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Prasasya RD, Caldwell BA, Liu Z, Wu S, Leu NA, Fowler JM, Cincotta SA, Laird DJ, Kohli RM, Bartolomei MS. Iterative oxidation by TET1 is required for reprogramming of imprinting control regions and patterning of mouse sperm hypomethylated regions. Dev Cell 2024; 59:1010-1027.e8. [PMID: 38569549 PMCID: PMC11042979 DOI: 10.1016/j.devcel.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 12/07/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Ten-eleven translocation (TET) enzymes iteratively oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during mammalian germline reprogramming remains unresolved due to the inability to decouple TET activities. Here, we generated two mouse lines expressing catalytically inactive TET1 (Tet1-HxD) and TET1 that stalls oxidation at 5hmC (Tet1-V). Tet1 knockout and catalytic mutant primordial germ cells (PGCs) fail to erase methylation at select imprinting control regions and promoters of meiosis-associated genes, validating the requirement for the iterative oxidation of 5mC for complete germline reprogramming. TET1V and TET1HxD rescue most hypermethylation of Tet1-/- sperm, suggesting the role of TET1 beyond its oxidative capability. We additionally identify a broader class of hypermethylated regions in Tet1 mutant mouse sperm that depend on TET oxidation for reprogramming. Our study demonstrates the link between TET1-mediated germline reprogramming and sperm methylome patterning.
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Affiliation(s)
- Rexxi D Prasasya
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Blake A Caldwell
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhengfeng Liu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Songze Wu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Johanna M Fowler
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven A Cincotta
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 84143, USA
| | - Diana J Laird
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 84143, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Choudhury S, Anne A, Singh M, Chaillet JR, Mohan KN. DNMT1 Y495C mutation interferes with maintenance methylation of imprinting control regions. Int J Biochem Cell Biol 2024; 169:106535. [PMID: 38281697 DOI: 10.1016/j.biocel.2024.106535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/05/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Hereditary Sensory and Autonomic Neuropathy Type 1E (HSAN1E) is a rare autosomal dominant neurological disorder due to missense mutations in DNA methyltransferase 1 (DNMT1). To investigate the nature of the dominant effect, we compared methylomes of transgenic R1wtDnmt1 and R1Dnmt1Y495C mouse embryonic stem cells (mESCs) overexpressing WT and the mutant mouse proteins respectively, with the R1 (wild-type) cells. In case of R1Dnmt1Y495C, 15 out of the 20 imprinting control regions were hypomethylated with transcript level dysregulation of multiple imprinted genes in ESCs and neurons. Non-imprinted regions, minor satellites, major satellites, LINE1 and IAP repeats were unaffected. These data mirror the specific imprinting defects associated with transient removal of DNMT1 in mESCs, deletion of the maternal-effect DNMT1o variant in preimplantation mouse embryos, and in part, reprogramming to naïve human iPSCs. This is the first DNMT1 mutation demonstrated to specifically affect Imprinting Control Regions (ICRs), and reinforces the differences in maintenance methylation of ICRs over non-imprinted regions. Consistent with nervous system abnormalities in the HSAN1E disorder and involvement of imprinted genes in normal development and neurogenesis, R1Dnmt1Y495C cells showed dysregulated pluripotency and neuron marker genes, and yielded more slender, shorter, and extensively branched neurons. We speculate that R1Dnmt1Y495C cells produce predominantly dimers containing mutant proteins, leading to a gradual and specific loss of ICR methylation during early human development.
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Affiliation(s)
- Sumana Choudhury
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - John Richard Chaillet
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India.
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3
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Prasasya RD, Caldwell BA, Liu Z, Wu S, Leu NA, Fowler JM, Cincotta SA, Laird DJ, Kohli RM, Bartolomei MS. TET1 Catalytic Activity is Required for Reprogramming of Imprinting Control Regions and Patterning of Sperm-Specific Hypomethylated Regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529426. [PMID: 36865267 PMCID: PMC9980038 DOI: 10.1101/2023.02.21.529426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
DNA methylation erasure is required for mammalian primordial germ cell reprogramming. TET enzymes iteratively oxidize 5-methylcytosine to generate 5-hyroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxycytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during germline reprogramming remains unresolved due to the lack of genetic models that decouple TET activities. Here, we generated two mouse lines expressing catalytically inactive TET1 ( Tet1-HxD ) and TET1 that stalls oxidation at 5hmC ( Tet1-V ). Tet1 -/- , Tet1 V/V , and Tet1 HxD/HxD sperm methylomes show that TET1 V and TET1 HxD rescue most Tet1 -/- hypermethylated regions, demonstrating the importance of TET1’s extra-catalytic functions. Imprinted regions, in contrast, require iterative oxidation. We further reveal a broader class of hypermethylated regions in sperm of Tet1 mutant mice that are excluded from de novo methylation during male germline development and depend on TET oxidation for reprogramming. Our study underscores the link between TET1-mediated demethylation during reprogramming and sperm methylome patterning.
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Mangiavacchi PM, Caldas-Bussiere MC, Mendonça MDS, Rumpf R, Lemos Júnior PES, Alves CS, Carneiro WDS, Dias AJB, Rios ÁFL. Multi-locus DNA methylation analysis of imprinted genes in cattle from somatic cell nuclear transfer. Theriogenology 2022; 186:95-107. [DOI: 10.1016/j.theriogenology.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 10/18/2022]
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Ishihara T, Griffith OW, Suzuki S, Renfree MB. Presence of H3K4me3 on Paternally Expressed Genes of the Paternal Genome From Sperm to Implantation. Front Cell Dev Biol 2022; 10:838684. [PMID: 35359448 PMCID: PMC8960379 DOI: 10.3389/fcell.2022.838684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting, parent-of-origin-specific gene expression, is controlled by differential epigenetic status of the parental chromosomes. While DNA methylation and suppressive histone modifications established during gametogenesis suppress imprinted genes on the inactive allele, how and when the expressed allele gains its active status is not clear. In this study, we asked whether the active histone-3 lysine-4 trimethylation (H3K4me3) marks remain at paternally expressed genes (PEGs) in sperm and embryos before and after fertilization using published data. Here we show that mouse sperm had the active H3K4me3 at more than half of known PEGs, and these genes were present even after fertilization. Using reciprocal cross data, we identified 13 new transient PEGs during zygotic genome activation. Next, we confirmed that the 12 out of the 13 new transient PEGs were associated with the paternal H3K4me3 in sperm. Nine out of the 12 genes were associated with the paternal H3K4me3 in zygotes. Our results show that paternal H3K4me3 marks escape inactivation during the histone-to-protamine transition that occurs during sperm maturation and are present in embryos from early zygotic stages up to implantation.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Oliver W. Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Marilyn B. Renfree,
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Wootton J, Soutoglou E. Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity. Front Genet 2022; 12:773426. [PMID: 34970302 PMCID: PMC8712883 DOI: 10.3389/fgene.2021.773426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.
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Affiliation(s)
- Jack Wootton
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Evi Soutoglou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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Abstract
Cardiovascular diseases show many sex-related differences in prevalence, etiology, phenotype expression, and outcomes. Complex molecular mechanisms underlie this diverse pathological manifestation, from sex-determined differential gene expression to sex hormones interaction with their specific receptors in different tissues. More recently, differential non-coding RNAs regulation also turned out to be an involved mechanism. This review focuses on sex impact on the various heart failure syndromes, including coronary artery disease, heart failure with preserved ejection fraction and with reduced ejection fraction, with particular attention to dilated cardiomyopathy. Despite similar genetic predisposition in terms of identified causative mutations, other causes, such as cardiotoxic drugs exposure or stress-induced cardiomyopathy, are more prevalent in women. Beyond this, differences in disease presentation and natural history reveal a more severe clinical onset with otherwise better long-term outcomes in women compared to men. Understanding the varying characteristics of disease manifestation and outcomes is warranted for a prompt and tailored treatment for both men and women. This is a mandatory step in the road to the personalized medicine. Moreover, despite a higher enrollment in the last years, the under-representation of females in clinical trials is the first obstacle to overcome in the long way to develop appropriate sex-based therapy approach.
