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Wanigasuriya I, Gouil Q, Kinkel SA, Tapia Del Fierro A, Beck T, Roper EA, Breslin K, Stringer J, Hutt K, Lee HJ, Keniry A, Ritchie ME, Blewitt ME. Smchd1 is a maternal effect gene required for genomic imprinting. eLife 2020; 9:55529. [PMID: 33186096 PMCID: PMC7665889 DOI: 10.7554/elife.55529] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic imprinting establishes parental allele-biased expression of a suite of mammalian genes based on parent-of-origin specific epigenetic marks. These marks are under the control of maternal effect proteins supplied in the oocyte. Here we report epigenetic repressor Smchd1 as a novel maternal effect gene that regulates the imprinted expression of ten genes in mice. We also found zygotic SMCHD1 had a dose-dependent effect on the imprinted expression of seven genes. Together, zygotic and maternal SMCHD1 regulate three classic imprinted clusters and eight other genes, including non-canonical imprinted genes. Interestingly, the loss of maternal SMCHD1 does not alter germline DNA methylation imprints pre-implantation or later in gestation. Instead, what appears to unite most imprinted genes sensitive to SMCHD1 is their reliance on polycomb-mediated methylation as germline or secondary imprints, therefore we propose that SMCHD1 acts downstream of polycomb imprints to mediate its function.
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Affiliation(s)
- Iromi Wanigasuriya
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Quentin Gouil
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Sarah A Kinkel
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andrés Tapia Del Fierro
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Tamara Beck
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Ellise A Roper
- Faculty of Health and Medicine, The University of Newcastle, Newcastle, Australia
| | - Kelsey Breslin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Jessica Stringer
- Monash Biomedicine Discovery institute, Monash University, Clayton, Australia
| | - Karla Hutt
- Monash Biomedicine Discovery institute, Monash University, Clayton, Australia
| | - Heather J Lee
- Faculty of Health and Medicine, The University of Newcastle, Newcastle, Australia
| | - Andrew Keniry
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia.,The Department of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Marnie E Blewitt
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,The Department of Medical Biology, The University of Melbourne, Parkville, Australia
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52
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Wang Y, Singh AR, Zhao Y, Du T, Huang Y, Wan X, Mukhopadhyay D, Wang Y, Wang N, Zhang P. TRIM28 regulates sprouting angiogenesis through VEGFR-DLL4-Notch signaling circuit. FASEB J 2020; 34:14710-14724. [PMID: 32918765 PMCID: PMC10115459 DOI: 10.1096/fj.202000186rrr] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023]
Abstract
Sprouting angiogenesis is a highly coordinately process controlled by vascular endothelial growth factor receptor (VEGFR)-Notch signaling. Here we investigated whether Tripartite motif-containing 28 (TRIM28), which is an epigenetic modifier implicated in gene transcription and cell differentiation, is essential to mediate sprouting angiogenesis. We observed that knockdown of TRIM28 ortholog in zebrafish resulted in developmental vascular defect with disorganized and reduced vasculatures. Consistently, TRIM28 knockdown inhibited angiogenic sprouting of cultured endothelial cells (ECs), which exhibited increased mRNA levels of VEGFR1, Delta-like (DLL) 3, and Notch2 but reduced levels of VEGFR2, DLL1, DLL4, Notch1, Notch3, and Notch4.The regulative effects of TRIM28 on these angiogenic factors were partially mediated by hypoxia-inducible factor 1 α (HIF-1α) and recombination signal-binding protein for immunoglobulin kappa J region (RBPJκ). In vitro DNA-binding assay showed that TRIM28 knockdown increased the association of RBPJκ with DNA sequences containing HIF-1α-binding sites. Moreover, the phosphorylation of TRIM28 was controlled by VEGF and Notch1 through a mechanism involving RBPJκ-dual-specificity phosphatase (DUSP)-p38 MAPK, indicating a negative feedback mechanism. These findings established TRIM28 as a crucial regulator of VEGFR-Notch signaling circuit through HIF-1α and RBPJκ in EC sprouting angiogenesis.
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Affiliation(s)
- Yinfang Wang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Angom Ramcharan Singh
- Department of Biochemistry and Molecular Biology, College of Medicine and Science, Mayo Clinic, Jacksonville, FL, USA
| | - Yuanyuan Zhao
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tao Du
- Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yitong Huang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaohong Wan
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, College of Medicine and Science, Mayo Clinic, Jacksonville, FL, USA
| | - Ying Wang
- Department of Biochemistry and Molecular Biology, College of Medicine and Science, Mayo Clinic, Jacksonville, FL, USA
| | - Nanping Wang
- The Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Peng Zhang
- Central Laboratory, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Cardiovascular Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Putuo Central School of Clinical Medicine, Anhui Medical University, Hefei, China
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53
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Lu HP, Lin CJ, Chen WC, Chang YJ, Lin SW, Wang HH, Chang CJ. TRIM28 Regulates Dlk1 Expression in Adipogenesis. Int J Mol Sci 2020; 21:ijms21197245. [PMID: 33008113 PMCID: PMC7582669 DOI: 10.3390/ijms21197245] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/20/2020] [Accepted: 09/27/2020] [Indexed: 12/23/2022] Open
Abstract
The tripartite motif-containing protein 28 (TRIM28) is a transcription corepressor, interacting with histone deacetylase and methyltransferase complexes. TRIM28 is a crucial regulator in development and differentiation. We would like to investigate its function and regulation in adipogenesis. Knockdown of Trim28 by transducing lentivirus-carrying shRNAs impairs the differentiation of 3T3-L1 preadipocytes, demonstrated by morphological observation and gene expression analysis. To understand the molecular mechanism of Trim28-mediated adipogenesis, the RNA-seq was performed to find out the possible Trim28-regulated genes. Dlk1 (delta-like homolog 1) was increased in Trim28 knockdown 3T3-L1 cells both untreated and induced to differentiation. Dlk1 is an imprinted gene and known as an inhibitor of adipogenesis. Further knockdown of Dlk1 in Trim28 knockdown 3T3-L1 would rescue cell differentiation. The epigenetic analysis showed that DNA methylation of Dlk1 promoter and differentially methylated regions (DMRs) was not altered significantly in Trim28 knockdown cells. However, compared to control cells, the histone methylation on the Dlk1 promoter was increased at H3K4 and decreased at H3K27 in Trim28 knockdown cells. Finally, we found Trim28 might be recruited by transcription factor E2f1 to regulate Dlk1 expression. The results imply Trim28-Dlk1 axis is critical for adipogenesis.
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Affiliation(s)
- Hsin-Pin Lu
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan; (H.-P.L.); (C.-J.L.); (W.-C.C.)
| | - Chieh-Ju Lin
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan; (H.-P.L.); (C.-J.L.); (W.-C.C.)
| | - Wen-Ching Chen
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan; (H.-P.L.); (C.-J.L.); (W.-C.C.)
| | - Yao-Jen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (Y.-J.C.); (S.-W.L.)
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (Y.-J.C.); (S.-W.L.)
| | - Hsin-Hui Wang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Department of Pediatrics, Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei 11217, Taiwan
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang-Ming University, Taipei 11217, Taiwan
| | - Ching-Jin Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan; (H.-P.L.); (C.-J.L.); (W.-C.C.)
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; (Y.-J.C.); (S.-W.L.)
- Correspondence:
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54
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Jeon KY, Ko EJ, Oh YL, Kim H, Eo WK, Kim A, Sun HG, Ock MS, Kim KH, Cha HJ. Analysis of KAP1 expression patterns and human endogenous retrovirus Env proteins in ovarian cancer. Genes Genomics 2020; 42:1145-1150. [PMID: 32785870 DOI: 10.1007/s13258-020-00979-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/27/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Human endogenous retroviruses (HERVs) constitute around 8% of the human genome and have important roles in human health and disease, including cancers. Previous studies showed that HERV envelope (Env) proteins are highly expressed in cancer tissues and co-related with cancer progression. KAP1 has been reported to play a key role in regulating retrotransposons, including HERV-K, through epigenetic silencing. OBJECTIVE The relationship between KAP-1 and HERV Envs expressions was analyzed only in tumor cell lines and has not yet been studied in cancer tissues. In this study, we analyzed the expression patterns and relationship between KAP1 and HERV Env proteins in ovarian cancer tissues. METHOD The expression patterns of KAP-1 and HERV Env proteins, including HERV-K and HERV-R, were analyzed in ovarian cancer tissue microarrays that contained 80 surgical specimens, including normal ovary and malignant ovarian cancers. RESULTS The expression of HERV-R Env and KAP1 proteins is significantly higher in ovarian cancer compared with normal ovary tissues. However, the expression of HERV-K Env did not change significantly in cancer tissues. The expression patterns of HERV-K Env and HERV-R Env significantly increased in early stages of cancer and KAP1 expression was higher in certain stage and types of cancers. However, the expression of HERV-K Env, HERV-R Env, and KAP1 did not change in different age groups. The correlation between the expression of KAP1 and HERV-Env, including HERV-K and HERV-R, was not significantly correlated. CONCLUSIONS The results of this study showed that there was no significant correlation between the expression of KAP1 and HERV Env proteins in ovarian cancer tissues, unlike studies with cell lines in vitro. These results suggest that the actual expression of HERV Env proteins in ovarian cancer tissues may be regulated through various complex factors as well as KAP1.
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Affiliation(s)
- Kyung-Yoon Jeon
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, South Korea
| | - Eun-Ji Ko
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, South Korea.,Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, South Korea
| | - Young Lim Oh
- Department of Obstetrics and Gynecology, Kosin University College of Medicine, Busan, South Korea
| | - Hongbae Kim
- Department of Obstetrics and Gynecology, Kangnam Sacred Heart Hospital, Hallym University Medical Center, Hallym University College of Medicine, Chuncheon, South Korea
| | - Wan Kyu Eo
- Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, South Korea
| | - Ari Kim
- Department of Obstetrics and Gynecology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, Vernon Hills, IL, USA
| | - Han Gyu Sun
- Department of Obstetrics and Gynecology, Ehwa Obstetrics and Gynecology Clinic, Cheongju, Korea
| | - Mee Sun Ock
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, South Korea
| | - Ki Hyung Kim
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea.
| | - Hee-Jae Cha
- Department of Parasitology and Genetics, Kosin University College of Medicine, Busan, South Korea.
