, their transcriptional silencing by DNA methylation is important for maintaining the transcriptomic integrity as well.
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81
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Abstract
The germ cell lineage originates early in development and undergoes a series of complex developmental processes that culminate in the generation of fully matured gametes, the spermatozoa and the oocytes. Remarkably, researchers have been recapitulating these developmental pathways using mouse and human pluripotent stem cells (PSCs). With further studies, including those involving non-human primate models, human gametogenesis may be fully reconstituted from PSCs, which would profoundly facilitate our understanding of human germ cell development and infertility. Here we discuss groundbreaking studies that lay the foundation for this achievement, the current state of the field, and challenges for deriving gametes from hPSCs.
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Affiliation(s)
- Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; Center for Induced Pluripotent Stem Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Hidetaka Miyauchi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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82
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Giannoulatou E, Maher GJ, Ding Z, Gillis AJM, Dorssers LCJ, Hoischen A, Rajpert-De Meyts E, McVean G, Wilkie AOM, Looijenga LHJ, Goriely A. Whole-genome sequencing of spermatocytic tumors provides insights into the mutational processes operating in the male germline. PLoS One 2017; 12:e0178169. [PMID: 28542371 PMCID: PMC5439955 DOI: 10.1371/journal.pone.0178169] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 12/31/2022] Open
Abstract
Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover, spermatogonia very rarely form tumors, so-called spermatocytic tumors (SpT). In line with the previous identification of FGFR3 and HRAS selfish mutations in a subset of cases, candidate gene screening of 29 SpTs identified an oncogenic NRAS mutation in two cases. To gain insights in the etiology of SpT and into properties of the male germline, we performed whole-genome sequencing of five tumors (4/5 with matched normal tissue). The acquired single nucleotide variant load was extremely low (~0.2 per Mb), with an average of 6 (2-9) non-synonymous variants per tumor, none of which is likely to be oncogenic. The observed mutational signature of SpTs is strikingly similar to that of germline de novo mutations, mostly involving C>T transitions with a significant enrichment in the ACG trinucleotide context. The tumors exhibited extensive aneuploidy (50-99 autosomes/tumor) involving whole-chromosomes, with recurrent gains of chr9 and chr20 and loss of chr7, suggesting that aneuploidy itself represents the initiating oncogenic event. We propose that SpT etiology recapitulates the unique properties of male germ cells; because of evolutionary constraints to maintain low point mutation rate, rare tumorigenic driver events are caused by a combination of gene imbalance mediated via whole-chromosome aneuploidy. Finally, we propose a general framework of male germ cell tumor pathology that accounts for their mutational landscape, timing and cellular origin.
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Affiliation(s)
- Eleni Giannoulatou
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Geoffrey J. Maher
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Zhihao Ding
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ad J. M. Gillis
- Department of Pathology, Erasmus MC—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lambert C. J. Dorssers
- Department of Pathology, Erasmus MC—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ewa Rajpert-De Meyts
- Department of Growth & Reproduction, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | | | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrew O. M. Wilkie
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Leendert H. J. Looijenga
- Department of Pathology, Erasmus MC—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anne Goriely
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
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83
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Ambrosi C, Manzo M, Baubec T. Dynamics and Context-Dependent Roles of DNA Methylation. J Mol Biol 2017; 429:1459-1475. [PMID: 28214512 DOI: 10.1016/j.jmb.2017.02.008] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/26/2017] [Accepted: 02/09/2017] [Indexed: 12/22/2022]
Abstract
DNA methylation is one of the most extensively studied epigenetic marks. It is involved in transcriptional gene silencing and plays important roles during mammalian development. Its perturbation is often associated with human diseases. In mammalian genomes, DNA methylation is a prevalent modification that decorates the majority of cytosines. It is found at the promoters and enhancers of inactive genes, at repetitive elements, and within transcribed gene bodies. Its presence at promoters is dynamically linked to gene activity, suggesting that it could directly influence gene expression patterns and cellular identity. The genome-wide distribution and dynamic behaviour of this mark have been studied in great detail in a variety of tissues and cell lines, including early embryonic development and in embryonic stem cells. In combination with functional studies, these genome-wide maps of DNA methylation revealed interesting features of this mark and provided important insights into its dynamic nature and potential functional role in genome regulation. In this review, we discuss how these recent observations, in combination with insights obtained from biochemical and functional genetics studies, have expanded our current knowledge about the regulation and context-dependent roles of DNA methylation in mammalian genomes.