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8
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Wang M, Ngo V, Wang W. Deciphering the genetic code of DNA methylation. Brief Bioinform 2021; 22:6082840. [PMID: 33432324 DOI: 10.1093/bib/bbaa424] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/03/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022] Open
Abstract
DNA methylation plays crucial roles in many biological processes and abnormal DNA methylation patterns are often observed in diseases. Recent studies have shed light on cis-acting DNA elements that regulate locus-specific DNA methylation, which involves transcription factors, histone modification and DNA secondary structures. In addition, several recent studies have surveyed DNA motifs that regulate DNA methylation and suggest potential applications in diagnosis and prognosis. Here, we discuss the current biological foundation for the cis-acting genetic code that regulates DNA methylation. We review the computational models that predict DNA methylation with genetic features and discuss the biological insights revealed from these models. We also provide an in-depth discussion on how to leverage such knowledge in clinical applications, particularly in the context of liquid biopsy for early cancer diagnosis and treatment.
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Affiliation(s)
- Mengchi Wang
- Bioinformatics and Systems Biology at University of California, USA
| | - Vu Ngo
- Bioinformatics and Systems Biology at University of California, USA
| | - Wei Wang
- Bioinformatics and Systems Biology, Department of Chemistry and Biochemistry, and Department of Cellular and Molecular Medicine at University of California, USA
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Rivera RM. Consequences of assisted reproductive techniques on the embryonic epigenome in cattle. Reprod Fertil Dev 2020; 32:65-81. [PMID: 32188559 DOI: 10.1071/rd19276] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Procedures used in assisted reproduction have been under constant scrutiny since their inception with the goal of improving the number and quality of embryos produced. However, invitro production of embryos is not without complications because many fertilised oocytes fail to become blastocysts, and even those that do often differ in the genetic output compared with their invivo counterparts. Thus only a portion of those transferred complete normal fetal development. An unwanted consequence of bovine assisted reproductive technology (ART) is the induction of a syndrome characterised by fetal overgrowth and placental abnormalities, namely large offspring syndrome; a condition associated with inappropriate control of the epigenome. Epigenetics is the study of chromatin and its effects on genetic output. Establishment and maintenance of epigenetic marks during gametogenesis and embryogenesis is imperative for the maintenance of cell identity and function. ARTs are implemented during times of vast epigenetic reprogramming; as a result, many studies have identified ART-induced deviations in epigenetic regulation in mammalian gametes and embryos. This review describes the various layers of epigenetic regulation and discusses findings pertaining to the effects of ART on the epigenome of bovine gametes and the preimplantation embryo.
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Affiliation(s)
- Rocío Melissa Rivera
- Division of Animal Science University of Missouri, Columbia, Missouri 65211, USA.
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10
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Mahadevan IA, Kumar S, Rao MRS. Linker histone variant H1t is closely associated with repressed repeat-element chromatin domains in pachytene spermatocytes. Epigenetics Chromatin 2020; 13:9. [PMID: 32131873 PMCID: PMC7057672 DOI: 10.1186/s13072-020-00335-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/20/2020] [Indexed: 12/22/2022] Open
Abstract
Background H1t is the major linker histone variant in pachytene spermatocytes, where it constitutes 50–60% of total H1. This linker histone variant was previously reported to localize in the nucleolar rDNA element in mouse spermatocytes. Our main aim was to determine the extra-nucleolar localization of this linker histone variant in pachytene spermatocytes. Results We generated H1t-specific antibodies in rabbits and validated its specificity by multiple assays like ELISA, western blot, etc. Genome-wide occupancy studies, as determined by ChIP-sequencing in P20 mouse testicular cells revealed that H1t did not closely associate with active gene promoters and open chromatin regions. Annotation of H1t-bound genomic regions revealed that H1t is depleted from DSB hotspots and TSS, but are predominantly associated with retrotransposable repeat elements like LINE and LTR in pachytene spermatocytes. These chromatin domains are repressed based on co-association of H1t observed with methylated CpGs and repressive histone marks like H3K9me3 and H4K20me3 in vivo. Mass spectrometric analysis of proteins associated with H1t-containing oligonucleosomes identified piRNA–PIWI pathway proteins, repeat repression-associated proteins and heterochromatin proteins confirming the association with repressed repeat-element genomic regions. We validated the interaction of key proteins with H1t-containing oligonucleosomes by use of ChIP-western blot assays. On the other hand, we observe majority of H1t peaks to be associated with the intergenic spacer of the rDNA element, also in association with SINE elements of the rDNA element. Thus, we have identified the genomic and chromatin features of both nucleolar and extranucleolar localization patterns of linker histone H1t in the context of pachytene spermatocytes. Conclusions H1t-containing repeat-element LINE and LTR chromatin domains are associated with repressive marks like methylated CpGs, histone modifications H3K9me3 and H4K20me3, and heterochromatin proteins like HP1β, Trim28, PIWIL1, etc. Apart from localization of H1t at the rDNA element, we demonstrate the extranucleolar association of this linker histone variant at repeat-associated chromatin domains in pachytene spermatocytes. We hypothesize that H1t might induce local chromatin relaxation to recruit heterochromatin and repeat repression-associated protein factors necessary for TE (transposable element) repression, the final biological effect being formation of closed chromatin repressed structures.
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Affiliation(s)
- Iyer Aditya Mahadevan
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Sanjeev Kumar
- BioCOS Life Sciences Private Limited, SAAMI Building, 851/A, AECS Layout, B-Block, Singasandra Hosur Road, Bangalore, India
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11
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Xavier MJ, Roman SD, Aitken RJ, Nixon B. Transgenerational inheritance: how impacts to the epigenetic and genetic information of parents affect offspring health. Hum Reprod Update 2019; 25:518-540. [DOI: 10.1093/humupd/dmz017] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/19/2019] [Accepted: 04/04/2019] [Indexed: 12/18/2022] Open
Abstract
Abstract
BACKGROUND
A defining feature of sexual reproduction is the transmission of genomic information from both parents to the offspring. There is now compelling evidence that the inheritance of such genetic information is accompanied by additional epigenetic marks, or stable heritable information that is not accounted for by variations in DNA sequence. The reversible nature of epigenetic marks coupled with multiple rounds of epigenetic reprogramming that erase the majority of existing patterns have made the investigation of this phenomenon challenging. However, continual advances in molecular methods are allowing closer examination of the dynamic alterations to histone composition and DNA methylation patterns that accompany development and, in particular, how these modifications can occur in an individual’s germline and be transmitted to the following generation. While the underlying mechanisms that permit this form of transgenerational inheritance remain unclear, it is increasingly apparent that a combination of genetic and epigenetic modifications plays major roles in determining the phenotypes of individuals and their offspring.
OBJECTIVE AND RATIONALE
Information pertaining to transgenerational inheritance was systematically reviewed focusing primarily on mammalian cells to the exclusion of inheritance in plants, due to inherent differences in the means by which information is transmitted between generations. The effects of environmental factors and biological processes on both epigenetic and genetic information were reviewed to determine their contribution to modulating inheritable phenotypes.
SEARCH METHODS
Articles indexed in PubMed were searched using keywords related to transgenerational inheritance, epigenetic modifications, paternal and maternal inheritable traits and environmental and biological factors influencing transgenerational modifications. We sought to clarify the role of epigenetic reprogramming events during the life cycle of mammals and provide a comprehensive review of how the genomic and epigenomic make-up of progenitors may determine the phenotype of its descendants.
OUTCOMES
We found strong evidence supporting the role of DNA methylation patterns, histone modifications and even non-protein-coding RNA in altering the epigenetic composition of individuals and producing stable epigenetic effects that were transmitted from parents to offspring, in both humans and rodent species. Multiple genomic domains and several histone modification sites were found to resist demethylation and endure genome-wide reprogramming events. Epigenetic modifications integrated into the genome of individuals were shown to modulate gene expression and activity at enhancer and promoter domains, while genetic mutations were shown to alter sequence availability for methylation and histone binding. Fundamentally, alterations to the nuclear composition of the germline in response to environmental factors, ageing, diet and toxicant exposure have the potential to become hereditably transmitted.