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55
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Singh PB, Belyakin SN, Laktionov PP. Biology and Physics of Heterochromatin- Like Domains/Complexes. Cells 2020; 9:E1881. [PMID: 32796726 PMCID: PMC7465696 DOI: 10.3390/cells9081881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 11/17/2022] Open
Abstract
The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the "unit of incompatibility" that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal "clutch", consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of "clutches" in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, Nur-Sultan City 010000, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Stepan N. Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
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56
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Deng M, Zhang G, Cai Y, Liu Z, Zhang Y, Meng F, Wang F, Wan Y. DNA methylation dynamics during zygotic genome activation in goat. Theriogenology 2020; 156:144-154. [PMID: 32731098 DOI: 10.1016/j.theriogenology.2020.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
Abstract
DNA methylation is a crucial element in the epigenetic regulation of mammalian embryonic development. However, the subtle changes in DNA methylation differ in species, and, little information is known regarding the dynamics of DNA methylation at the single-base resolution in goat. In the present study, we studied the DNA methylation dynamics during goat zygotic genome activation (ZGA) at global and single-base resolution using immunostaining and reduced representation bisulfite sequencing, respectively. We showed that DNA methylation was decreased both at global and single-base resolution, and the expression of TET1 was increased while DNMT1 was decreased during ZGA in goat. We identified 51058 tiles of differential methylation regions (DMRs), which were enriched in the developmental process, the regulation of developmental process, AMPK signaling pathway, mTOR signaling pathway, autophagy, and lysosome, as revealed by GO and KEGG enrichment analysis. Furthermore, we found an association between the methylation level and the expression of imprinted genes (IGF2R, PEG3, and ZFP64), maternal genes (TRIM28, SETD1A, SIN3A, and NPM2), and zygotic genes (DUXA, IGF2BP1, WT1, and ZIM3), suggesting that DNA methylation is in the tight control of ZGA in goat by regulating the expression of the critical genes. Our data will help to understand the stochastic ZGA events to achieve better development of goat embryos in vitro and provide an excellent source for further ZGA studies.
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Affiliation(s)
- Mingtian Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guomin Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Cai
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zifei Liu
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fanxing Meng
- National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongjie Wan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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57
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Żylicz JJ, Heard E. Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. Annu Rev Biochem 2020; 89:255-282. [PMID: 32259458 DOI: 10.1146/annurev-biochem-062917-012655] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
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Affiliation(s)
- Jan J Żylicz
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, PSL University, 75248 Paris Cedex 05, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, United Kingdom
| | - Edith Heard
- Directors' Research, EMBL Heidelberg, 69117 Heidelberg, Germany;
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58
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Chen Z, Zhang Y. Maternal H3K27me3-dependent autosomal and X chromosome imprinting. Nat Rev Genet 2020; 21:555-571. [PMID: 32514155 DOI: 10.1038/s41576-020-0245-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 12/19/2022]
Abstract
Genomic imprinting and X-chromosome inactivation (XCI) are classic epigenetic phenomena that involve transcriptional silencing of one parental allele. Germline-derived differential DNA methylation is the best-studied epigenetic mark that initiates imprinting, but evidence indicates that other mechanisms exist. Recent studies have revealed that maternal trimethylation of H3 on lysine 27 (H3K27me3) mediates autosomal maternal allele-specific gene silencing and has an important role in imprinted XCI through repression of maternal Xist. Furthermore, loss of H3K27me3-mediated imprinting contributes to the developmental defects observed in cloned embryos. This novel maternal H3K27me3-mediated non-canonical imprinting mechanism further emphasizes the important role of parental chromatin in development and could provide the basis for improving the efficiency of embryo cloning.
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Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA. .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. .,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Boston, MA, USA.
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59
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The influence of DNA methylation on monoallelic expression. Essays Biochem 2020; 63:663-676. [PMID: 31782494 PMCID: PMC6923323 DOI: 10.1042/ebc20190034] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 01/02/2023]
Abstract
Monoallelic gene expression occurs in diploid cells when only one of the two alleles of a gene is active. There are three main classes of genes that display monoallelic expression in mammalian genomes: (1) imprinted genes that are monoallelically expressed in a parent-of-origin dependent manner; (2) X-linked genes that undergo random X-chromosome inactivation in female cells; (3) random monoallelically expressed single and clustered genes located on autosomes. The heritability of monoallelic expression patterns during cell divisions implies that epigenetic mechanisms are involved in the cellular memory of these expression states. Among these, methylation of CpG sites on DNA is one of the best described modification to explain somatic inheritance. Here, we discuss the relevance of DNA methylation for the establishment and maintenance of monoallelic expression patterns among these three groups of genes, and how this is intrinsically linked to development and cellular states.
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60
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Sadeghi H, Nazemalhosseini-Mojarad E, Yassaee VR, Savabkar S, Ghasemian M, Aghdaei HA, Zali MR, Mirfakhraie R. Could CYP24A1 promoter methylation status affect the gene expression in the colorectal cancer patients? Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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61
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Biwer C, Kawam B, Chapelle V, Silvestre F. The Role of Stochasticity in the Origin of Epigenetic Variation in Animal Populations. Integr Comp Biol 2020; 60:1544-1557. [PMID: 32470118 DOI: 10.1093/icb/icaa047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic mechanisms such as DNA methylation modulate gene expression in a complex fashion are consequently recognized as among the most important contributors to phenotypic variation in natural populations of plants, animals, and microorganisms. Interactions between genetics and epigenetics are multifaceted and epigenetic variation stands at the crossroad between genetic and environmental variance, which make these mechanisms prominent in the processes of adaptive evolution. DNA methylation patterns depend on the genotype and can be reshaped by environmental conditions, while transgenerational epigenetic inheritance has been reported in various species. On the other hand, DNA methylation can influence the genetic mutation rate and directly affect the evolutionary potential of a population. The origin of epigenetic variance can be attributed to genetic, environmental, or stochastic factors. Generally less investigated than the first two components, variation lacking any predictable order is nevertheless present in natural populations and stochastic epigenetic variation, also referred to spontaneous epimutations, can sustain phenotypic diversity. Here, potential sources of such stochastic epigenetic variability in animals are explored, with a focus on DNA methylation. To this day, quantifying the importance of stochasticity in epigenetic variability remains a challenge. However, comparisons between the mutation and the epimutation rates showed a high level of the latter, suggesting a significant role of spontaneous epimutations in adaptation. The implications of stochastic epigenetic variability are multifold: by affecting development and subsequently phenotype, random changes in epigenetic marks may provide additional phenotypic diversity, which can help natural populations when facing fluctuating environments. In isogenic lineages and asexually reproducing organisms, poor or absent genetic diversity can hence be tolerated. Further implication of stochastic epigenetic variability in adaptation is found in bottlenecked invasive species populations and populations using a bet-hedging strategy.
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Affiliation(s)
| | | | | | - F Silvestre
- Institute of Earth, Life and Environment (ILEE), University of Namur, 61 rue de Bruxelles, Namur, 5000, Belgium
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62
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Ivanova E, Canovas S, Garcia-Martínez S, Romar R, Lopes JS, Rizos D, Sanchez-Calabuig MJ, Krueger F, Andrews S, Perez-Sanz F, Kelsey G, Coy P. DNA methylation changes during preimplantation development reveal inter-species differences and reprogramming events at imprinted genes. Clin Epigenetics 2020; 12:64. [PMID: 32393379 PMCID: PMC7216732 DOI: 10.1186/s13148-020-00857-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/23/2020] [Indexed: 02/08/2023] Open
Abstract
Preimplantation embryos experience profound resetting of epigenetic information inherited from the gametes. Genome-wide analysis at single-base resolution has shown similarities but also species differences between human and mouse preimplantation embryos in DNA methylation patterns and reprogramming. Here, we have extended such analysis to two key livestock species, the pig and the cow. We generated genome-wide DNA methylation and whole-transcriptome datasets from gametes to blastocysts in both species. In oocytes from both species, a distinctive bimodal methylation landscape is present, with hypermethylated domains prevalent over hypomethylated domains, similar to human, while in the mouse the proportions are reversed.An oocyte-like pattern of methylation persists in the cleavage stages, albeit with some reduction in methylation level, persisting to blastocysts in cow, while pig blastocysts have a highly hypomethylated landscape. In the pig, there was evidence of transient de novo methylation at the 8-16 cell stages of domains unmethylated in oocytes, revealing a complex dynamic of methylation reprogramming. The methylation datasets were used to identify germline differentially methylated regions (gDMRs) of known imprinted genes and for the basis of detection of novel imprinted loci. Strikingly in the pig, we detected a consistent reduction in gDMR methylation at the 8-16 cell stages, followed by recovery to the blastocyst stage, suggesting an active period of imprint stabilization in preimplantation embryos. Transcriptome analysis revealed absence of expression in oocytes of both species of ZFP57, a key factor in the mouse for gDMR methylation maintenance, but presence of the alternative imprint regulator ZNF445. In conclusion, our study reveals species differences in DNA methylation reprogramming and suggests that porcine or bovine models may be closer to human in key aspects than in the mouse model.
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Affiliation(s)
- Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Sebastian Canovas
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Soledad Garcia-Martínez
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
| | - Raquel Romar
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Jordana S Lopes
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain
| | | | | | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Fernando Perez-Sanz
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
| | - Pilar Coy
- Physiology of Reproduction Group, Departamento de Fisiología, Universidad de Murcia, Campus Mare Nostrum, 30100, Murcia, Spain.
- Instituto Murciano de Investigación Biosanitaria, IMIB-Arrixaca-UMU, 30120, Murcia, Spain.
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Abstract
As the maternal–foetal interface, the placenta is essential for the establishment and progression of healthy pregnancy, regulating both foetal growth and maternal adaptation to pregnancy. The evolution and functional importance of genomic imprinting are inextricably linked to mammalian placentation. Recent technological advances in mapping and manipulating the epigenome in embryogenesis in mouse models have revealed novel mechanisms regulating genomic imprinting in placental trophoblast, the physiological implications of which are only just beginning to be explored. This review will highlight important recent discoveries and exciting new directions in the study of placental imprinting. The placenta is essential for healthy pregnancy because it supports the growth of the baby, helps the mother’s body adapt, and provides a connection between mother and the developing baby. Studying gene regulation and the early steps in placental development is challenging in human pregnancy, so mouse models have been key in building our understanding of these processes. In particular, these studies have identified a subset of genes that are essential for placentation, termed imprinted genes. Imprinted genes are those that are expressed from only one copy, depending on whether they were inherited from mom or dad. In this review, I describe recent novel approaches used to study the mechanisms regulating these imprinted genes in mouse models, and I highlight several new discoveries. It has become apparent that the regulation of imprinted genes in placenta is often unique from other tissues and that there are species-specific mechanisms allowing the evolution of new imprinted genes specifically in the placenta.