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Affiliation(s)
- Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program of the Life Sciences Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program of the Life Sciences Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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84
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Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, LaSalle JM. Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns. Stem Cells 2017; 35:981-988. [PMID: 28032673 DOI: 10.1002/stem.2563] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/27/2016] [Accepted: 12/12/2016] [Indexed: 12/20/2022]
Abstract
Early embryonic stages of pluripotency are modeled for epigenomic studies primarily with human embryonic stem cells (ESC) or induced pluripotent stem cells (iPSCs). For analysis of DNA methylation however, ESCs and iPSCs do not accurately reflect the DNA methylation levels found in preimplantation embryos. Whole genome bisulfite sequencing (WGBS) approaches have revealed the presence of large partially methylated domains (PMDs) covering 30%-40% of the genome in oocytes, preimplantation embryos, and placenta. In contrast, ESCs and iPSCs show abnormally high levels of DNA methylation compared to inner cell mass (ICM) or placenta. Here we show that dental pulp stem cells (DPSCs), derived from baby teeth and cultured in serum-containing media, have PMDs and mimic the ICM and placental methylome more closely than iPSCs and ESCs. By principal component analysis, DPSC methylation patterns were more similar to two other neural stem cell types of human derivation (EPI-NCSC and LUHMES) and placenta than were iPSCs, ESCs or other human cell lines (SH-SY5Y, B lymphoblast, IMR90). To test the suitability of DPSCs in modeling epigenetic differences associated with disease, we compared methylation patterns of DPSCs derived from children with chromosome 15q11.2-q13.3 maternal duplication (Dup15q) to controls. Differential methylation region (DMR) analyses revealed the expected Dup15q hypermethylation at the imprinting control region, as well as hypomethylation over SNORD116, and novel DMRs over 147 genes, including several autism candidate genes. Together these data suggest that DPSCs are a useful model for epigenomic and functional studies of human neurodevelopmental disorders. Stem Cells 2017;35:981-988.
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Affiliation(s)
- Keith Dunaway
- Medical Microbiology and Immunology, UC Davis, Davis, California, USA.,Genome Center, UC Davis, Davis, California, USA.,MIND Institute, UC Davis, Davis, California, USA.,Center for Children's Environmental Health, UC Davis, Davis, California, USA
| | - Sarita Goorha
- Department of Neurology, UTHSC, Memphis, Tennessee, USA.,Department of Pediatrics, UTHSC, Memphis, Tennessee, USA.,Department of Anatomy and Neurobiology, UTHSC, Memphis, Tennessee, USA
| | - Lauren Matelski
- MIND Institute, UC Davis, Davis, California, USA.,Center for Children's Environmental Health, UC Davis, Davis, California, USA.,Internal Medicine, UC Davis, Davis, California, USA
| | - Nora Urraca
- Department of Neurology, UTHSC, Memphis, Tennessee, USA
| | - Pamela J Lein
- MIND Institute, UC Davis, Davis, California, USA.,Center for Children's Environmental Health, UC Davis, Davis, California, USA.,Molecular Biosciences, UC Davis, Davis, California, USA
| | - Ian Korf
- Genome Center, UC Davis, Davis, California, USA.,Molecular and Cellular Biology, UC Davis, Davis, California, USA
| | - Lawrence T Reiter
- Department of Neurology, UTHSC, Memphis, Tennessee, USA.,Department of Pediatrics, UTHSC, Memphis, Tennessee, USA.,Department of Anatomy and Neurobiology, UTHSC, Memphis, Tennessee, USA
| | - Janine M LaSalle
- Medical Microbiology and Immunology, UC Davis, Davis, California, USA.,Genome Center, UC Davis, Davis, California, USA.,MIND Institute, UC Davis, Davis, California, USA.,Center for Children's Environmental Health, UC Davis, Davis, California, USA
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85