WIDER IMPLICATIONS
The environment influences the health and well-being of progeny by working through the germline to introduce spontaneous genetic mutations as well as a variety of epigenetic changes, including alterations in DNA methylation status and the post-translational modification of histones. In evolutionary terms, these changes create the phenotypic diversity that fuels the fires of natural selection. However, rather than being adaptive, such variation may also generate a plethora of pathological disease states ranging from dominant genetic disorders to neurological conditions, including spontaneous schizophrenia and autism.
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Affiliation(s)
- Miguel João Xavier
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Shaun D Roman
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Chemical Biology and Clinical Pharmacology, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - R John Aitken
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Brett Nixon
- Reproductive Science Group, Faculty of Science, The University of Newcastle, Callaghan, NSW 2308, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW 2308, Australia
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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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13
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Wang C, Zhan L, Wu M, Ma R, Yao J, Xiong Y, Pan Y, Guan S, Zhang X, Zang J. Spindlin-1 recognizes methylations of K20 and R23 of histone H4 tail. FEBS Lett 2018; 592:4098-4110. [PMID: 30381828 DOI: 10.1002/1873-3468.13281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/08/2022]
Abstract
Using methods combining cross-linking, pull-down assays, and stable isotope labeling by amino acids in cell culture with mass spectrometry, we identified that the Tudor domain-containing protein Spindlin-1 recognizes trimethylation of histone H4 lysine 20 (H4K20me3). The binding affinity of Spindlin-1 to H4K20me3 is weaker than that to H3K4me3, indicating H4K20me3 as a secondary substrate for Spindlin-1. Structural studies of Spindlin-1 in complex with the H4K20me3 peptide indicate that Spindlin-1 attains a distinct binding mode for H4K20me3 recognition. Further biochemical analysis identified that Spindlin-1 also binds methylated R23 of H4, providing new clues for the function of Spindlin-1.
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Affiliation(s)
- Chengliang Wang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Li Zhan
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Minhao Wu
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Rongsheng Ma
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Jun Yao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ying Xiong
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Yang Pan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Shenheng Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Xuan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
| | - Jianye Zang
- Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, China
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14
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Huang H, Zhang D, Wang Y, Perez-Neut M, Han Z, Zheng YG, Hao Q, Zhao Y. Lysine benzoylation is a histone mark regulated by SIRT2. Nat Commun 2018; 9:3374. [PMID: 30154464 PMCID: PMC6113264 DOI: 10.1038/s41467-018-05567-w] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/11/2018] [Indexed: 02/06/2023] Open
Abstract
Metabolic regulation of histone marks is associated with diverse biological processes through dynamically modulating chromatin structure and functions. Here we report the identification and characterization of a histone mark, lysine benzoylation (Kbz). Our study identifies 22 Kbz sites on histones from HepG2 and RAW cells. This type of histone mark can be stimulated by sodium benzoate (SB), an FDA-approved drug and a widely used chemical food preservative, via generation of benzoyl CoA. By ChIP-seq and RNA-seq analysis, we demonstrate that histone Kbz marks are associated with gene expression and have physiological relevance distinct from histone acetylation. In addition, we demonstrate that SIRT2, a NAD+-dependent protein deacetylase, removes histone Kbz both in vitro and in vivo. This study therefore reveals a new type of histone marks with potential physiological relevance and identifies possible non-canonical functions of a widely used chemical food preservative. Histone marks regulate chromatin structure and function. Here the authors identify and characterize lysine benzoylation, a histone mark that can be modulated by sodium benzoate, a widely used chemical food preservative, associated with specific regulation of gene expression.
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Affiliation(s)
- He Huang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Di Zhang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Yi Wang
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Mathew Perez-Neut
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Zhen Han
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, 60637, USA.
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15
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Mishra LN, Shalini V, Gupta N, Ghosh K, Suthar N, Bhaduri U, Rao MRS. Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements. Epigenetics Chromatin 2018; 11:43. [PMID: 30068355 PMCID: PMC6069787 DOI: 10.1186/s13072-018-0214-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linker histones establish and maintain higher-order chromatin structure. Eleven linker histone subtypes have been reported in mammals. HILS1 is a spermatid-specific linker histone, and its expression overlaps with the histone-protamine exchange process during mammalian spermiogenesis. However, the role of HILS1 in spermatid chromatin remodeling is largely unknown. RESULTS In this study, we demonstrate using circular dichroism spectroscopy that HILS1 is a poor condenser of DNA and chromatin compared to somatic linker histone H1d. Genome-wide occupancy study in elongating/condensing spermatids revealed the preferential binding of HILS1 to the LINE-1 (L1) elements within the intergenic and intronic regions of rat spermatid genome. We observed specific enrichment of the histone PTMs like H3K9me3, H4K20me3 and H4 acetylation marks (H4K5ac and H4K12ac) in the HILS1-bound chromatin complex, whereas H3K4me3 and H3K27me3 marks were absent. CONCLUSIONS HILS1 possesses significantly lower α-helicity compared to other linker histones such as H1t and H1d. Interestingly, in contrast to the somatic histone variant H1d, HILS1 is a poor condenser of chromatin which demonstrate the idea that this particular linker histone variant may have distinct role in histone to protamine replacement. Based on HILS1 ChIP-seq analysis of elongating/condensing spermatids, we speculate that HILS1 may provide a platform for the structural transitions and forms the higher-order chromatin structures encompassing LINE-1 elements during spermiogenesis.
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Affiliation(s)
- Laxmi Narayan Mishra
- Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India.,Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Vasantha Shalini
- Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India
| | - Nikhil Gupta
- Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India.,Epigenetics and Cell Fate, UMR7216, CNRS, University Paris Diderot, Sorbonne Paris Cite, 75013, Paris, France
| | - Krittika Ghosh
- InterpretOmics India Pvt. Ltd., #329, 7th Main, HAL II Stage 80 Feet Road, Indira Nagar, Bangalore, 560008, India
| | - Neeraj Suthar
- InterpretOmics India Pvt. Ltd., #329, 7th Main, HAL II Stage 80 Feet Road, Indira Nagar, Bangalore, 560008, India
| | - Utsa Bhaduri
- Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India
| | - M R Satyanarayana Rao
- Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India.
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16
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Ventura-Clapier R, Dworatzek E, Seeland U, Kararigas G, Arnal JF, Brunelleschi S, Carpenter TC, Erdmann J, Franconi F, Giannetta E, Glezerman M, Hofmann SM, Junien C, Katai M, Kublickiene K, König IR, Majdic G, Malorni W, Mieth C, Miller VM, Reynolds RM, Shimokawa H, Tannenbaum C, D'Ursi AM, Regitz-Zagrosek V. Sex in basic research: concepts in the cardiovascular field. Cardiovasc Res 2018; 113:711-724. [PMID: 28472454 DOI: 10.1093/cvr/cvx066] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 05/01/2017] [Indexed: 01/01/2023] Open
Abstract
Women and men, female and male animals and cells are biologically different, and acknowledgement of this fact is critical to advancing medicine. However, incorporating concepts of sex-specific analysis in basic research is largely neglected, introducing bias into translational findings, clinical concepts and drug development. Research funding agencies recently approached these issues but implementation of policy changes in the scientific community is still limited, probably due to deficits in concepts, knowledge and proper methodology. This expert review is based on the EUGenMed project (www.eugenmed.eu) developing a roadmap for implementing sex and gender in biomedical and health research. For sake of clarity and conciseness, examples are mainly taken from the cardiovascular field that may serve as a paradigm for others, since a significant amount of knowledge how sex and oestrogen determine the manifestation of many cardiovascular diseases (CVD) has been accumulated. As main concepts for implementation of sex in basic research, the study of primary cell and animals of both sexes, the study of the influence of genetic vs. hormonal factors and the analysis of sex chromosomes and sex specific statistics in genome wide association studies (GWAS) are discussed. The review also discusses methodological issues, and analyses strength, weaknesses, opportunities and threats in implementing sex-sensitive aspects into basic research.