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Affiliation(s)
- Courtney W. Hanna
- Centre for Trophoblast Research, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- * E-mail:
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Tan JHL, Wollmann H, van Pelt AMM, Kaldis P, Messerschmidt DM. Infertility-Causing Haploinsufficiency Reveals TRIM28/KAP1 Requirement in Spermatogonia. Stem Cell Reports 2020; 14:818-827. [PMID: 32302554 PMCID: PMC7220855 DOI: 10.1016/j.stemcr.2020.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 01/21/2023] Open
Abstract
Spermatogenesis relies on exquisite stem cell homeostasis, the carefully balanced self-renewal and differentiation of spermatogonial stem cells (SSCs). Disturbing this equilibrium will likely manifest through sub- or infertility, a global health issue with often idiopathic presentation. In this respect, disease phenotypes caused by haploinsufficiency of otherwise vital developmental genes are of particular interest. Here, we show that mice heterozygous for Trim28, an essential epigenetic regulator, suffer gradual testicular degeneration. Contrary to previous reports we detect Trim28 expression in spermatogonia, albeit at low levels. Further reduction through Trim28 heterozygosity increases the propensity of SSCs to differentiate at the cost of self-renewal. TRIM28/KAP1 haploinsufficiency causes testicular degeneration and infertility TRIM28/KAP1 is expressed in spermatogonia stem cell compartment Stem cell homeostasis in the testis is dependent on proper TRIM28/KAP1 levels
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Affiliation(s)
- Joel H L Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore; NUS Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore 119077, Singapore
| | - Heike Wollmann
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Ans M M van Pelt
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore
| | - Daniel M Messerschmidt
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138673, Singapore.
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Abstract
In 1993, Denise Barlow proposed that genomic imprinting might have arisen from a host defense mechanism designed to inactivate retrotransposons. Although there were few examples at hand, she suggested that there should be maternal-specific and paternal-specific factors involved, with cognate imprinting boxes that they recognized; furthermore, the system should build on conserved biochemical factors, including DNA methylation, and maternal control should predominate for imprints. Here, we revisit this hypothesis in the light of recent advances in our understanding of host defense and DNA methylation and in particular, the link with Krüppel-associated box–zinc finger (KRAB-ZF) proteins.
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Affiliation(s)
- Miroslava Ondičová
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Rebecca J. Oakey
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Colum P. Walsh
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
- * E-mail:
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66
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Deng M, Liu Z, Chen B, Wan Y, Yang H, Zhang Y, Cai Y, Zhou J, Wang F. Aberrant DNA and histone methylation during zygotic genome activation in goat cloned embryos. Theriogenology 2020; 148:27-36. [PMID: 32126393 DOI: 10.1016/j.theriogenology.2020.02.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/17/2020] [Accepted: 02/22/2020] [Indexed: 01/23/2023]
Abstract
In somatic cell nuclear transfer (SCNT) embryos, developmental defects first appear at the time of zygotic genome activation (ZGA), a process that is under the control of DNA and histone methylation. However, dynamics of 5-mC and 5-hmC during ZGA differ between porcine and bovine SCNT embryos, and histone methylation during ZGA in goat SCNT embryos remains poorly understood. Therefore, in the present study, we investigated the dynamic changes of 5-mC, 5-hmC, H3K4me2/3, and H3K9me3, as well as the expression of key genes related to these epigenetic modifications, during ZGA in goat cloned embryos. Compared with the IVF embryos, the 5-mC signal intensity was significantly increased at the 2- and 4-cell stage SCNT embryos, and the H3K4me3 and H3K9me3 signal intensity was significantly increased at 2- to 8-cell stage SCNT embryos, while the 5-hmC and H3K4me2 signal intensity was significantly lower at the 4- and 8-cell stage SCNT embryos. Of note, the H3K9me3 level was also significantly higher, whereas H3K4me3 signal intensity showed no statistical difference in the pronuclear stage SCNT embryos. Moreover, the expression of TET2, DNMT3B, KDM4A, SUV39H1, G9A, and SETDB1 was significantly increased, while the expression of UHRF1, PCNA, KDM4B, KDM4D, KDM5A, KDM5B, and KDM5C was significantly decreased at the 8-cell stage SCNT embryos. Our data revealed aberrant DNA and histone methylation during ZGA in goat cloned embryos. We further inferred that the abnormally higher level of 5-mC, H3K4me3, and H3K9me3 might serve as epigenetic barriers of the reprogramming and modifying these aberrant modifications might be a promising strategy to improve cloning efficiency in goat.
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Affiliation(s)
- Mingtian Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zifei Liu
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baobao Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongjie Wan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Yang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Cai
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianguo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; National Experimental Teaching Demonstration Center of Animal Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Elbracht M, Mackay D, Begemann M, Kagan KO, Eggermann T. Disturbed genomic imprinting and its relevance for human reproduction: causes and clinical consequences. Hum Reprod Update 2020; 26:197-213. [DOI: 10.1093/humupd/dmz045] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/07/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022] Open
Abstract
Abstract
BACKGROUND
Human reproductive issues affecting fetal and maternal health are caused by numerous exogenous and endogenous factors, of which the latter undoubtedly include genetic changes. Pathogenic variants in either maternal or offspring DNA are associated with effects on the offspring including clinical disorders and nonviable outcomes. Conversely, both fetal and maternal factors can affect maternal health during pregnancy. Recently, it has become evident that mammalian reproduction is influenced by genomic imprinting, an epigenetic phenomenon that regulates the expression of genes according to their parent from whom they are inherited. About 1% of human genes are normally expressed from only the maternally or paternally inherited gene copy. Since numerous imprinted genes are involved in (embryonic) growth and development, disturbance of their balanced expression can adversely affect these processes.
OBJECTIVE AND RATIONALE
This review summarises current our understanding of genomic imprinting in relation to human ontogenesis and pregnancy and its relevance for reproductive medicine.
SEARCH METHODS
Literature databases (Pubmed, Medline) were thoroughly searched for the role of imprinting in human reproductive failure. In particular, the terms ‘multilocus imprinting disturbances, SCMC, NLRP/NALP, imprinting and reproduction’ were used in various combinations.
OUTCOMES
A range of molecular changes to specific groups of imprinted genes are associated with imprinting disorders, i.e. syndromes with recognisable clinical features including distinctive prenatal features. Whereas the majority of affected individuals exhibit alterations at single imprinted loci, some have multi-locus imprinting disturbances (MLID) with less predictable clinical features. Imprinting disturbances are also seen in some nonviable pregnancy outcomes, such as (recurrent) hydatidiform moles, which can therefore be regarded as a severe form of imprinting disorders. There is growing evidence that MLID can be caused by variants in the maternal genome altering the imprinting status of the oocyte and the embryo, i.e. maternal effect mutations. Pregnancies of women carrying maternal affect mutations can have different courses, ranging from miscarriages to birth of children with clinical features of various imprinting disorders.
WIDER IMPLICATIONS
Increasing understanding of imprinting disturbances and their clinical consequences have significant impacts on diagnostics, counselling and management in the context of human reproduction. Defining criteria for identifying pregnancies complicated by imprinting disorders facilitates early diagnosis and personalised management of both the mother and offspring. Identifying the molecular lesions underlying imprinting disturbances (e.g. maternal effect mutations) allows targeted counselling of the family and focused medical care in further pregnancies.
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Affiliation(s)
- Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Deborah Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Karl Oliver Kagan
- Obstetrics and Gynaecology, University Hospital of Tübingen, Tübingen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
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Hansel, Gretel, and the Consequences of Failing to Remove Histone Methylation Breadcrumbs. Trends Genet 2020; 36:160-176. [PMID: 32007289 PMCID: PMC10047806 DOI: 10.1016/j.tig.2019.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/20/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023]
Abstract
Like breadcrumbs in the forest, cotranscriptionally acquired histone methylation acts as a memory of prior transcription. Because it can be retained through cell divisions, transcriptional memory allows cells to coordinate complex transcriptional programs during development. However, if not reprogrammed properly during cell fate transitions, it can also disrupt cellular identity. In this review, we discuss the consequences of failure to reprogram histone methylation during three crucial epigenetic reprogramming windows: maternal reprogramming at fertilization, embryonic stem cell (ESC) differentiation, and the continuous maintenance of cell identity in differentiated cells. In addition, we discuss how following the wrong breadcrumb trail of transcriptional memory provides a framework for understanding how heterozygous loss-of-function mutations in histone-modifying enzymes may cause severe neurodevelopmental disorders.
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69
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Matsuzaki H, Kuramochi D, Okamura E, Hirakawa K, Ushiki A, Tanimoto K. Recapitulation of gametic DNA methylation and its post-fertilization maintenance with reassembled DNA elements at the mouse Igf2/H19 locus. Epigenetics Chromatin 2020; 13:2. [PMID: 31937365 PMCID: PMC6958606 DOI: 10.1186/s13072-019-0326-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/30/2019] [Indexed: 12/23/2022] Open
Abstract
Background Paternal allele-specific DNA methylation of the H19 imprinting control region (ICR) regulates imprinted expression of the Igf2/H19 genes. The molecular mechanism by which differential methylation of the H19 ICR is established during gametogenesis and maintained after fertilization, however, is not fully understood. We previously showed that a 2.9-kb H19 ICR fragment in transgenic mice was differentially methylated only after fertilization, demonstrating that two separable events, gametic and post-fertilization methylation, occur at the H19 ICR. We then determined that CTCF/Sox-Oct motifs and the 478-bp sequence of the H19 ICR are essential for maintaining its maternal hypomethylation status and for acquisition of paternal methylation, respectively, during the post-fertilization period. Results Using a series of 5′-truncated H19 ICR transgenes to dissect the 478-bp sequence, we identified a 118-bp region required for post-fertilization methylation activity. Deletion of the sequence from the paternal endogenous H19 ICR caused loss of methylation after fertilization, indicating that methylation activity of the sequence is required to protect endogenous H19 ICR from genome-wide reprogramming. We then reconstructed a synthetic DNA fragment in which the CTCF binding sites, Sox-Oct motifs, as well as the 118-bp sequence, were inserted into lambda DNA, and used it to replace the endogenous H19 ICR. The fragment was methylated during spermatogenesis; moreover, its allele-specific methylation status was faithfully maintained after fertilization, and imprinted expression of the both Igf2 and H19 genes was recapitulated. Conclusions Our results identified a 118-bp region within the H19 ICR that is required for de novo DNA methylation of the paternally inherited H19 ICR during pre-implantation period. A lambda DNA-based artificial fragment that contains the 118-bp sequence, in addition to the previously identified cis elements, could fully replace the function of the H19 ICR in the mouse genome.