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Toh H, Shirane K, Miura F, Kubo N, Ichiyanagi K, Hayashi K, Saitou M, Suyama M, Ito T, Sasaki H. Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing. BMC Genomics 2017; 18:31. [PMID: 28056787 PMCID: PMC5217569 DOI: 10.1186/s12864-016-3392-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 12/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methylation of cytosine in genomic DNA is a well-characterized epigenetic modification involved in many cellular processes and diseases. Whole-genome bisulfite sequencing (WGBS), such as MethylC-seq and post-bisulfite adaptor tagging sequencing (PBAT-seq), uses the power of high-throughput DNA sequencers and provides genome-wide DNA methylation profiles at single-base resolution. However, the accuracy and consistency of WGBS outputs in relation to the operating conditions of high-throughput sequencers have not been explored. RESULTS We have used the Illumina HiSeq platform for our PBAT-based WGBS, and found that different versions of HiSeq Control Software (HCS) and Real-Time Analysis (RTA) installed on the system provided different global CpG methylation levels (approximately 5% overall difference) for the same libraries. This problem was reproduced multiple times with different WGBS libraries and likely to be associated with the low sequence diversity of bisulfite-converted DNA. We found that HCS was the major determinant in the observed differences. To determine which version of HCS is most suitable for WGBS, we used substrates with predetermined CpG methylation levels, and found that HCS v2.0.5 is the best among the examined versions. HCS v2.0.12 showed the poorest performance and provided artificially lower CpG methylation levels when 5-methylcytosine is read as guanine (first read of PBAT-seq and second read of MethylC-seq). In addition, paired-end sequencing of low diversity libraries using HCS v2.2.38 or the latest HCS v2.2.58 was greatly affected by cluster densities. CONCLUSIONS Software updates in the Illumina HiSeq platform can affect the outputs from low-diversity sequencing libraries such as WGBS libraries. More recent versions are not necessarily the better, and HCS v2.0.5 is currently the best for WGBS among the examined HCS versions. Thus, together with other experimental conditions, special care has to be taken on this point when CpG methylation levels are to be compared between different samples by WGBS.
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Affiliation(s)
- Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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86
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Ishikura Y, Yabuta Y, Ohta H, Hayashi K, Nakamura T, Okamoto I, Yamamoto T, Kurimoto K, Shirane K, Sasaki H, Saitou M. In Vitro Derivation and Propagation of Spermatogonial Stem Cell Activity from Mouse Pluripotent Stem Cells. Cell Rep 2016; 17:2789-2804. [DOI: 10.1016/j.celrep.2016.11.026] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 09/23/2016] [Accepted: 11/02/2016] [Indexed: 01/11/2023] Open
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87
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Wippermann A, Rupp O, Brinkrolf K, Hoffrogge R, Noll T. Integrative analysis of DNA methylation and gene expression in butyrate-treated CHO cells. J Biotechnol 2016; 257:150-161. [PMID: 27890772 DOI: 10.1016/j.jbiotec.2016.11.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 01/01/2023]
Abstract
The cellular mechanisms responsible for the versatile properties of CHO cells as the major production cell line for biopharmaceutical molecules are not entirely understood yet, although several 'omics' data facilitate the understanding of CHO cells and their reactions to environmental conditions. However, genome-wide studies of epigenetic processes such as DNA methylation are still limited. To prove the applicability and usefulness of integrating DNA methylation and gene expression data in a biotechnological context, we exemplarily analyzed the time course of cellular reactions upon butyrate addition in antibody-producing CHO cells by whole-genome bisulfite sequencing and CHO-specific cDNA microarrays. Gene expression and DNA methylation analyses showed that pathways known to be affected by butyrate, including cell cycle and apoptosis, as well as pathways potentially involved in butyrate-induced hyperproductivity such as central energy metabolism and protein biosynthesis were affected. Differentially methylated regions were furthermore found to contain binding-site motifs of specific transcription factors and were hypothesized to represent regulatory regions closely connected to the cellular response to butyrate. Generally, our experiment underlines the benefit of integrating DNA methylation and gene expression data, as it provided potential novel candidate genes for rational cell line development and allowed for new insights into the butyrate effect on CHO cells.