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Affiliation(s)
- Renée Ventura-Clapier
- Signalisation et Physiopathologie Cardiovasculaire UMR-S 1180, Inserm, Univ. Paris-Sud, Université Paris-Saclay, 92296 Châtenay-Malabry, France
| | - Elke Dworatzek
- Institute of Gender in Medicine and Center for Cardiovascular Research, Charité Universitaetsmedizin Berlin, 10115 Berlin, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Germany
| | - Ute Seeland
- Institute of Gender in Medicine and Center for Cardiovascular Research, Charité Universitaetsmedizin Berlin, 10115 Berlin, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Germany
| | - Georgios Kararigas
- Institute of Gender in Medicine and Center for Cardiovascular Research, Charité Universitaetsmedizin Berlin, 10115 Berlin, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Germany
| | - Jean-Francois Arnal
- Faculté Médecine Toulouse-Rangueil, Université de Toulouse, Toulouse, France
| | - Sandra Brunelleschi
- Department of Health Sciences, School of Medicine, University of Eastern Piedmont, Novara, Italy
| | - Thomas C Carpenter
- College of Medicine and Veterinary Medicine, University of Edinburgh, EH16 4TJ Edinburgh, UK
| | - Jeanette Erdmann
- Institut für Kardiogenetik, Universität zu Lübeck, 23562 Lübeck, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Germany
| | - Flavia Franconi
- Department of Biomedical Science, University of Sassari,Sassari, Italy
| | - Elisa Giannetta
- Ricercatore TD in Endocrinologia, Dipartimento di Medicina Sperimentale, Sezione di Fisiopatologia Medica, Sapienza University of Rome, Roma, Italy
| | - Marek Glezerman
- International Society for Gender Medicine, Research Center for Medicine, Rabin Medical Center, and Tel Aviv University, Israel
| | - Susanna M Hofmann
- Medizinische Klinik und Poliklinik IV, Klinikum der LMU München, Munich 80336, Germany; Institute for Diabetes and Regeneration, Helmholtz Center Munich, Germany; German Center for Diabetes Research (DZD) München-Neuherberg, Germany
| | - Claudine Junien
- BDR Biologie du Développement et Reproduction Developmental Biology and Reproduction UMR, INRA, France
| | - Miyuki Katai
- Section of Gender Medicine, Department of General Medicine, Tokyo Women's Medical University, 162-8666 Tokyo, Japan
| | - Karolina Kublickiene
- Centre for Gender Medicine and Departments of Obstetrics and Gynecology and Renal Medicine, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Inke R König
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Germany.,Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, 235620 Lübeck, Germany
| | - Gregor Majdic
- Institute for Preclinical Sciences, Veterinary Faculty, University of Ljubljana & Institute of Physiology, Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Walter Malorni
- National Center for Gender-Specific Medicine, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Christin Mieth
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Germany.,Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft (MDC), Berlin, Germany
| | | | - Rebecca M Reynolds
- Center for Cardiovascular Science, Queen's Medical Research Institute, EH16 4TJ Edinburgh, UK
| | - Hiroaki Shimokawa
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Japan
| | - Cara Tannenbaum
- Institute of Gender and Health, Canadian Institutes of Health Research (CIHR), Canada
| | - Anna Maria D'Ursi
- Medicinal Chemistry DIFARMA, Università di Salerno, 84084 Fisciano, Italy
| | - Vera Regitz-Zagrosek
- Institute of Gender in Medicine and Center for Cardiovascular Research, Charité Universitaetsmedizin Berlin, 10115 Berlin, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Germany
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17
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Dumasia K, Kumar A, Deshpande S, Balasinor NH. Estrogen, through estrogen receptor 1, regulates histone modifications and chromatin remodeling during spermatogenesis in adult rats. Epigenetics 2017; 12:953-963. [PMID: 28949791 DOI: 10.1080/15592294.2017.1382786] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Estrogen receptors (ESR1 and ESR2) play crucial roles in various processes during spermatogenesis. To elucidate individual roles of ESRs in male fertility, we developed in vivo selective ESR agonist administration models. Adult male rats treated with ESR1 and ESR2 agonist for 60 days show spermatogenic defects leading to reduced sperm counts and fertility. While studying epigenetic changes in the male germ line that could have affected fertility, we earlier observed a decrease in DNA methylation and its machinery upon ESR2 agonist treatment. Here, we explored the effects on histone modifications, which could contribute to decreased male fertility upon ESR agonist administration. ESR1 agonist treatment affected testicular levels of histone modifications associated with active and repressed chromatin states, along with heterochromatin marks. This was concomitant with deregulation of corresponding histone modifying enzymes in the testis. In addition, there was increased retention of histones along with protamine deficiency in the caudal spermatozoa after ESR1 agonist treatment. This could be due to the observed decrease in several chromatin remodeling proteins implicated in mediating histone-to-protamine exchange during spermiogenesis. The activating and repressing histone marks in spermatozoa, which play a critical role in early embryo development, were deregulated after both the ESR agonist treatments. Together, these epigenetic defects in the male germ line could affect the spermatozoa quality and lead to the observed decrease in fertility. Our results thus highlight the importance of ESRs in regulating different epigenetic processes during spermatogenesis, which are crucial for male fertility.
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Affiliation(s)
- Kushaan Dumasia
- a Department of Neuroendocrinology , National Institute for Research in Reproductive Health (Indian Council of Medical Research), Parel , Mumbai , India
| | - Anita Kumar
- a Department of Neuroendocrinology , National Institute for Research in Reproductive Health (Indian Council of Medical Research), Parel , Mumbai , India
| | - Sharvari Deshpande
- a Department of Neuroendocrinology , National Institute for Research in Reproductive Health (Indian Council of Medical Research), Parel , Mumbai , India
| | - Nafisa H Balasinor
- a Department of Neuroendocrinology , National Institute for Research in Reproductive Health (Indian Council of Medical Research), Parel , Mumbai , India
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18
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Liu Y, Ding Z. Obesity, a serious etiologic factor for male subfertility in modern society. Reproduction 2017; 154:R123-R131. [DOI: 10.1530/rep-17-0161] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/02/2017] [Accepted: 07/26/2017] [Indexed: 12/14/2022]
Abstract
Obesity, defined as excessive accumulation of fat in adipose tissue, is a metabolic disorder resulting from behavioral, environmental and heritable causes. Obesity increases the risks of hypertension, diabetes, cardiovascular disease, sleep apnea, respiratory problems, osteoarthritis and cancer. Meanwhile, the negative impact of obesity on male reproduction is gradually recognized. According to the clinical investigations and animal experiments, obesity is correlated with reductions in sperm concentration and motility, increase in sperm DNA damage and changes in reproductive hormones. Several mechanisms can elucidate the effects of obesity on sperm functions and male subfertility, i.e., the excessive conversion of androgens into estrogens in redundant adipose tissue causes sexual hormone imbalance, subsequently resulting in hypogonadism. Secondly, adipokines produced by adipose tissue induce severe inflammation and oxidative stress in male reproductive tract, directly impairing testicular and epididymal tissues. Moreover, increased scrotal adiposity leads to increase gonadal heat, continuously hurting spermatogenesis. Therefore, obesity alters the systematic and regional environment crucial for spermatogenesis in testis and sperm maturation in epididymis, and finally results in poor sperm quality including decreased sperm motility, abnormal sperm morphology and acrosome reaction, changed membrane lipids and increased DNA damage. Furthermore, recent studies indicate that epigenetic changes may be a consequence of increased adiposity. A major effort to identify epigenetic determinants of obesity revealed that sperm DNA methylation and non-coding RNA modification are associated with BMI changes and proposed to inherit metabolic comorbidities across generations. This review will explain how obesity-related changes in males to influence sperm function and male fertility as well.