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Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan
| | - Daichi Kuramochi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Eiichi Okamura
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Katsuhiko Hirakawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Aki Ushiki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan.
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70
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Wen L, Liu Q, Xu J, Liu X, Shi C, Yang Z, Zhang Y, Xu H, Liu J, Yang H, Huang H, Qiao J, Tang F, Chen ZJ. Recent advances in mammalian reproductive biology. SCIENCE CHINA. LIFE SCIENCES 2020; 63:18-58. [PMID: 31813094 DOI: 10.1007/s11427-019-1572-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/22/2019] [Indexed: 01/05/2023]
Abstract
Reproductive biology is a uniquely important topic since it is about germ cells, which are central for transmitting genetic information from generation to generation. In this review, we discuss recent advances in mammalian germ cell development, including preimplantation development, fetal germ cell development and postnatal development of oocytes and sperm. We also discuss the etiologies of female and male infertility and describe the emerging technologies for studying reproductive biology such as gene editing and single-cell technologies.
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Affiliation(s)
- Lu Wen
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qiang Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jingjing Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Xixi Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Chaoyi Shi
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Zuwei Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Yili Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Hong Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Hefeng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Zi-Jiang Chen
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250021, China.
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71
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Lee A, Zhu Y, Sabo Y, Goff SP. Embryonic Cells Redistribute SUMO1 upon Forced SUMO1 Overexpression. mBio 2019; 10:e01856-19. [PMID: 31796536 PMCID: PMC6890988 DOI: 10.1128/mbio.01856-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/23/2019] [Indexed: 12/28/2022] Open
Abstract
Conjugation of small ubiquitin-like modifiers (SUMOs) to substrate proteins is a posttranslational protein modification that affects a diverse range of physiological processes. Global inhibition of SUMO conjugation in mice results in embryonic lethality, reflecting the importance of the SUMO pathways for embryonic development. Here, we demonstrated that SUMO1 overexpression was not well tolerated in murine embryonic carcinoma and embryonic stem (ES) cells and that only a few clones were recovered after transduction with vectors delivering SUMO1 expression constructs. Differentiated NIH/3T3 cells overexpress SUMO1 without deleterious effects and maintain high levels of both conjugated and free forms of SUMO1. The few embryonic cells surviving after forced overexpression retained all their SUMO1 in the form of a few high-molecular-weight conjugates and maintained undetectable levels of free SUMO1. The absence of free SUMO in embryonic cells was seen specifically upon overexpression of SUMO1, but not SUMO2. Moreover, blocking SUMO1 conjugation to endogenous substrates by C-terminal mutations of SUMO1 or by overexpression of a SUMO1 substrate "sponge" or by overexpression of the deSUMOylating enzyme SUMO-specific peptidase 1 (SENP1) dramatically restored free SUMO1 overexpression. The data suggest that overexpression of SUMO1 protein leading to an excess accumulation of critical SUMO1-conjugated substrates is not tolerated in embryonic cells. Surviving embryonic cells exhibit SUMO1 conjugation to allowed substrates but a complete absence of free SUMO1.IMPORTANCE Embryonic stem (ES) cells exhibit unusual transcriptional, proteomic, and signal response profiles, reflecting their unusual needs for rapid differentiation and replication. The work reported here demonstrated that mouse embryonic cell lines did not tolerate the overexpression of SUMO1, the small ubiquitin-like modifier protein that is covalently attached to many substrates to alter their intracellular localization and functionality. Forced SUMO1 overexpression is toxic to ES cells, and surviving cell populations adapt by dramatically reducing the levels of free SUMO1. Such a response is not seen in differentiated cells or with SUMO2 or with nonconjugatable SUMO1 mutants or in the presence of a SUMO1 "sponge" substrate that accepts the modification. The findings suggest that excess SUMO1 modification of specific substrates is not tolerated by embryonic cells and highlight a distinctive need for these cells to control the levels of SUMO1 available for conjugation.
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Affiliation(s)
- Andreia Lee
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Yiping Zhu
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York, New York, USA
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Yosef Sabo
- Department of Medicine, Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York, New York, USA
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Columbia University Medical Center, Columbia University, New York, New York, USA
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Farhadova S, Gomez-Velazquez M, Feil R. Stability and Lability of Parental Methylation Imprints in Development and Disease. Genes (Basel) 2019; 10:genes10120999. [PMID: 31810366 PMCID: PMC6947649 DOI: 10.3390/genes10120999] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
DNA methylation plays essential roles in mammals. Of particular interest are parental methylation marks that originate from the oocyte or the sperm, and bring about mono-allelic gene expression at defined chromosomal regions. The remarkable somatic stability of these parental imprints in the pre-implantation embryo—where they resist global waves of DNA demethylation—is not fully understood despite the importance of this phenomenon. After implantation, some methylation imprints persist in the placenta only, a tissue in which many genes are imprinted. Again here, the underlying epigenetic mechanisms are not clear. Mouse studies have pinpointed the involvement of transcription factors, covalent histone modifications, and histone variants. These and other features linked to the stability of methylation imprints are instructive as concerns their conservation in humans, in which different congenital disorders are caused by perturbed parental imprints. Here, we discuss DNA and histone methylation imprints, and why unravelling maintenance mechanisms is important for understanding imprinting disorders in humans.
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74
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Liu H, Chen H, Deng X, Peng Y, Zeng Q, Song Z, He W, Zhang L, Xiao T, Gao G, Li B. Knockdown of TRIM28 inhibits PDGF-BB-induced vascular smooth muscle cell proliferation and migration. Chem Biol Interact 2019; 311:108772. [PMID: 31351049 DOI: 10.1016/j.cbi.2019.108772] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/04/2019] [Accepted: 07/24/2019] [Indexed: 11/18/2022]
Abstract
Atherosclerosis is a common type of cardiovascular disease (CVD), remaining one of the leading causes of global death. Tripartite motif-containing 28 (TRIM28) is a member of TRIM family that has been found to be involved in atherosclerosis. However, the role of TRIM28 in atherosclerosis remains unknown. This study aimed to investigate the effects of TRIM28 on the phenotypic switching of human aortic smooth muscle cells (HASMCs), which is considered as a fundamental event during the development of atherosclerosis. The results showed that TRIM28 was highly expressed in human atherosclerotic tissues, as well in cultured HASMCs stimulated by platelet-derived growth factor subunit B homodimer (PDGF-BB). Knockdown of TRIM28 by transfection with siRNA targeting TRIM28 (si-TRIM28) significantly suppressed the PDGF-BB-induced cell proliferation and migration of HASMCs. Besides, knockdown of TRIM28 inhibited the expressions of matrix metalloproteinase (MMP)-2 and MMP-9. The VSMC markers including α-smooth muscle actin (α-SMA), calponin and SM22α were upregulated in TRIM28 knocked down HASMCs. Furthermore, knockdown of TRIM28 blocked PDGF-BB-induced NF-κB activation in HASMCs. Collectively, knockdown of TRIM28 prevented PDGF-BB-induced phenotypic switching of HASMCs, which might be mediated by the regulation of NF-κB signaling pathway.
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Affiliation(s)
- Hongtao Liu
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China.
| | - Hongwei Chen
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China
| | - Xia Deng
- Pharmacy Department, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China
| | - Yudong Peng
- Department of Institute of Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei Province, China
| | - Qiutang Zeng
- Department of Institute of Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei Province, China
| | - Zongren Song
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China
| | - Wenping He
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China
| | - Le Zhang
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China
| | - Ting Xiao
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China
| | - Gan Gao
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China
| | - Bailin Li
- Department of Cardiovascular Medicine, Shenzhen Longhua District Central Hospital, Longhua Central Hospital Affiliated Guangdong Medical University, Shenzhen, 518110, Guangdong Province, China
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75
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The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol 2019; 20:590-607. [PMID: 31399642 DOI: 10.1038/s41580-019-0159-6] [Citation(s) in RCA: 1129] [Impact Index Per Article: 225.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.
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76
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ZFP57 regulation of transposable elements and gene expression within and beyond imprinted domains. Epigenetics Chromatin 2019; 12:49. [PMID: 31399135 PMCID: PMC6688207 DOI: 10.1186/s13072-019-0295-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND KRAB zinc finger proteins (KZFPs) represent one of the largest families of DNA-binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. ZFP57 is required to maintain the post-fertilization DNA methylation memory of parental origin at genomic imprints. Here we conduct RNA-seq and ChIP-seq analyses in normal and ZFP57 mutant mouse ES cells to understand the relative importance of ZFP57 at imprints, unique and repetitive regions of the genome. RESULTS Over 80% of ZFP57 targets are TEs, however, ZFP57 is not essential for their repression. The remaining targets lie within unique imprinted and non-imprinted sequences. Though the loss of ZFP57 influences imprinted genes as expected, the majority of unique gene targets lose H3K9me3 with little effect on DNA methylation and very few exhibit alterations in expression. Comparison of ZFP57 mutants with DNA methyltransferase-deleted ES cells (TKO) identifies a remarkably similar pattern of H3K9me3 loss across the genome. These data define regions where H3K9me3 is secondary to DNA methylation and we propose that ZFP57 is the principal if not sole methylation-sensitive KZFP in mouse ES cells. Finally, we examine dynamics of DNA and H3K9 methylation during pre-implantation development and show that sites bound by ZFP57 in ES cells maintain DNA methylation and H3K9me3 at imprints and at non-imprinted regions on the maternally inherited chromosome throughout preimplantation development. CONCLUSION Our analyses suggest the evolution of a rare DNA methylation-sensitive KZFP that is not essential for repeat silencing, but whose primary function is to maintain DNA methylation and repressive histone marks at germline-derived imprinting control regions.