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Affiliation(s)
- Anna Wippermann
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany; Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Karina Brinkrolf
- Department of Biorescources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Gießen, Germany
| | - Raimund Hoffrogge
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany; Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Thomas Noll
- Institute of Cell Culture Technology, Bielefeld University, Bielefeld, Germany; Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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88
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Kobayashi N, Okae H, Hiura H, Chiba H, Shirakata Y, Hara K, Tanemura K, Arima T. Genome-Scale Assessment of Age-Related DNA Methylation Changes in Mouse Spermatozoa. PLoS One 2016; 11:e0167127. [PMID: 27880848 PMCID: PMC5120852 DOI: 10.1371/journal.pone.0167127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/09/2016] [Indexed: 01/10/2023] Open
Abstract
DNA methylation plays important roles in the production and functioning of spermatozoa. Recent studies have suggested that DNA methylation patterns in spermatozoa can change with age, but the regions susceptible to age-related methylation changes remain to be fully elucidated. In this study, we conducted genome-scale DNA methylation profiling of spermatozoa obtained from C57BL/6N mice at 8 weeks (8w), 18 weeks (18w) and 17 months of age (17m). There was no substantial difference in the global DNA methylation patterns between 18w and 17m samples except for a slight increase of methylation levels in long interspersed nuclear elements in the 17m samples. We found that maternally methylated imprinting control regions (mICRs) and spermatogenesis-related gene promoters had 5–10% higher methylation levels in 8w samples than in 18w or 17m samples. Analysis of individual sequence reads suggested that these regions were fully methylated (80–100%) in a subset of 8w spermatozoa. These regions are also known to be highly methylated in a subset of postnatal spermatogonia, which might be the source of the increased DNA methylation in 8w spermatozoa. Another possible source was contamination by somatic cells. Although we carefully purified the spermatozoa, it was difficult to completely exclude the possibility of somatic cell contamination. Further studies are needed to clarify the source of the small increase in DNA methylation in the 8w samples. Overall, our findings suggest that DNA methylation patterns in mouse spermatozoa are relatively stable throughout reproductive life.
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Affiliation(s)
- Norio Kobayashi
- Department of Informative Genetics, Tohoku University Graduate School of Medicine, 2–1 Seiryo-cho, Aoba-ku, Sendai, 980–8575, Japan
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, 1–1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, 981–8555, Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Tohoku University Graduate School of Medicine, 2–1 Seiryo-cho, Aoba-ku, Sendai, 980–8575, Japan
| | - Hitoshi Hiura
- Department of Informative Genetics, Tohoku University Graduate School of Medicine, 2–1 Seiryo-cho, Aoba-ku, Sendai, 980–8575, Japan
| | - Hatsune Chiba
- Department of Informative Genetics, Tohoku University Graduate School of Medicine, 2–1 Seiryo-cho, Aoba-ku, Sendai, 980–8575, Japan
| | - Yoshiki Shirakata
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, 1–1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, 981–8555, Japan
| | - Kenshiro Hara
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, 1–1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, 981–8555, Japan
| | - Kentaro Tanemura
- Laboratory of Animal Reproduction and Development, Graduate School of Agricultural Science, Tohoku University, 1–1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, 981–8555, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Tohoku University Graduate School of Medicine, 2–1 Seiryo-cho, Aoba-ku, Sendai, 980–8575, Japan