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19
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Lee CC, Peng SH, Shen L, Lee CF, Du TH, Kang ML, Xu GL, Upadhyay AK, Cheng X, Yan YT, Zhang Y, Juan LJ. The Role of N-α-acetyltransferase 10 Protein in DNA Methylation and Genomic Imprinting. Mol Cell 2017; 68:89-103.e7. [PMID: 28943313 DOI: 10.1016/j.molcel.2017.08.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/13/2017] [Accepted: 08/24/2017] [Indexed: 01/21/2023]
Abstract
Genomic imprinting is an allelic gene expression phenomenon primarily controlled by allele-specific DNA methylation at the imprinting control region (ICR), but the underlying mechanism remains largely unclear. N-α-acetyltransferase 10 protein (Naa10p) catalyzes N-α-acetylation of nascent proteins, and mutation of human Naa10p is linked to severe developmental delays. Here we report that Naa10-null mice display partial embryonic lethality, growth retardation, brain disorders, and maternal effect lethality, phenotypes commonly observed in defective genomic imprinting. Genome-wide analyses further revealed global DNA hypomethylation and enriched dysregulation of imprinted genes in Naa10p-knockout embryos and embryonic stem cells. Mechanistically, Naa10p facilitates binding of DNA methyltransferase 1 (Dnmt1) to DNA substrates, including the ICRs of the imprinted allele during S phase. Moreover, the lethal Ogden syndrome-associated mutation of human Naa10p disrupts its binding to the ICR of H19 and Dnmt1 recruitment. Our study thus links Naa10p mutation-associated Ogden syndrome to defective DNA methylation and genomic imprinting.
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Affiliation(s)
- Chen-Cheng Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Shih-Huan Peng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC; Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan, ROC
| | - Li Shen
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Chung-Fan Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Ting-Huei Du
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Ming-Lun Kang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Guo-Liang Xu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Anup K Upadhyay
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yu-Ting Yan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Yi Zhang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Li-Jung Juan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC.
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20
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Mettl3-mediated m 6A regulates spermatogonial differentiation and meiosis initiation. Cell Res 2017; 27:1100-1114. [PMID: 28809392 DOI: 10.1038/cr.2017.100] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 06/27/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022] Open
Abstract
METTL3 catalyzes the formation of N6-methyl-adenosine (m6A) which has important roles in regulating various biological processes. However, the in vivo function of Mettl3 remains largely unknown in mammals. Here we generated germ cell-specific Mettl3 knockout mice and demonstrated that Mettl3 was essential for male fertility and spermatogenesis. The ablation of Mettl3 in germ cells severely inhibited spermatogonial differentiation and blocked the initiation of meiosis. Transcriptome and m6A profiling analysis revealed that genes functioning in spermatogenesis had altered profiles of expression and alternative splicing. Our findings provide novel insights into the function and regulatory mechanisms of Mettl3-mediated m6A modification in spermatogenesis and reproduction in mammals.
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21
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Disparities in Cervical Cancer Incidence and Mortality: Can Epigenetics Contribute to Eliminating Disparities? Adv Cancer Res 2017; 133:129-156. [PMID: 28052819 DOI: 10.1016/bs.acr.2016.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Screening for uterine cervical intraepithelial neoplasia (CIN) followed by aggressive treatment has reduced invasive cervical cancer (ICC) incidence and mortality. However, ICC cases and carcinoma in situ (CIS) continue to be diagnosed annually in the United States, with minorities bearing the brunt of this burden. Because ICC peak incidence and mortality are 10-15 years earlier than other solid cancers, the number of potential years of life lost to this cancer is substantial. Screening for early signs of CIN is still the mainstay of many cervical cancer control programs. However, the accuracy of existing screening tests remains suboptimal. Changes in epigenetic patterns that occur as a result of human papillomavirus infection contribute to CIN progression to cancer, and can be harnessed to improve existing screening tests. However, this requires a concerted effort to identify the epigenomic landscape that is reliably altered by HPV infection specific to ICC, distinct from transient changes.
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22
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Taylor DH, McLean CM, Wu WL, Wang AB, Soloway PD. Imprinted DNA methylation reconstituted at a non-imprinted locus. Epigenetics Chromatin 2016; 9:41. [PMID: 27688812 PMCID: PMC5034545 DOI: 10.1186/s13072-016-0094-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/14/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammals, tight regulation of cytosine methylation is required for embryonic development and cellular differentiation. The trans-acting DNA methyltransferases that catalyze this modification have been identified and characterized; however, these proteins lack sequence specificity, leaving the mechanism of targeting unknown. A cis-acting regulator within the Rasgrf1 imprinting control region (ICR) is necessary for establishment and maintenance of local imprinted methylation. Here, we investigate whether 3-kb of sequence from the Rasgrf1 ICR is sufficient to direct appropriate imprinted methylation and target gene expression patterns when ectopically inserted at the Wnt1 locus. RESULTS The Rasgrf1 ICR at Wnt1 lacked somatic methylation when maternally transmitted and was fully methylated upon paternal transmission, consistent with its behavior at the Rasgrf1 locus. It was unmethylated in the female germline and was enriched for methylation in the male germline, though not to the levels seen at the endogenous Rasgrf1 allele. Wnt1 expression was not imprinted by the ectopic ICR, likely due to additional sequences being required for this function. CONCLUSIONS We have identified sequences that are sufficient for partial establishment and full maintenance of the imprinted DNA methylation patterns. Because full somatic methylation can occur without full gametic methylation, we infer that somatic methylation of the Rasgrf1 ICR is not simply a consequence of maintained gametic methylation.
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Affiliation(s)
- David H Taylor
- Field of Genetics, Genomics, and Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY USA
| | - Chelsea M McLean
- Field of Genetics, Genomics, and Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY USA ; Department of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan, Amsterdam, The Netherlands
| | - Warren L Wu
- Division of Nutritional Sciences, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY USA
| | - Alex B Wang
- Field of Biochemistry, Molecular and Cell Biology, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY USA
| | - Paul D Soloway
- Field of Genetics, Genomics, and Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY USA ; Division of Nutritional Sciences, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY USA ; Field of Biochemistry, Molecular and Cell Biology, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY USA
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23
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Hur SK, Freschi A, Ideraabdullah F, Thorvaldsen JL, Luense LJ, Weller AH, Berger SL, Cerrato F, Riccio A, Bartolomei MS. Humanized H19/Igf2 locus reveals diverged imprinting mechanism between mouse and human and reflects Silver-Russell syndrome phenotypes. Proc Natl Acad Sci U S A 2016; 113:10938-43. [PMID: 27621468 PMCID: PMC5047210 DOI: 10.1073/pnas.1603066113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic imprinting affects a subset of genes in mammals, such that they are expressed in a monoallelic, parent-of-origin-specific manner. These genes are regulated by imprinting control regions (ICRs), cis-regulatory elements that exhibit allele-specific differential DNA methylation. Although genomic imprinting is conserved in mammals, ICRs are genetically divergent across species. This raises the fundamental question of whether the ICR plays a species-specific role in regulating imprinting at a given locus. We addressed this question at the H19/insulin-like growth factor 2 (Igf2) imprinted locus, the misregulation of which is associated with the human imprinting disorders Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS). We generated a knock-in mouse in which the endogenous H19/Igf2 ICR (mIC1) is replaced by the orthologous human ICR (hIC1) sequence, designated H19(hIC1) We show that hIC1 can functionally replace mIC1 on the maternal allele. In contrast, paternally transmitted hIC1 leads to growth restriction, abnormal hIC1 methylation, and loss of H19 and Igf2 imprinted expression. Imprint establishment at hIC1 is impaired in the male germ line, which is associated with an abnormal composition of histone posttranslational modifications compared with mIC1. Overall, this study reveals evolutionarily divergent paternal imprinting at IC1 between mice and humans. The conserved maternal imprinting mechanism and function at IC1 demonstrates the possibility of modeling maternal transmission of hIC1 mutations associated with BWS in mice. In addition, we propose that further analyses in the paternal knock-in H19(+/hIC1) mice will elucidate the molecular mechanisms that may underlie SRS.