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77
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Genomic imprinting disorders: lessons on how genome, epigenome and environment interact. Nat Rev Genet 2019; 20:235-248. [PMID: 30647469 DOI: 10.1038/s41576-018-0092-0] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genomic imprinting, the monoallelic and parent-of-origin-dependent expression of a subset of genes, is required for normal development, and its disruption leads to human disease. Imprinting defects can involve isolated or multilocus epigenetic changes that may have no evident genetic cause, or imprinting disruption can be traced back to alterations of cis-acting elements or trans-acting factors that control the establishment, maintenance and erasure of germline epigenetic imprints. Recent insights into the dynamics of the epigenome, including the effect of environmental factors, suggest that the developmental outcomes and heritability of imprinting disorders are influenced by interactions between the genome, the epigenome and the environment in germ cells and early embryos.
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78
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Seah MKY, Wang Y, Goy PA, Loh HM, Peh WJ, Low DHP, Han BY, Wong E, Leong EL, Wolf G, Mzoughi S, Wollmann H, Macfarlan TS, Guccione E, Messerschmidt DM. The KRAB-zinc-finger protein ZFP708 mediates epigenetic repression at RMER19B retrotransposons. Development 2019; 146:dev.170266. [PMID: 30846446 PMCID: PMC6803371 DOI: 10.1242/dev.170266] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022]
Abstract
Global epigenetic reprogramming is vital to purge germ cell-specific epigenetic features to establish the totipotent state of the embryo. This process transpires to be carefully regulated and is not an undirected, radical erasure of parental epigenomes. The TRIM28 complex has been shown to be crucial in embryonic epigenetic reprogramming by regionally opposing DNA demethylation to preserve vital parental information to be inherited from germline to soma. Yet the DNA-binding factors guiding this complex to specific targets are largely unknown. Here, we uncover and characterize a novel, maternally expressed, TRIM28-interacting KRAB zinc-finger protein: ZFP708. It recruits the repressive TRIM28 complex to RMER19B retrotransposons to evoke regional heterochromatin formation. ZFP708 binding to these hitherto unknown TRIM28 targets is DNA methylation and H3K9me3 independent. ZFP708 mutant mice are viable and fertile, yet embryos fail to inherit and maintain DNA methylation at ZFP708 target sites. This can result in activation of RMER19B-adjacent genes, while ectopic expression of ZFP708 results in transcriptional repression. Finally, we describe the evolutionary conservation of ZFP708 in mice and rats, which is linked to the conserved presence of the targeted RMER19B retrotransposons in these species. Summary: Analysis of the function and targets of a maternal KRAB-zinc-finger protein, ZFP708, found to specifically mediate maintenance of DNA methylation at a subset of LTR retrotransposons during embryonic epigenetic reprogramming.
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Affiliation(s)
- Michelle K Y Seah
- Developmental Epigenetics and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Yaju Wang
- Developmental Epigenetics and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Pierre-Alexis Goy
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore
| | - Hui Mun Loh
- Developmental Epigenetics and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Wen Jun Peh
- Developmental Epigenetics and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Diana H P Low
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Brenda Y Han
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Esther Wong
- KOre - Knock Out resource, IMB, A*STAR, 138648, Singapore
| | - Ei Leen Leong
- KOre - Knock Out resource, IMB, A*STAR, 138648, Singapore
| | - Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Slim Mzoughi
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore
| | - Heike Wollmann
- NGS Unit of DNA Sequencing Facility, IMCB, A*STAR, 138673, Singapore
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Ernesto Guccione
- Methyltransferases in Development and Disease Group, IMCB, A*STAR, 138673, Singapore
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79
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Gheldof A, Mackay DJG, Cheong Y, Verpoest W. Genetic diagnosis of subfertility: the impact of meiosis and maternal effects. J Med Genet 2019; 56:271-282. [PMID: 30728173 PMCID: PMC6581078 DOI: 10.1136/jmedgenet-2018-105513] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 12/24/2018] [Accepted: 12/27/2018] [Indexed: 02/06/2023]
Abstract
During reproductive age, approximately one in seven couples are confronted with fertility problems. While the aetiology is diverse, including infections, metabolic diseases, hormonal imbalances and iatrogenic effects, it is becoming increasingly clear that genetic factors have a significant contribution. Due to the complex nature of infertility that often hints at a multifactorial cause, the search for potentially causal gene mutations in idiopathic infertile couples has remained difficult. Idiopathic infertility patients with a suspicion of an underlying genetic cause can be expected to have mutations in genes that do not readily affect general health but are only essential in certain processes connected to fertility. In this review, we specifically focus on genes involved in meiosis and maternal-effect processes, which are of critical importance for reproduction and initial embryonic development. We give an overview of genes that have already been linked to infertility in human, as well as good candidates which have been described in other organisms. Finally, we propose a phenotypic range in which we expect an optimal diagnostic yield of a meiotic/maternal-effect gene panel.
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Affiliation(s)
- Alexander Gheldof
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Brussels, Belgium
- Reproduction and Genetics Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Deborah J G Mackay
- Faculty of Medicine, University of Southampton, Southampton University Hospital, Southampton, UK
| | - Ying Cheong
- Complete Fertility, Human Development of Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Willem Verpoest
- Reproduction and Genetics Department, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, Brussels, Belgium
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80
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Zeng Y, Chen T. DNA Methylation Reprogramming during Mammalian Development. Genes (Basel) 2019; 10:E257. [PMID: 30934924 PMCID: PMC6523607 DOI: 10.3390/genes10040257] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
DNA methylation (5-methylcytosine, 5mC) is a major form of DNA modification in the mammalian genome that plays critical roles in chromatin structure and gene expression. In general, DNA methylation is stably maintained in somatic tissues. However, DNA methylation patterns and levels show dynamic changes during development. Specifically, the genome undergoes two waves of global demethylation and remethylation for the purpose of producing the next generation. The first wave occurs in the germline, initiated with the erasure of global methylation in primordial germ cells (PGCs) and completed with the establishment of sex-specific methylation patterns during later stages of germ cell development. The second wave occurs after fertilization, including the erasure of most methylation marks inherited from the gametes and the subsequent establishment of the embryonic methylation pattern. The two waves of DNA methylation reprogramming involve both distinct and shared mechanisms. In this review article, we provide an overview of the key reprogramming events, focusing on the important players in these processes, including DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) family of 5mC dioxygenases.
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Affiliation(s)
- Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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81
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Smith HL, Stevens A, Minogue B, Sneddon S, Shaw L, Wood L, Adeniyi T, Xiao H, Lio P, Kimber SJ, Brison DR. Systems based analysis of human embryos and gene networks involved in cell lineage allocation. BMC Genomics 2019; 20:171. [PMID: 30836937 PMCID: PMC6399968 DOI: 10.1186/s12864-019-5558-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Little is understood of the molecular mechanisms involved in the earliest cell fate decision in human development, leading to the establishment of the trophectoderm (TE) and inner cell mass (ICM) stem cell population. Notably, there is a lack of understanding of how transcriptional networks arise during reorganisation of the embryonic genome post-fertilisation. RESULTS We identified a hierarchical structure of preimplantation gene network modules around the time of embryonic genome activation (EGA). Using network models along with eukaryotic initiation factor (EIF) and epigenetic-associated gene expression we defined two sets of blastomeres that exhibited diverging tendencies towards ICM or TE. Analysis of the developmental networks demonstrated stage specific EIF expression and revealed that histone modifications may be an important epigenetic regulatory mechanism in preimplantation human embryos. Comparison to published RNAseq data confirmed that during EGA the individual 8-cell blastomeres are transcriptionally primed for the first lineage decision in development towards ICM or TE. CONCLUSIONS Using multiple systems biology approaches to compare developmental stages in the early human embryo with single cell transcript data from blastomeres, we have shown that blastomeres considered to be totipotent are not transcriptionally equivalent. Furthermore we have linked the developmental interactome to individual blastomeres and to later cell lineage. This has clinical implications for understanding the impact of fertility treatments and developmental programming of long term health.
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Affiliation(s)
- H. L. Smith
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - A. Stevens
- Division of Developmental Biology & Medicine, School of Medical Sciences, University of Manchester, Manchester Academic Health Sciences Centre, 5th Floor Research, Royal Manchester Children’s Hospital, Oxford Road, Manchester, M13 9WL UK
| | - B. Minogue
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - S. Sneddon
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - L. Shaw
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - L. Wood
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - T. Adeniyi
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - H. Xiao
- Computer Laboratory, William Gates Building, University of Cambridge, Cambridge, UK
| | - P. Lio
- Computer Laboratory, William Gates Building, University of Cambridge, Cambridge, UK
| | - S. J. Kimber
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
| | - D. R. Brison
- Maternal and Fetal Health Research Centre, University of Manchester, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
- Department of Reproductive Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Oxford Road, Manchester, M13 9WL UK
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82
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Yang CH, Andrew Pospisilik J. Polyphenism - A Window Into Gene-Environment Interactions and Phenotypic Plasticity. Front Genet 2019; 10:132. [PMID: 30863426 PMCID: PMC6399471 DOI: 10.3389/fgene.2019.00132] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/08/2019] [Indexed: 02/01/2023] Open
Abstract
Phenotypic plasticity describes the capacity of a single genotype to exhibit a variety of phenotypes as well as the mechanisms that translate environmental variation into reproducible phenotypic modifications. Polyphenism describes the unique sub-type of phenotypic plasticity where the outputs are not continuous, but rather discrete and multi-stable, resulting in several distinct phenotypes on the same genetic background. Epigenetic regulation underpins the stable phenotypic divergences that exemplify polyphenism and their evolutionary origin. Here, we briefly summarize the apparent ubiquity and diversity of polyphenisms across the animal kingdom. We briefly review the best characterized models across taxa and highlight the consistent themes both in their epidemiology and what little we know about molecular mechanisms. Finally, we highlight work that supports the possibility that humans may have a subtle polyphenism at the level of metabolism.