- * E-mail:
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89
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Langenstroth-Röwer D, Gromoll J, Wistuba J, Tröndle I, Laurentino S, Schlatt S, Neuhaus N. De novo methylation in male germ cells of the common marmoset monkey occurs during postnatal development and is maintained in vitro. Epigenetics 2016; 12:527-539. [PMID: 27786608 DOI: 10.1080/15592294.2016.1248007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The timing of de novo DNA methylation in male germ cells during human testicular development is yet unsolved. Apart from that, the stability of established imprinting patterns in vitro is controversially discussed. This study aimed at determining the timing of DNA de novo methylation and at assessing the stability of the methylation status in vitro. We employed the marmoset monkey (Callithrix jacchus) as it is considered the best non-human primate model for human testicular development. We selected neonatal, pre-pubertal, pubertal, and adult animals (n = 3, each) and assessed germ cell global DNA methylation levels by 5-methyl cytosine staining, and Alu elements and gene-specific methylation (H19, LIT1, SNRPN, MEST, OCT4, MAGE-A4, and DDX-4) by pyrosequencing. De novo methylation is progressively established during postnatal primate development and continues until adulthood, a process that is different in most other species. Importantly, once established, methylation patterns remained stable, as demonstrated using in vitro cultures. Thus, the marmoset monkey is a unique model for the study of postnatal DNA methylation mechanisms in germ cells and for the identification of epimutations and their causes.
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Affiliation(s)
| | - Jörg Gromoll
- a Centre of Reproductive Medicine and Andrology , Albert-Schweitzer-Campus 1, Münster , Germany
| | - Joachim Wistuba
- a Centre of Reproductive Medicine and Andrology , Albert-Schweitzer-Campus 1, Münster , Germany
| | - Ina Tröndle
- a Centre of Reproductive Medicine and Andrology , Albert-Schweitzer-Campus 1, Münster , Germany
| | - Sandra Laurentino
- a Centre of Reproductive Medicine and Andrology , Albert-Schweitzer-Campus 1, Münster , Germany
| | - Stefan Schlatt
- a Centre of Reproductive Medicine and Andrology , Albert-Schweitzer-Campus 1, Münster , Germany
| | - Nina Neuhaus
- a Centre of Reproductive Medicine and Andrology , Albert-Schweitzer-Campus 1, Münster , Germany
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90
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Epigenetic Remodeling in Male Germline Development. Stem Cells Int 2016; 2016:3152173. [PMID: 27818689 PMCID: PMC5081465 DOI: 10.1155/2016/3152173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/26/2016] [Indexed: 12/31/2022] Open
Abstract
In mammals, germ cells guarantee the inheritance of genetic and epigenetic information across generations and are the origin of a new organism. During embryo development, the blastocyst is formed in the early stage, is comprised of an inner cell mass which is pluripotent, and could give rise to the embryonic stem cells (ESCs). The inner cell mass undergoes demethylation processes and will reestablish a methylated state that is similar to that of somatic cells later in epiblast stage. Primordial germ cells (PGCs) will be formed very soon and accompanied by the process of genome-wide demethylation. With the input of male sex determination genes, spermatogonial stem cells (SSCs) are generated and undergo the process of spermatogenesis. Spermatogenesis is a delicately regulated process in which various regulations are launched to guarantee normal mitosis and meiosis in SSCs. During all these processes, especially during spermatid development, DNA methylation profile and histone modifications are of crucial importance. In this review, we will discuss the epigenetic modifications from zygote formation to mature sperm generation and their significance to these development processes.