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Affiliation(s)
- Stella K Hur
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Andrea Freschi
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Folami Ideraabdullah
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Joanne L Thorvaldsen
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Lacey J Luense
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Angela H Weller
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Flavia Cerrato
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy;
| | - Andrea Riccio
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy; Institute of Genetics and Biophysics A. Buzzati-Traverso, 80131 Naples, Italy
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104;
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Cui X, Jing X, Wu X, Yan M, Li Q, Shen Y, Wang Z. DNA methylation in spermatogenesis and male infertility. Exp Ther Med 2016; 12:1973-1979. [PMID: 27698683 DOI: 10.3892/etm.2016.3569] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/06/2016] [Indexed: 12/12/2022] Open
Abstract
Infertility is a significant problem for human reproduction, with males and females equally affected. However, the molecular mechanisms underlying male infertility remain unclear. Spermatogenesis is a highly complex process involving mitotic cell division, meiosis cell division and spermiogenesis; during this period, unique and extensive chromatin and epigenetic modifications occur to bring about specific epigenetic profiles in spermatozoa. It has recently been suggested that the dysregulation of epigenetic modifications, in particular the methylation of sperm genomic DNA, may serve an important role in the development of numerous diseases. The present study is a comprehensive review on the topic of male infertility, aiming to elucidate the association between sperm genomic DNA methylation and poor semen quality in male infertility. In addition, the current status of the genetic and epigenetic determinants of spermatogenesis in humans is discussed.
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Affiliation(s)
- Xiangrong Cui
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China; Division of Clinical Microbiology The Center Hospital of Linfen, Linfen, Shanxi 041000, P.R. China
| | - Xuan Jing
- Clinical Laboratory, Shanxi Province People's Hospital, Taiyuan, Shanxi 030001, P.R. China
| | - Xueqing Wu
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
| | - Meiqin Yan
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
| | - Qiang Li
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
| | - Yan Shen
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
| | - Zhenqiang Wang
- Reproductive Medicine Center, Children's Hospital of Shanxi and Women Health Center of Shanxi, Taiyuan, Shanxi 030000, P.R. China
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25
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Matsumura Y, Nakaki R, Inagaki T, Yoshida A, Kano Y, Kimura H, Tanaka T, Tsutsumi S, Nakao M, Doi T, Fukami K, Osborne TF, Kodama T, Aburatani H, Sakai J. H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation. Mol Cell 2016; 60:584-96. [PMID: 26590716 DOI: 10.1016/j.molcel.2015.10.025] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/11/2015] [Accepted: 10/12/2015] [Indexed: 12/29/2022]
Abstract
Bivalent H3K4me3 and H3K27me3 chromatin domains in embryonic stem cells keep active developmental regulatory genes expressed at very low levels and poised for activation. Here, we show an alternative and previously unknown bivalent modified histone signature in lineage-committed mesenchymal stem cells and preadipocytes that pairs H3K4me3 with H3K9me3 to maintain adipogenic master regulatory genes (Cebpa and Pparg) expressed at low levels yet poised for activation when differentiation is required. We show lineage-specific gene-body DNA methylation recruits H3K9 methyltransferase SETDB1, which methylates H3K9 immediately downstream of transcription start sites marked with H3K4me3 to establish the bivalent domain. At the Cebpa locus, this prevents transcription factor C/EBPβ binding, histone acetylation, and further H3K4me3 deposition and is associated with pausing of RNA polymerase II, which limits Cebpa gene expression and adipogenesis.
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Affiliation(s)
- Yoshihiro Matsumura
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Ryo Nakaki
- Genome Science Division, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takeshi Inagaki
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ayano Yoshida
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; Laboratory of Genome and Biosignals, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan
| | - Yuka Kano
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Toshiya Tanaka
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takefumi Doi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kiyoko Fukami
- Laboratory of Genome and Biosignals, Tokyo University of Pharmacy and Life Science, Tokyo 192-0392, Japan
| | - Timothy F Osborne
- Metabolic Disease Program, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan; The Translational Systems Biology and Medicine Initiative (TSBMI), Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
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26
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Hammoud SS, Low DHP, Yi C, Lee CL, Oatley JM, Payne CJ, Carrell DT, Guccione E, Cairns BR. Transcription and imprinting dynamics in developing postnatal male germline stem cells. Genes Dev 2016; 29:2312-24. [PMID: 26545815 PMCID: PMC4647563 DOI: 10.1101/gad.261925.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hammoud et al. conducted extensive genomic profiling and classified three broad spermatogonial stem cell (SSC) populations in juveniles: (1) epithelial-like SSCs, (2) more abundant mesenchymal-like SSCs, and (3) (in older juveniles) abundant cells committing to gametogenesis. Mesenchymal-like SSCs lacked imprinting specifically at paternally imprinted loci but fully restored imprinting prior to puberty. Mesenchymal-like SSCs also displayed developmentally linked DNA demethylation at meiotic genes and also at certain monoallelic neural genes. Postnatal spermatogonial stem cells (SSCs) progress through proliferative and developmental stages to populate the testicular niche prior to productive spermatogenesis. To better understand, we conducted extensive genomic profiling at multiple postnatal stages on subpopulations enriched for particular markers (THY1, KIT, OCT4, ID4, or GFRa1). Overall, our profiles suggest three broad populations of spermatogonia in juveniles: (1) epithelial-like spermatogonia (THY1+; high OCT4, ID4, and GFRa1), (2) more abundant mesenchymal-like spermatogonia (THY1+; moderate OCT4 and ID4; high mesenchymal markers), and (3) (in older juveniles) abundant spermatogonia committing to gametogenesis (high KIT+). Epithelial-like spermatogonia displayed the expected imprinting patterns, but, surprisingly, mesenchymal-like spermatogonia lacked imprinting specifically at paternally imprinted loci but fully restored imprinting prior to puberty. Furthermore, mesenchymal-like spermatogonia also displayed developmentally linked DNA demethylation at meiotic genes and also at certain monoallelic neural genes (e.g., protocadherins and olfactory receptors). We also reveal novel candidate receptor–ligand networks involving SSCs and the developing niche. Taken together, neonates/juveniles contain heterogeneous epithelial-like or mesenchymal-like spermatogonial populations, with the latter displaying extensive DNA methylation/chromatin dynamics. We speculate that this plasticity helps SSCs proliferate and migrate within the developing seminiferous tubule, with proper niche interaction and membrane attachment reverting mesenchymal-like spermatogonial subtype cells back to an epithelial-like state with normal imprinting profiles.
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Affiliation(s)
- Saher Sue Hammoud
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Diana H P Low
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Chongil Yi
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Chee Leng Lee
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Jon M Oatley
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
| | - Christopher J Payne
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA; Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA; Human Molecular Genetics Program, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60614, USA
| | - Douglas T Carrell
- Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Ernesto Guccione
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Bradley R Cairns
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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27
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Zamudio N, Barau J, Teissandier A, Walter M, Borsos M, Servant N, Bourc'his D. DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination. Genes Dev 2015; 29:1256-70. [PMID: 26109049 PMCID: PMC4495397 DOI: 10.1101/gad.257840.114] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Zamudio et al. demonstrate that DNA methylation restrains transposons from adopting chromatin characteristics amenable to meiotic recombination, which they propose prevents the occurrence of erratic chromosomal events. DNA methylation is essential for protecting the mammalian germline against transposons. When DNA methylation-based transposon control is defective, meiotic chromosome pairing is consistently impaired during spermatogenesis: How and why meiosis is vulnerable to transposon activity is unknown. Using two DNA methylation-deficient backgrounds, the Dnmt3L and Miwi2 mutant mice, we reveal that DNA methylation is largely dispensable for silencing transposons before meiosis onset. After this, it becomes crucial to back up to a developmentally programmed H3K9me2 loss. Massive retrotransposition does not occur following transposon derepression, but the meiotic chromatin landscape is profoundly affected. Indeed, H3K4me3 marks gained over transcriptionally active transposons correlate with formation of SPO11-dependent double-strand breaks and recruitment of the DMC1 repair enzyme in Dnmt3L−/− meiotic cells, whereas these features are normally exclusive to meiotic recombination hot spots. Here, we demonstrate that DNA methylation restrains transposons from adopting chromatin characteristics amenable to meiotic recombination, which we propose prevents the occurrence of erratic chromosomal events.