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Affiliation(s)
- Chih-Hsiang Yang
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Van Andel Research Institute, Grand Rapids, MI, United States
| | - John Andrew Pospisilik
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Van Andel Research Institute, Grand Rapids, MI, United States
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83
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Diets IJ, Hoyer J, Ekici AB, Popp B, Hoogerbrugge N, van Reijmersdal SV, Bhaskaran R, Hadjihannas M, Vasileiou G, Thiel CT, Seven D, Uebe S, Ilencikova D, Waanders E, Mavinkurve-Groothuis AMC, Roeleveld N, de Krijger RR, Wegert J, Graf N, Vokuhl C, Agaimy A, Gessler M, Reis A, Kuiper RP, Jongmans MCJ, Metzler M. TRIM28 haploinsufficiency predisposes to Wilms tumor. Int J Cancer 2019; 145:941-951. [PMID: 30694527 DOI: 10.1002/ijc.32167] [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] [Received: 10/08/2018] [Revised: 12/08/2018] [Accepted: 01/15/2019] [Indexed: 12/21/2022]
Abstract
Two percent of patients with Wilms tumors have a positive family history. In many of these cases the genetic cause remains unresolved. By applying germline exome sequencing in two families with two affected individuals with Wilms tumors, we identified truncating mutations in TRIM28. Subsequent mutational screening of germline and tumor DNA of 269 children affected by Wilms tumor was performed, and revealed seven additional individuals with germline truncating mutations, and one individual with a somatic truncating mutation in TRIM28. TRIM28 encodes a complex scaffold protein involved in many different processes, including gene silencing, DNA repair and maintenance of genomic integrity. Expression studies on mRNA and protein level showed reduction of TRIM28, confirming a loss-of-function effect of the mutations identified. The tumors showed an epithelial-type histology that stained negative for TRIM28 by immunohistochemistry. The tumors were bilateral in six patients, and 10/11 tumors are accompanied by perilobar nephrogenic rests. Exome sequencing on eight tumor DNA samples from six individuals showed loss-of-heterozygosity (LOH) of the TRIM28-locus by mitotic recombination in seven tumors, suggesting that TRIM28 functions as a tumor suppressor gene in Wilms tumor development. Additionally, the tumors showed very few mutations in known Wilms tumor driver genes, suggesting that loss of TRIM28 is the main driver of tumorigenesis. In conclusion, we identified heterozygous germline truncating mutations in TRIM28 in 11 children with mainly epithelial-type Wilms tumors, which become homozygous in tumor tissue. These data establish TRIM28 as a novel Wilms tumor predisposition gene, acting as a tumor suppressor gene by LOH.
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Affiliation(s)
- Illja J Diets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Juliane Hoyer
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Arif B Ekici
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Bernt Popp
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Simon V van Reijmersdal
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Rajith Bhaskaran
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Michel Hadjihannas
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Georgia Vasileiou
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Christian T Thiel
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Didem Seven
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany.,Department of Medical Biology, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Steffen Uebe
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Denisa Ilencikova
- Department of Pediatrics, Children's University Hospital, Comenius University, Bratislava, Slovakia
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Nel Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands.,Department of Pediatrics, Radboudumc Amalia's Children's Hospital, Nijmegen, The Netherlands
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Norbert Graf
- Department of Pediatric Hematology and Oncology, Saarland University, Medical Center Homburg/Saar, Homburg, Germany
| | - Christian Vokuhl
- Kiel Pediatric Tumor Registry, Section of Pediatric Pathology, Department of Pathology, Christian Albrechts University, Kiel, Germany
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, and Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - André Reis
- Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Institute of Human Genetics, Erlangen, Germany
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Markus Metzler
- Department of Pediatrics and Adolescent Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
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Singh PB, Shloma VV, Belyakin SN. Maternal regulation of chromosomal imprinting in animals. Chromosoma 2019; 128:69-80. [PMID: 30719566 PMCID: PMC6536480 DOI: 10.1007/s00412-018-00690-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/24/2018] [Accepted: 12/28/2018] [Indexed: 11/29/2022]
Abstract
Chromosomal imprinting requires an epigenetic system that "imprints" one of the two parental chromosomes such that it results in a heritable (cell-to-cell) change in behavior of the "imprinted" chromosome. Imprinting takes place when the parental genomes are separate, which occurs during gamete formation in the respective germ-lines and post-fertilization during the period when the parental pro-nuclei lie separately within the ooplasm of the zygote. In the mouse, chromosomal imprinting is regulated by germ-line specific DNA methylation. But the methylation machinery in the respective germ-lines does not discriminate between imprinted and non-imprinted regions. As a consequence, the mouse oocyte nucleus contains over a thousand oocyte-specific germ-line differentially methylated regions (gDMRs). Upon fertilization, the sperm provides a few hundred sperm-specific gDMRs of its own. Combined, there are around 1600 imprinted and non-imprinted gDMRs in the pro-nuclei of the newly fertilized zygote. It is a remarkable fact that beginning in the maternal ooplasm, there are mechanisms that manage to preserve DNA methylation at ~ 26 known imprinted gDMRs in the face of the ongoing genome-wide DNA de-methylation that characterizes pre-implantation development. Specificity is achieved through the binding of KRAB-zinc finger proteins to their cognate recognition sequences within the gDMRs of imprinted genes. This in turn nucleates the assembly of localized heterochromatin-like complexes that preserve methylation at imprinted gDMRs through recruitment of the maintenance methyl transferase Dnmt1. These studies have shown that a germ-line imprint may cause parent-of-origin-specific behavior only if "licensed" by mechanisms that operate post-fertilization. Study of the germ-line and post-fertilization contributions to the imprinting of chromosomes in classical insect systems (Coccidae and Sciaridae) show that the ooplasm is the likely site where imprinting takes place. By comparing molecular and genetic studies across these three species, we suggest that mechanisms which operate post-fertilization play a key role in chromosomal imprinting phenomena in animals and conserved components of heterochromatin are shared by these mechanisms.
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Affiliation(s)
- Prim B Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Astana, Z05K4F4, Kazakhstan.
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation.
| | - Victor V Shloma
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation
- Genomics Laboratory, Institute of Molecular and Cellular Biology SD RAS, Lavrentyev ave, 8/2, Novosibirsk, 630090, Russian Federation
| | - Stepan N Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation
- Genomics Laboratory, Institute of Molecular and Cellular Biology SD RAS, Lavrentyev ave, 8/2, Novosibirsk, 630090, Russian Federation
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85
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Abstract
SummaryTRIM28/KAP1/TIF1β was identified as a universal transcriptional co-repressor and is critical for regulating post-fertilization methylation reprogramming in preimplantation embryos. In this study, three siRNAs (si647, si742, and si1153) were designed to target the TRIM28 mRNA sequence. After transfection of the mixture of the three siRNA (siMix) into bovine fibroblast cells, the most effective one for TRIM28 knockdown was selected. By injecting RNAi directed against TRIM28 mRNA, we found that TRIM28 knockdown in oocytes had the most effect on the H19 gene, in which differentially methylated region (DMR) methylation was almost completely absent at the 2-cell stage (1.4%), while control embryos showed 74% methylation. In addition, global H3K9me3 levels at the 2-cell stage were significantly higher in the in vitro fertilization (IVF) group than in the TRIM28 knockdown group (P<0.05). We further show that TRIM28 is highly expressed during oocyte maturation and reaches peak levels at the 2-cell stage. In contrast, at this stage, TRIM28 expression in somatic cell nuclear transfer (SCNT) embryos decreased significantly (P<0.05), suggesting that Trim28 transcripts are lost during SCNT. TRIM28 is required for the maintenance of methylation imprints in bovine preimplantation embryos, and the loss of TRIM28 during SCNT may contribute to the unfaithful maintenance of imprints in cloned embryos.
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86
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Li J, Shen H, Xie H, Ying Y, Jin K, Yan H, Wang S, Xu M, Wang X, Xu X, Xie L. Dysregulation of ncRNAs located at the DLK1‑DIO3 imprinted domain: involvement in urological cancers. Cancer Manag Res 2019; 11:777-787. [PMID: 30697070 PMCID: PMC6339654 DOI: 10.2147/cmar.s190764] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genomic imprinting has been found to be involved in human physical development and several diseases. The DLK1-DIO3 imprinted domain is located on human chromosome 14 and contains paternally expressed protein-coding genes (DLK1, RTL1, DIO3) and numerous maternally expressed ncRNA genes (MEG3, MEG8, antisense RTL1, miRNAs, piRNAs, and snoRNAs). Emerging evidence has implicated that dysregulation of the DLK1-DIO3 imprinted domain especially the imprinted ncRNAs is critical for tumor progressions. Multiple miRNAs and lncRNAs have been investigated in urological cancers, of which several are transcribed from this domain. In this review, we present current data about the associated miRNAs, lncRNAs, and piRNAs and the regulation of differentially methylated regions methylation status in the progression of urological cancers and preliminarily propose certain concepts about the potential regulatory networks involved in DLK1-DIO3 imprinted domain.
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Affiliation(s)
- Jiangfeng Li
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Haixiang Shen
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Haiyun Xie
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Yufan Ying
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Ke Jin
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Huaqing Yan
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Song Wang
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Mingjie Xu
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Xiao Wang
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Xin Xu
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
| | - Liping Xie
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China, ;
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87
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Jarred EG, Bildsoe H, Western PS. Out of sight, out of mind? Germ cells and the potential impacts of epigenomic drugs. F1000Res 2018; 7. [PMID: 30613387 PMCID: PMC6305226 DOI: 10.12688/f1000research.15935.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications, including DNA methylation and histone modifications, determine the way DNA is packaged within the nucleus and regulate cell-specific gene expression. The heritability of these modifications provides a memory of cell identity and function. Common dysregulation of epigenetic modifications in cancer has driven substantial interest in the development of epigenetic modifying drugs. Although these drugs have the potential to be highly beneficial for patients, they act systemically and may have “off-target” effects in other cells such as the patients’ sperm or eggs. This review discusses the potential for epigenomic drugs to impact on the germline epigenome and subsequent offspring and aims to foster further examination into the possible effects of these drugs on gametes. Ultimately, the information gained by further research may improve the clinical guidelines for the use of such drugs in patients of reproductive age.