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91
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Global Landscape and Regulatory Principles of DNA Methylation Reprogramming for Germ Cell Specification by Mouse Pluripotent Stem Cells. Dev Cell 2016; 39:87-103. [PMID: 27642137 DOI: 10.1016/j.devcel.2016.08.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 06/29/2016] [Accepted: 08/19/2016] [Indexed: 11/22/2022]
Abstract
Specification of primordial germ cells (PGCs) activates epigenetic reprogramming for totipotency, the elucidation of which remains a fundamental challenge. Here, we uncover regulatory principles for DNA methylation reprogramming during in vitro PGC specification, in which mouse embryonic stem cells (ESCs) are induced into epiblast-like cells (EpiLCs) and then PGC-like cells (PGCLCs). While ESCs reorganize their methylome to form EpiLCs, PGCLCs essentially dilute the EpiLC methylome at constant, yet different, rates between unique sequence regions and repeats. ESCs form hypomethylated domains around pluripotency regulators for their activation, whereas PGCLCs create demethylation-sensitive domains around developmental regulators by accumulating abundant H3K27me3 for their repression. Loss of PRDM14 globally upregulates methylation and diminishes the hypomethylated domains, but it preserves demethylation-sensitive domains. Notably, female ESCs form hypomethylated lamina-associated domains, while female PGCLCs effectively reverse such states into a more normal configuration. Our findings illuminate the unique orchestration of DNA methylation and histone modification reprogramming during PGC specification.
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92
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Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X. Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic Acids Res 2016; 44:10177-10185. [PMID: 27596594 PMCID: PMC5137437 DOI: 10.1093/nar/gkw774] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/06/2023] Open
Abstract
Reprogramming of mammalian genome methylation is critically important but poorly understood. Klf4, a transcription factor directing reprogramming, contains a DNA binding domain with three consecutive C2H2 zinc fingers. Klf4 recognizes CpG or TpG within a specific sequence. Mouse Klf4 DNA binding domain has roughly equal affinity for methylated CpG or TpG, and slightly lower affinity for unmodified CpG. The structural basis for this key preference is unclear, though the side chain of Glu446 is known to contact the methyl group of 5-methylcytosine (5mC) or thymine (5-methyluracil). We examined the role of Glu446 by mutagenesis. Substituting Glu446 with aspartate (E446D) resulted in preference for unmodified cytosine, due to decreased affinity for 5mC. In contrast, substituting Glu446 with proline (E446P) increased affinity for 5mC by two orders of magnitude. Structural analysis revealed hydrophobic interaction between the proline's aliphatic cyclic structure and the 5-methyl group of the pyrimidine (5mC or T). As in wild-type Klf4 (E446), the proline at position 446 does not interact directly with either the 5mC N4 nitrogen or the thymine O4 oxygen. In contrast, the unmethylated cytosine's exocyclic N4 amino group (NH2) and its ring carbon C5 atom hydrogen bond directly with the aspartate carboxylate of the E446D variant. Both of these interactions would provide a preference for cytosine over thymine, and the latter one could explain the E446D preference for unmethylated cytosine. Finally, we evaluated the ability of these Klf4 mutants to regulate transcription of methylated and unmethylated promoters in a luciferase reporter assay.
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Affiliation(s)
| | - Dongxue Wang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Alyse N Steves
- Genetics and Molecular Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology & Immunology and Program in Bioinformatics, The University of Toledo College of Medicine & Life Sciences, Toledo, Ohio 43614, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA .,Genetics and Molecular Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
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93
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Al-Soudy AS, Nakanishi T, Mizuno S, Hasegawa Y, Shawki HH, Katoh MC, Basha WA, Ibrahim AE, El-Shemy HA, Iseki H, Yoshiki A, Hiromori Y, Nagase H, Takahashi S, Oishi H, Sugiyama F. Germline recombination in a novel Cre transgenic line, Prl3b1-Cre mouse. Genesis 2016; 54:389-97. [PMID: 27124574 DOI: 10.1002/dvg.22944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/12/2016] [Accepted: 04/24/2016] [Indexed: 11/09/2022]
Abstract