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Affiliation(s)
- Natasha Zamudio
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
| | - Joan Barau
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
| | - Aurélie Teissandier
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France; U900, INSERM, Paris 75005, France; Mines ParisTech, Institut Curie, Paris 75005, France
| | - Marius Walter
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
| | - Maté Borsos
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
| | - Nicolas Servant
- U900, INSERM, Paris 75005, France; Mines ParisTech, Institut Curie, Paris 75005, France
| | - Déborah Bourc'his
- UMR3215, CNRS, Paris 75005, France; U934, INSERM Institut Curie, Paris 75005, France
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28
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Huan Y, Zhu J, Huang B, Mu Y, Kong Q, Liu Z. Trichostatin A rescues the disrupted imprinting induced by somatic cell nuclear transfer in pigs. PLoS One 2015; 10:e0126607. [PMID: 25962071 PMCID: PMC4427324 DOI: 10.1371/journal.pone.0126607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/06/2015] [Indexed: 11/25/2022] Open
Abstract
Imprinting disorders induced by somatic cell nuclear transfer (SCNT) usually lead to the abnormalities of cloned animals and low cloning efficiency. Histone deacetylase inhibitors have been shown to improve gene expression, genomic methylation reprogramming and the development of cloned embryos, however, the imprinting statuses in these treated embryos and during their subsequent development remain poorly studied. In this study, we investigated the dynamics of H19/Igf2 methylation and transcription in porcine cloned embryos treated with trichostatin A (TSA), and examined H19/Igf2 imprinting patterns in cloned fetuses and piglets. Our results showed that compared with the maintenance of H19/Igf2 methylation in fertilized embryos, cloned embryos displayed aberrant H19/Igf2 methylation and lower H19/Igf2 transcripts. When TSA enhanced the development of cloned embryos, the disrupted H19/Igf2 imprinting was largely rescued in these treated embryos, more similar to those detected in fertilized counterparts. Further studies displayed that TSA effectively rescued the disrupted imprinting of H19/Igf2 in cloned fetuses and piglets, prevented the occurrence of cloned fetus and piglet abnormalities, and enhanced the full-term development of cloned embryos. In conclusion, our results demonstrated that aberrant imprinting induced by SCNT led to the abnormalities of cloned fetuses and piglets and low cloning efficiency, and TSA rescued the disrupted imprinting in cloned embryos, fetuses and piglets, and prevented the occurrence of cloned fetus and piglet abnormalities, thereby improving the development of cloned embryos. This study would have important implications in improving cloning efficiency and the health of cloned animals.
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Affiliation(s)
- Yanjun Huan
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong Province, China
| | - Jiang Zhu
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
| | - Bo Huang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
| | - Yanshuang Mu
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
| | - Qingran Kong
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
- * E-mail:
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29
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Monk D. Germline-derived DNA methylation and early embryo epigenetic reprogramming: The selected survival of imprints. Int J Biochem Cell Biol 2015; 67:128-38. [PMID: 25966912 DOI: 10.1016/j.biocel.2015.04.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/27/2015] [Indexed: 12/27/2022]
Abstract
DNA methylation is an essential epigenetic mechanism involved in many essential cellular processes. During development epigenetic reprograming takes place during gametogenesis and then again in the pre-implantation embryo. These two reprograming windows ensure genome-wide removal of methylation in the primordial germ cells so that sex-specific signatures can be acquired in the sperm and oocyte. Following fertilization the majority of this epigenetic information is erased to give the developing embryo an epigenetic profile coherent with pluripotency. It is estimated that ∼65% of the genome is differentially methylated between the gametes, however following embryonic reprogramming only parent-of-origin methylation at known imprinted loci remains. This suggests that trans-acting factors such as Zfp57 can discriminate imprinted differentially methylated regions (DMRs) from the thousands of CpG rich regions that are differentially marked in the gametes. Recently transient imprinted DMRs have been identified suggesting that these loci are also protected from pre-implantation reprograming but succumb to de novo remethylation at the implantation stage. This highlights that "ubiquitous" imprinted loci are also resilient to gaining methylation by protecting their unmethylated alleles. In this review I examine the processes involved in epigenetic reprograming and the mechanisms that ensure allelic methylation at imprinted loci is retained throughout the life of the organism, discussing the critical differences between mouse and humans. This article is part of a Directed Issue entitled: Epigenetics Dynamics in development and disease.
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Affiliation(s)
- David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona 08908, Spain.
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30
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O'Doherty AM, MacHugh DE, Spillane C, Magee DA. Genomic imprinting effects on complex traits in domesticated animal species. Front Genet 2015; 6:156. [PMID: 25964798 PMCID: PMC4408863 DOI: 10.3389/fgene.2015.00156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/06/2015] [Indexed: 11/13/2022] Open
Abstract
Monoallelically expressed genes that exert their phenotypic effect in a parent-of-origin specific manner are considered to be subject to genomic imprinting, the most well understood form of epigenetic regulation of gene expression in mammals. The observed differences in allele specific gene expression for imprinted genes are not attributable to differences in DNA sequence information, but to specific chemical modifications of DNA and chromatin proteins. Since the discovery of genomic imprinting some three decades ago, over 100 imprinted mammalian genes have been identified and considerable advances have been made in uncovering the molecular mechanisms regulating imprinted gene expression. While most genomic imprinting studies have focused on mouse models and human biomedical disorders, recent work has highlighted the contributions of imprinted genes to complex trait variation in domestic livestock species. Consequently, greater understanding of genomic imprinting and its effect on agriculturally important traits is predicted to have major implications for the future of animal breeding and husbandry. In this review, we discuss genomic imprinting in mammals with particular emphasis on domestic livestock species and consider how this information can be used in animal breeding research and genetic improvement programs.
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Affiliation(s)
- Alan M O'Doherty
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Ireland
| | - David E MacHugh
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Ireland ; Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, Galway Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield Ireland ; Department of Animal Science, University of Connecticut, Storrs, CT USA
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31
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Qi S, Wang Z, Li P, Wu Q, Shi T, Li J, Wong J. Non-germ Line Restoration of Genomic Imprinting for a Small Subset of Imprinted Genes in Ubiquitin-like PHD and RING Finger Domain-Containing 1 (Uhrf1) Null Mouse Embryonic Stem Cells. J Biol Chem 2015; 290:14181-91. [PMID: 25900245 DOI: 10.1074/jbc.m114.626697] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 01/23/2023] Open
Abstract
The underlying mechanism for the establishment and maintenance of differential DNA methylation in imprinted genes is largely unknown. Previous studies using Dnmt1 knock-out embryonic stem (ES) cells demonstrated that, although re-expression of DNMT1 restored DNA methylation in the non-imprinted regions, the methylation patterns of imprinted genes could be restored only through germ line passage. Knock-out of Uhrf1, an accessory factor essential for DNMT1-mediated DNA methylation, in mouse ES cells also led to impaired global DNA methylation and loss of genomic imprinting. Here, we demonstrate that, although re-expression of UHRF1 in Uhrf1(-/-) ES cells restored DNA methylation for the bulk genome but not for most of the imprinted genes, it did rescue DNA methylation for the imprinted H19, Nnat, and Dlk1 genes. Analysis of histone modifications at the differential methylated regions of the imprinted genes by ChIP assays revealed that for the imprinted genes whose DNA methylation could be restored upon re-expression of UHRF1, the active histone markers (especially H3K4me3) were maintained at considerably low levels, and low levels were maintained even in Uhrf1(-/-) ES cells. In contrast, for the imprinted genes whose DNA methylation could not be restored upon UHRF1 re-expression, the active histone markers (especially H3K4me3) were relatively high and became even higher in Uhrf1(-/-) ES cells. Our study thus supports a role for histone modifications in determining the establishment of imprinting-related DNA methylation and demonstrates that mouse ES cells can be a valuable model for mechanistic study of the establishment and maintenance of differential DNA methylation in imprinted genes.