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Affiliation(s)
- Ellen G Jarred
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia
| | - Heidi Bildsoe
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia
| | - Patrick S Western
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia
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88
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Chen F, Fu Q, Pu L, Zhang P, Huang Y, Hou Z, Xu Z, Chen D, Huang F, Deng T, Liang X, Lu Y, Zhang M. Integrated Analysis of Quantitative Proteome and Transcriptional Profiles Reveals the Dynamic Function of Maternally Expressed Proteins After Parthenogenetic Activation of Buffalo Oocyte. Mol Cell Proteomics 2018; 17:1875-1891. [PMID: 30002204 PMCID: PMC6166679 DOI: 10.1074/mcp.ra118.000556] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/16/2018] [Indexed: 01/09/2023] Open
Abstract
Maternal-effect genes are especially critical for early embryonic development after fertilization and until massive activation of the embryonic genome occurs. By applying a tandem mass tag (TMT)-labeled quantitative proteomics combined with RNA sequencing approach, the proteome of the buffalo was quantitatively analyzed during parthenogenesis of mature oocytes and the two-cell stage embryo. Of 1908 quantified proteins, 123 differed significantly. The transcriptome was analyzed eight stages (GV, MII, 2-cell, 4-cell, 8-cell, 16-cell, morula, blastocyst) of Buffalo using the RNA sequencing approach, and a total of 3567 unique genes were identified to be differently expressed between all consecutive stages of pre-implantation development. Validation of proteomics results (TUBB3, CTNNA1, CDH3, MAP2K1), which are involved in tight junction and gap junction, revealing that the maternal expression of the proteins possibly plays a role in the formation of cellular junctions firstly after parthenogenetic activation. Correlation and hierarchical analyses of transcriptional profiles and the expression of NPM2 and NLRP5 mRNA of buffalo in vitro developed oocytes and parthenogenetic embryos indicated that the "maternal-to-zygotic transition" (MZT) process might exist in the model of parthenogenesis, which is similar to a normally fertilized embryo, and may occur between the 8-cell to 16-cell stage. These data provide a rich resource for further studies on maternal proteins and genes and are conducive to improving nuclear transfer technology.
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Affiliation(s)
- Fumei Chen
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Qiang Fu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Liping Pu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Pengfei Zhang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Yulin Huang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhen Hou
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhuangzhuang Xu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Dongrong Chen
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Fengling Huang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China
| | - Tingxian Deng
- §Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, Guangxi 530001, China
| | - Xianwei Liang
- §Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, Guangxi 530001, China
| | - Yangqing Lu
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China;
| | - Ming Zhang
- From the ‡State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource, Animal Reproduction Institute, Guangxi University, Nanning, Guangxi 530004, China;
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89
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Abstract
Epigenetic mechanisms allow the establishment and maintenance of multiple cellular phenotypes from a single genomic code. At the initiation of development, the oocyte and spermatozoa provide their fully differentiated chromatin that soon after fertilization undergo extensive remodeling, resulting in a totipotent state that can then drive cellular differentiation towards all cell types. These remodeling involves different epigenetic modifications, including DNA methylation, post-translational modifications of histones, non-coding RNAs, and large-scale chromatin conformation changes. Moreover, epigenetic remodeling is responsible for reprogramming somatic cells to totipotency upon somatic cell nuclear transfer/cloning, which is often incomplete and inefficient. Given that environmental factors, such as assisted reproductive techniques (ARTs), can affect epigenetic remodeling, there is interest in understanding the mechanisms driving these changes. We describe and discuss our current understanding of mechanisms responsible for the epigenetic remodeling that ensues during preimplantation development of mammals, presenting findings from studies of mouse embryos and when available comparing them to what is known for human and cattle embryos.
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Affiliation(s)
- Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, CA, United States
| | - Rafael V Sampaio
- Department of Animal Science, University of California Davis, Davis, CA, United States.,Department of Animal Science, University of California Davis, Davis, CA, United States
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90
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Hanna CW, Demond H, Kelsey G. Epigenetic regulation in development: is the mouse a good model for the human? Hum Reprod Update 2018; 24:556-576. [PMID: 29992283 PMCID: PMC6093373 DOI: 10.1093/humupd/dmy021] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/20/2018] [Accepted: 06/05/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Over the past few years, advances in molecular technologies have allowed unprecedented mapping of epigenetic modifications in gametes and during early embryonic development. This work is allowing a detailed genomic analysis, which for the first time can answer long-standing questions about epigenetic regulation and reprogramming, and highlights differences between mouse and human, the implications of which are only beginning to be explored. OBJECTIVE AND RATIONALE In this review, we summarise new low-cell molecular methods enabling the interrogation of epigenetic information in gametes and early embryos, the mechanistic insights these have provided, and contrast the findings in mouse and human. SEARCH METHODS Relevant studies were identified by PubMed search. OUTCOMES We discuss the levels of epigenetic regulation, from DNA modifications to chromatin organisation, during mouse gametogenesis, fertilisation and pre- and post-implantation development. The recently characterised features of the oocyte epigenome highlight its exceptionally unique regulatory landscape. The chromatin organisation and epigenetic landscape of both gametic genomes are rapidly reprogrammed after fertilisation. This extensive epigenetic remodelling is necessary for zygotic genome activation, but the mechanistic link remains unclear. While the vast majority of epigenetic information from the gametes is erased in pre-implantation development, new insights suggest that repressive histone modifications from the oocyte may mediate a novel mechanism of imprinting. To date, the characterisation of epigenetics in human development has been almost exclusively limited to DNA methylation profiling; these data reinforce that the global dynamics are conserved between mouse and human. However, as we look closer, it is becoming apparent that the mechanisms regulating these dynamics are distinct. These early findings emphasise the importance of investigations of fundamental epigenetic mechanisms in both mouse and humans. WIDER IMPLICATIONS Failures in epigenetic regulation have been implicated in human disease and infertility. With increasing maternal age and use of reproductive technologies in countries all over the world, it is becoming ever more important to understand the necessary processes required to establish a developmentally competent embryo. Furthermore, it is essential to evaluate the extent to which these epigenetic patterns are sensitive to such technologies and other adverse environmental exposures.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Hannah Demond
- Epigenetics programme, Babraham Institute, Cambridge, UK
| | - Gavin Kelsey
- Epigenetics programme, Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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91
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SanMiguel JM, Bartolomei MS. DNA methylation dynamics of genomic imprinting in mouse development. Biol Reprod 2018; 99:252-262. [PMID: 29462489 PMCID: PMC6044325 DOI: 10.1093/biolre/ioy036] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 01/05/2023] Open
Abstract
DNA methylation is an essential epigenetic mark crucial for normal mammalian development. This modification controls the expression of a unique class of genes, designated as imprinted, which are expressed monoallelically and in a parent-of-origin-specific manner. Proper parental allele-specific DNA methylation at imprinting control regions (ICRs) is necessary for appropriate imprinting. Processes that deregulate DNA methylation of imprinted loci cause disease in humans. DNA methylation patterns dramatically change during mammalian development: first, the majority of the genome, with the exception of ICRs, is demethylated after fertilization, and subsequently undergoes genome-wide de novo DNA methylation. Secondly, after primordial germ cells are specified in the embryo, another wave of demethylation occurs, with ICR demethylation occurring late in the process. Lastly, ICRs reacquire DNA methylation imprints in developing germ cells. We describe the past discoveries and current literature defining these crucial dynamics in relation to imprinted genes and the rest of the genome.
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Affiliation(s)
- Jennifer M SanMiguel
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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92
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Matsuzaki H, Okamura E, Kuramochi D, Ushiki A, Hirakawa K, Fukamizu A, Tanimoto K. Synthetic DNA fragments bearing ICR cis elements become differentially methylated and recapitulate genomic imprinting in transgenic mice. Epigenetics Chromatin 2018; 11:36. [PMID: 29958543 PMCID: PMC6027785 DOI: 10.1186/s13072-018-0207-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/01/2018] [Indexed: 11/24/2022] Open
Abstract
Background Genomic imprinting is governed by allele-specific DNA methylation at imprinting control regions (ICRs), and the mechanism controlling its differential methylation establishment during gametogenesis has been a subject of intensive research interest. However, recent studies have reported that gamete methylation is not restricted at the ICRs, thus highlighting the significance of ICR methylation maintenance during the preimplantation period where genome-wide epigenetic reprogramming takes place. Using transgenic mice (TgM), we previously demonstrated that the H19 ICR possesses autonomous activity to acquire paternal-allele-specific DNA methylation after fertilization. Furthermore, this activity is indispensable for the maintenance of imprinted methylation at the endogenous H19 ICR during the preimplantation period. In addition, we showed that a specific 5′ fragment of the H19 ICR is required for its paternal methylation after fertilization, while CTCF and Sox-Oct motifs are essential for its maternal protection from undesirable methylation after implantation. Results To ask whether specific cis elements are sufficient to reconstitute imprinted methylation status, we employed a TgM co-placement strategy for facilitating detection of postfertilization methylation activity and precise comparison of test sequences. Bacteriophage lambda DNA becomes highly methylated regardless of its parental origin and thus can be used as a neutral sequence bearing no inclination for differential DNA methylation. We previously showed that insertion of only CTCF and Sox-Oct binding motifs from the H19 ICR into a lambda DNA (LCb) decreased its methylation level after both paternal and maternal transmission. We therefore appended a 478-bp 5′ sequence from the H19 ICR into the LCb fragment and found that it acquired paternal-allele-specific methylation, the dynamics of which was identical to that of the H19 ICR, in TgM. Crucially, transgene expression also became imprinted. Although there are potential binding sites for ZFP57 (a candidate protein thought to control the methylation imprint) in the larger H19 ICR, they are not found in the 478-bp fragment, rendering the role of ZFP57 in postfertilization H19 ICR methylation a still open question. Conclusions Our results demonstrate that a differentially methylated region can be reconstituted by combining the activities of specific imprinting elements and that these elements together determine the activity of a genomically imprinted region in vivo. Electronic supplementary material The online version of this article (10.1186/s13072-018-0207-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Eiichi Okamura
- Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Daichi Kuramochi
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Aki Ushiki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan
| | - Katsuhiko Hirakawa
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Akiyoshi Fukamizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan. .,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
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93
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Halliday BJ, Fukuzawa R, Markie DM, Grundy RG, Ludgate JL, Black MA, Skeen JE, Weeks RJ, Catchpoole DR, Roberts AGK, Reeve AE, Morison IM. Germline mutations and somatic inactivation of TRIM28 in Wilms tumour. PLoS Genet 2018; 14:e1007399. [PMID: 29912901 PMCID: PMC6005459 DOI: 10.1371/journal.pgen.1007399] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 05/08/2018] [Indexed: 12/21/2022] Open
Abstract
Wilms tumour is a childhood tumour that arises as a consequence of somatic and rare germline mutations, the characterisation of which has refined our understanding of nephrogenesis and carcinogenesis. Here we report that germline loss of function mutations in TRIM28 predispose children to Wilms tumour. Loss of function of this transcriptional co-repressor, which has a role in nephrogenesis, has not previously been associated with cancer. Inactivation of TRIM28, either germline or somatic, occurred through inactivating mutations, loss of heterozygosity or epigenetic silencing. TRIM28-mutated tumours had a monomorphic epithelial histology that is uncommon for Wilms tumour. Critically, these tumours were negative for TRIM28 immunohistochemical staining whereas the epithelial component in normal tissue and other Wilms tumours stained positively. These data, together with a characteristic gene expression profile, suggest that inactivation of TRIM28 provides the molecular basis for defining a previously described subtype of Wilms tumour, that has early age of onset and excellent prognosis. The germline and somatic molecular events associated with Wilms tumour, a childhood kidney cancer, have been progressively defined over the past three decades. Among the uncharacterised tumours are a group of tumours that have monomorphic epithelial histology, familial association, distinctively clustered gene-expression patterns, early age of diagnosis, and excellent prognosis. Here, we describe germline mutations and loss of function of TRIM28 in familial Wilms tumours, along with somatic loss of function in a non-familial Wilms tumour. All TRIM28-mutant tumours showed the rare monomorphic epithelial histology, suggesting that loss of TRIM28 expression could be a useful marker to define a group of tumours with excellent prognosis. Future studies could lead to identification and reassurance of families that carry TRIM28 mutations, and to the use of reduced intensity of treatment for children who develop TRIM28-null tumours.