Spermatogenesis is a complex and highly regulated process by which spermatogonial stem cells differentiate into spermatozoa. To better understand the molecular mechanisms of the process, the Cre/loxP system has been widely utilized for conditional gene knockout in mice. In this study, we generated a transgenic mouse line that expresses Cre recombinase under the control of the 2.5 kbp of the Prolactin family 3, subfamily b, member 1 (Prl3b1) gene promoter (Prl3b1-cre). Prl3b1 was initially reported to code for placental lactogen 2 (PL-2) protein in placenta along with increased expression toward the end of pregnancy. PL-2 was found to be expressed in germ cells in the testis, especially in spermatocytes. To analyze the specificity and efficiency of Cre recombinase activity in Prl3b1-cre mice, the mice were mated with reporter R26GRR mice, which express GFP ubiquitously before and tdsRed exclusively after Cre recombination. The systemic examination of Prl3b1-cre;R26GRR mice revealed that tdsRed-positive cells were detected only in the testis and epididymis. Fluorescence imaging of Prl3b1-cre;R26GRR testes suggested that Cre-mediated recombination took place in the germ cells with approximately 74% efficiency determined by in vitro fertilization. In conclusion, our results suggest that the Prl3b1-cre mice line provides a unique resource to understand testicular germ-cell development. genesis 54:389-397, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Al-Sayed Al-Soudy
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Animal Genetic Resource Department, National Gene Bank, Giza, Egypt.,Department of Anatomy and Embryology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tsuyoshi Nakanishi
- Laboratory of Hygienic Chemistry and Molecular Toxicology, Gifu Pharmaceutical University, Gifu, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshikazu Hasegawa
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hossam H Shawki
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Animal Genetic Resource Department, National Gene Bank, Giza, Egypt.,Department of Anatomy and Embryology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Megumi C Katoh
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Department of Anatomy and Embryology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Walaa A Basha
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Department of Anatomy and Embryology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Department of Anatomy and Embryology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Abdelaziz E Ibrahim
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Hany A El-Shemy
- Cairo University Research Park, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hiroyoshi Iseki
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, Riken BioResource Center, Tsukuba, Japan
| | - Youhei Hiromori
- Laboratory of Hygienic Chemistry and Molecular Toxicology, Gifu Pharmaceutical University, Gifu, Japan.,Department of Pharmacy, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Hisamitsu Nagase
- Laboratory of Hygienic Chemistry and Molecular Toxicology, Gifu Pharmaceutical University, Gifu, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Department of Anatomy and Embryology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hisashi Oishi
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Department of Anatomy and Embryology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
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94
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Hammoud SS, Low DHP, Yi C, Lee CL, Oatley JM, Payne CJ, Carrell DT, Guccione E, Cairns BR. Transcription and imprinting dynamics in developing postnatal male germline stem cells. Genes Dev 2016; 29:2312-24. [PMID: 26545815 PMCID: PMC4647563 DOI: 10.1101/gad.261925.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hammoud et al. conducted extensive genomic profiling and classified three broad spermatogonial stem cell (SSC) populations in juveniles: (1) epithelial-like SSCs, (2) more abundant mesenchymal-like SSCs, and (3) (in older juveniles) abundant cells committing to gametogenesis. Mesenchymal-like SSCs lacked imprinting specifically at paternally imprinted loci but fully restored imprinting prior to puberty. Mesenchymal-like SSCs also displayed developmentally linked DNA demethylation at meiotic genes and also at certain monoallelic neural genes. Postnatal spermatogonial stem cells (SSCs) progress through proliferative and developmental stages to populate the testicular niche prior to productive spermatogenesis. To better understand, we conducted extensive genomic profiling at multiple postnatal stages on subpopulations enriched for particular markers (THY1, KIT, OCT4, ID4, or GFRa1). Overall, our profiles suggest three broad populations of spermatogonia in juveniles: (1) epithelial-like spermatogonia (THY1+; high OCT4, ID4, and GFRa1), (2) more abundant mesenchymal-like spermatogonia (THY1+; moderate OCT4 and ID4; high mesenchymal markers), and (3) (in older juveniles) abundant spermatogonia committing to gametogenesis (high KIT+). Epithelial-like spermatogonia displayed the expected imprinting patterns, but, surprisingly, mesenchymal-like spermatogonia lacked imprinting specifically at paternally imprinted loci but fully restored imprinting prior to puberty. Furthermore, mesenchymal-like spermatogonia also displayed developmentally linked DNA demethylation at meiotic genes and also at certain monoallelic neural genes (e.g., protocadherins and olfactory receptors). We also reveal novel candidate receptor–ligand networks involving SSCs and the developing niche. Taken together, neonates/juveniles contain heterogeneous epithelial-like or mesenchymal-like spermatogonial populations, with the latter displaying extensive DNA methylation/chromatin dynamics. We speculate that this plasticity helps SSCs proliferate and migrate within the developing seminiferous tubule, with proper niche interaction and membrane attachment reverting mesenchymal-like spermatogonial subtype cells back to an epithelial-like state with normal imprinting profiles.
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Affiliation(s)
- Saher Sue Hammoud
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Diana H P Low
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Chongil Yi
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Chee Leng Lee
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Jon M Oatley
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Christopher J Payne
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA; Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA; Human Molecular Genetics Program, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60614, USA
| | - Douglas T Carrell
- Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Ernesto Guccione
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Bradley R Cairns
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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95
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Patel A, Hashimoto H, Zhang X, Cheng X. Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins. Methods Enzymol 2016; 573:387-401. [PMID: 27372763 DOI: 10.1016/bs.mie.2016.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Much is known about vertebrate DNA methylation and oxidation; however, much less is known about how modified cytosine residues within particular sequences are recognized. Among the known methylated DNA-binding domains, the Cys2-His2 zinc finger (ZnF) protein superfamily is the largest with hundreds of members, each containing tandem ZnFs ranging from 3 to >30 fingers. We have begun to biochemically and structurally characterize these ZnFs not only on their sequence specificity but also on their sensitivity to various DNA modifications. Rather than following published methods of refolding insoluble ZnF arrays, we have expressed and purified soluble forms of ZnFs, ranging in size from a tandem array of two to six ZnFs, from seven different proteins. We also describe a fluorescence polarization assay to measure ZnFs affinity with oligonucleotides containing various modifications and our approaches for cocrystallization of ZnFs with oligonucleotides.
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Affiliation(s)
- A Patel
- Emory University School of Medicine, Atlanta, GA, United States
| | - H Hashimoto
- Emory University School of Medicine, Atlanta, GA, United States
| | - X Zhang
- Emory University School of Medicine, Atlanta, GA, United States.
| | - X Cheng
- Emory University School of Medicine, Atlanta, GA, United States.
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96
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Weyrich A, Lenz D, Jeschek M, Chung TH, Rübensam K, Göritz F, Jewgenow K, Fickel J. Paternal intergenerational epigenetic response to heat exposure in male Wild guinea pigs. Mol Ecol 2015; 25:1729-40. [DOI: 10.1111/mec.13494] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/17/2015] [Accepted: 11/19/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Alexandra Weyrich
- Leibniz‐Institute for Zoo and Wildlife Research (IZW) Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
| | - Dorina Lenz
- Leibniz‐Institute for Zoo and Wildlife Research (IZW) Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
| | - Marie Jeschek
- Leibniz‐Institute for Zoo and Wildlife Research (IZW) Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
- Berlin Center for Genomics in Biodiversity Research Königin‐Luise‐Str 6‐8 14195 Berlin Germany
| | - Tzu Hung Chung
- Zymoresearch, EpiQuest 17062 Murphy Ave. Irvine CA 92614 USA
| | - Kathrin Rübensam
- Leibniz‐Institute for Zoo and Wildlife Research (IZW) Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
| | - Frank Göritz
- Leibniz‐Institute for Zoo and Wildlife Research (IZW) Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
| | - Katarina Jewgenow
- Leibniz‐Institute for Zoo and Wildlife Research (IZW) Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
| | - Jörns Fickel
- Leibniz‐Institute for Zoo and Wildlife Research (IZW) Alfred‐Kowalke‐Str. 17 10315 Berlin Germany
- Potsdam University Karl‐Liebknecht‐Str. 22‐24 14476 Potsdam Germany
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