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Affiliation(s)
- Benjamin J. Halliday
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Ryuji Fukuzawa
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- Department of Pathology, International University of Health and Welfare, School of Medicine, Narita, Japan
| | - David M. Markie
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Richard G. Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, United Kingdom
| | - Jackie L. Ludgate
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Michael A. Black
- Cancer Genetics Laboratory, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Robert J. Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Daniel R. Catchpoole
- Tumour Bank, Children’s Cancer Research Unit, The Children’s Hospital at Westmead, Westmead, NSW, Australia
| | - Aedan G. K. Roberts
- Tumour Bank, Children’s Cancer Research Unit, The Children’s Hospital at Westmead, Westmead, NSW, Australia
| | - Anthony E. Reeve
- Cancer Genetics Laboratory, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ian M. Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- * E-mail:
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94
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Western PS. Epigenomic drugs and the germline: Collateral damage in the home of heritability? Mol Cell Endocrinol 2018; 468:121-133. [PMID: 29471014 DOI: 10.1016/j.mce.2018.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 02/07/2023]
Abstract
The testis and ovary provide specialised environments that nurture germ cells and facilitate their maturation, culminating in the production of mature gametes that can found the following generation. The sperm and egg not only transmit genetic information, but also epigenetic modifications that affect the development and physiology of offspring. Importantly, the epigenetic information contained in mature sperm and oocytes can be influenced by a range of environmental factors, such as diet, chemicals and drugs. An increasing range of studies are revealing how gene-environment interactions are mediated through the germline. Outside the germline, altered epigenetic state is common in a range of diseases, including many cancers. As epigenetic modifications are reversible, pharmaceuticals that directly target epigenetic modifying proteins have been developed and are delivering substantial benefits to patients, particularly in oncology. While providing the most effective patient treatment is clearly the primary concern, some patients will want to conceive children after treatment. However, the impacts of epigenomic drugs on the male and female gametes are poorly understood and whether these drugs will have lasting effects on patients' germline epigenome and subsequent offspring remains largely undetermined. Currently, evidence based clinical guidelines for use of epigenomic drugs in patients of reproductive age are limited in this context. Developing a deeper understanding of the epigenetic mechanisms regulating the germline epigenome and its impact on inherited traits and disease susceptibility is required to determine how specific epigenomic drugs might affect the germline and inheritance. Understanding these potential effects will facilitate the development of informed clinical guidelines appropriate for the use of epigenomic drugs in patients of reproductive age, ultimately improving the safety of these therapies in the clinic.
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Affiliation(s)
- Patrick S Western
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia.
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95
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Abstract
Environmental factors, particularly during early life, are important for the later metabolic health of the individual. In our obesogenic environment, it is of major socio-economic importance to investigate the mechanisms that contribute to the risk of metabolic ill health. Increasing evidence from a variety of model organisms suggests that non-genetically determined phenotypes, including metabolic effects such as glucose intolerance and obesity, can be passed between generations, which encourages us to revisit heredity. Inheritance of altered epigenetic information through the germ line has been proposed as one plausible mechanism. Whether the germline epigenome can be altered by environmental conditions such as diet and the extent to which this occurs in humans are the subject of intense current interest and debate, especially given that extensive germline epigenetic reprogramming is known to occur. As epigenetic mechanisms are often highly conserved between organisms, studying epigenetic inheritance in plants and lower metazoans has the potential to inform our investigation in mammals. This Review explores the extent to which epigenetic inheritance contributes to heredity in these different organisms, whether the environment can affect epigenetic inheritance and whether there is any evidence for the inheritance of acquired phenotypes.
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Affiliation(s)
- Elizabeth J Radford
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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96
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Champroux A, Cocquet J, Henry-Berger J, Drevet JR, Kocer A. A Decade of Exploring the Mammalian Sperm Epigenome: Paternal Epigenetic and Transgenerational Inheritance. Front Cell Dev Biol 2018; 6:50. [PMID: 29868581 PMCID: PMC5962689 DOI: 10.3389/fcell.2018.00050] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/18/2018] [Indexed: 12/12/2022] Open
Abstract
The past decade has seen a tremendous increase in interest and progress in the field of sperm epigenetics. Studies have shown that chromatin regulation during male germline development is multiple and complex, and that the spermatozoon possesses a unique epigenome. Its DNA methylation profile, DNA-associated proteins, nucleo-protamine distribution pattern and non-coding RNA set up a unique epigenetic landscape which is delivered, along with its haploid genome, to the oocyte upon fertilization, and therefore can contribute to embryogenesis and to the offspring health. An emerging body of compelling data demonstrates that environmental exposures and paternal lifestyle can change the sperm epigenome and, consequently, may affect both the embryonic developmental program and the health of future generations. This short review will attempt to provide an overview of what is currently known about sperm epigenome and the existence of transgenerational epigenetic inheritance of paternally acquired traits that may contribute to the offspring phenotype.
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Affiliation(s)
- Alexandre Champroux
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julie Cocquet
- INSERM U1016, Institut Cochin, Centre National de la Recherche Scientifique UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Joëlle Henry-Berger
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Joël R. Drevet
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ayhan Kocer
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
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97
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Mackin SJ, Thakur A, Walsh CP. Imprint stability and plasticity during development. Reproduction 2018; 156:R43-R55. [PMID: 29743259 DOI: 10.1530/rep-18-0051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022]
Abstract
There have been a number of recent insights in the area of genomic imprinting, the phenomenon whereby one of two autosomal alleles is selected for expression based on the parent of origin. This is due in part to a proliferation of new techniques for interrogating the genome that are leading researchers working on organisms other than mouse and human, where imprinting has been most studied, to become interested in looking for potential imprinting effects. Here, we recap what is known about the importance of imprints for growth and body size, as well as the main types of locus control. Interestingly, work from a number of labs has now shown that maintenance of the imprint post implantation appears to be a more crucial step than previously appreciated. We ask whether imprints can be reprogrammed somatically, how many loci there are and how conserved imprinted regions are in other species. Finally, we survey some of the methods available for examining DNA methylation genome-wide and look to the future of this burgeoning field.
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Affiliation(s)
- Sarah-Jayne Mackin
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Avinash Thakur
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Colum P Walsh
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
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98
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The Vast Complexity of the Epigenetic Landscape during Neurodevelopment: An Open Frame to Understanding Brain Function. Int J Mol Sci 2018; 19:ijms19051333. [PMID: 29723958 PMCID: PMC5983638 DOI: 10.3390/ijms19051333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/16/2018] [Accepted: 04/26/2018] [Indexed: 12/31/2022] Open
Abstract
Development is a well-defined stage-to-stage process that allows the coordination and maintenance of the structure and function of cells and their progenitors, in a complete organism embedded in an environment that, in turn, will shape cellular responses to external stimuli. Epigenetic mechanisms comprise a group of process that regulate genetic expression without changing the DNA sequence, and they contribute to the necessary plasticity of individuals to face a constantly changing medium. These mechanisms act in conjunction with genetic pools and their correct interactions will be crucial to zygote formation, embryo development, and brain tissue organization. In this work, we will summarize the main findings related to DNA methylation and histone modifications in embryonic stem cells and throughout early development phases. Furthermore, we will critically outline some key observations on how epigenetic mechanisms influence the rest of the developmental process and how long its footprint is extended from fecundation to adulthood.
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99
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Karemaker ID, Vermeulen M. Single-Cell DNA Methylation Profiling: Technologies and Biological Applications. Trends Biotechnol 2018; 36:952-965. [PMID: 29724495 DOI: 10.1016/j.tibtech.2018.04.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 12/18/2022]
Abstract
DNA methylation is an epigenetic modification that plays an important role in gene expression regulation, development, and disease. Recent technological innovations have spurred the development of methods that enable us to study the occurrence and biology of this mark at the single-cell level. Apart from answering fundamental biological questions about heterogeneous systems or rare cell types, low-input methods also bring clinical applications within reach. Ultimately, integrating these data with other single-cell data sets will allow deciphering multiple layers of gene expression regulation within each individual cell. Here, we review the approaches that have been developed to facilitate single-cell DNA methylation profiling, their biological applications, and how these will further our understanding of the biology of DNA methylation.
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Affiliation(s)
- Ino D Karemaker
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
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100
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Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat Cell Biol 2018; 20:620-631. [DOI: 10.1038/s41556-018-0093-4] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 03/21/2018] [Indexed: 12/24/2022]
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