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Affiliation(s)
- Shankang Qi
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241 and
| | - Zhiqiang Wang
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241 and
| | - Pishun Li
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241 and
| | - Qihan Wu
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241 and
| | - Tieliu Shi
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241 and
| | - Jiwen Li
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241 and
| | - Jiemin Wong
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241 and the Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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32
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Sanli I, Feil R. Chromatin mechanisms in the developmental control of imprinted gene expression. Int J Biochem Cell Biol 2015; 67:139-47. [PMID: 25908531 DOI: 10.1016/j.biocel.2015.04.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
Hundreds of protein-coding genes and regulatory non-coding RNAs (ncRNAs) are subject to genomic imprinting. The mono-allelic DNA methylation marks that control imprinted gene expression are somatically maintained throughout development, and this process is linked to specific chromatin features. Yet, at many imprinted genes, the mono-allelic expression is lineage or tissue-specific. Recent studies provide mechanistic insights into the developmentally-restricted action of the 'imprinting control regions' (ICRs). At several imprinted domains, the ICR expresses a long ncRNA that mediates chromatin repression in cis (and probably in trans as well). ICRs at other imprinted domains mediate higher-order chromatin structuration that enhances, or prevents, transcription of close-by genes. Here, we present how chromatin and ncRNAs contribute to developmental control of imprinted gene expression and discuss implications for disease. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Ildem Sanli
- Institute of Molecular Genetics (IGMM), UMR-5535, CNRS, University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), UMR-5535, CNRS, University of Montpellier, 1919 route de Mende, 34293 Montpellier, France.
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Kamimura S, Hatanaka Y, Hirasawa R, Matsumoto K, Oikawa M, Lee J, Matoba S, Mizutani E, Ogonuki N, Inoue K, Kohda T, Ishino F, Ogura A. Establishment of Paternal Genomic Imprinting in Mouse Prospermatogonia Analyzed by Nuclear Transfer1. Biol Reprod 2014; 91:120. [DOI: 10.1095/biolreprod.114.120451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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34
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Kota SK, Llères D, Bouschet T, Hirasawa R, Marchand A, Begon-Pescia C, Sanli I, Arnaud P, Journot L, Girardot M, Feil R. ICR noncoding RNA expression controls imprinting and DNA replication at the Dlk1-Dio3 domain. Dev Cell 2014; 31:19-33. [PMID: 25263792 DOI: 10.1016/j.devcel.2014.08.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 07/04/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
Imprinted genes play essential roles in development, and their allelic expression is mediated by imprinting control regions (ICRs). The Dlk1-Dio3 locus is among the few imprinted domains controlled by a paternally methylated ICR. The unmethylated maternal copy activates imprinted expression early in development through an unknown mechanism. We find that in mouse embryonic stem cells (ESCs) and in blastocysts, this function is linked to maternal, bidirectional expression of noncoding RNAs (ncRNAs) from the ICR. Disruption of ICR ncRNA expression in ESCs affected gene expression in cis, led to acquisition of aberrant histone and DNA methylation, delayed replication timing along the domain on the maternal chromosome, and changed its subnuclear localization. The epigenetic alterations persisted during differentiation and affected the neurogenic potential of the stem cells. Our data indicate that monoallelic expression at an ICR of enhancer RNA-like ncRNAs controls imprinted gene expression, epigenetic maintenance processes, and DNA replication in embryonic cells.
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Affiliation(s)
- Satya K Kota
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Tristan Bouschet
- Institute of Functional Genomics (IGF), CNRS and University of Montpellier, 141 rue de la Cardonille, Montpellier 34090, France
| | - Ryutaro Hirasawa
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Alice Marchand
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Christina Begon-Pescia
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Ildem Sanli
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Philippe Arnaud
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Laurent Journot
- Institute of Functional Genomics (IGF), CNRS and University of Montpellier, 141 rue de la Cardonille, Montpellier 34090, France
| | - Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 Route de Mende, Montpellier 34293, France.
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Deb M, Kar S, Sengupta D, Shilpi A, Parbin S, Rath SK, Londhe VA, Patra SK. Chromatin dynamics: H3K4 methylation and H3 variant replacement during development and in cancer. Cell Mol Life Sci 2014; 71:3439-63. [PMID: 24676717 PMCID: PMC11113154 DOI: 10.1007/s00018-014-1605-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 02/11/2014] [Accepted: 03/06/2014] [Indexed: 12/11/2022]
Abstract
The dynamic nature of chromatin and its myriad modifications play a crucial role in gene regulation (expression and repression) during development, cellular survival, homeostasis, ageing, and apoptosis/death. Histone 3 lysine 4 methylation (H3K4 methylation) catalyzed by H3K4 specific histone methyltransferases is one of the more critical chromatin modifications that is generally associated with gene activation. Additionally, the deposition of H3 variant(s) in conjunction with H3K4 methylation generates an intricately reliable epigenetic regulatory circuit that guides transcriptional activity in normal development and homeostasis. Consequently, alterations in this epigenetic circuit may trigger disease development. The mechanistic relationship between H3 variant deposition and H3K4 methylation during normal development has remained foggy. However, recent investigations in the field of chromatin dynamics in various model organisms, tumors, cancer tissues, and cell lines cultured without and with therapeutic agents, as well as from model reconstituted chromatins reveal that there may be different subsets of chromatin assemblage with specific patterns of histone replacement executing similar functions. In this light, we attempt to explain the intricate control system that maintains chromatin structure and dynamics during normal development as well as during tumor development and cancer progression in this review. Our focus is to highlight the contribution of H3K4 methylation-histone variant crosstalk in regulating chromatin architecture and subsequently its function.
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Affiliation(s)
- Moonmoon Deb
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Dipta Sengupta
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Arunima Shilpi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sabnam Parbin
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sandip K. Rath
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Vedang A. Londhe
- Division of Neonatology and Developmental Biology, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1752 USA
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
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Kim JH, Jee BC, Lee JM, Suh CS, Kim SH. Histone acetylation level and histone acetyltransferase/deacetylase activity in ejaculated sperm from normozoospermic men. Yonsei Med J 2014; 55:1333-40. [PMID: 25048493 PMCID: PMC4108820 DOI: 10.3349/ymj.2014.55.5.1333] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
PURPOSE The aim of this work was to evaluate nuclear histone acetylation level and total histone acetyltransferase (HAT) and deacetylase (HDAC) activity in ejaculated sperm and their relevance to conventional sperm parameters. MATERIALS AND METHODS Thirty-three normozoospermic men were included in this study. Semen samples were processed by swim-up and then immunostained by six acetylation antibodies (H3K9ac, H3K14ac, H4K5ac, H4K8ac, H4K12ac, and H4K16ac). Our preliminary study verified the expression of HAT/HDAC1 in mature human sperm. From vitrified-warmed sperm samples, total HAT/HDAC activity was measured by commercially available kits. Nuclear DNA integrity was also measured by TUNEL assay. RESULTS The levels of six acetylation marks were not related with conventional sperm parameters including sperm DNA fragmentation index (DFI) as well as HAT/HDAC activity. However, sperm DFI was positively correlated with HAT activity (r=0.038 after adjustment, p<0.02). HAT activity showed a negative relationship with HDAC activity (r=-0.51, p<0.01). Strict morphology was negatively correlated with acetylation enzyme index (=HAT activity/HDAC activity) (r=-0.53, p<0.01). CONCLUSION Our works demonstrated a significant relationship of acetylation-associated enzyme activity and strict morphology or sperm DFI.
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Affiliation(s)
- Jee Hyun Kim
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea. ; Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Byung Chul Jee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea. ; Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Jang Mi Lee
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Chang Suk Suh
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea. ; Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Seok Hyun Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea. ; Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
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Lambrot R, Xu C, Saint-Phar S, Chountalos G, Cohen T, Paquet M, Suderman M, Hallett M, Kimmins S. Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes. Nat Commun 2014; 4:2889. [PMID: 24326934 PMCID: PMC3863903 DOI: 10.1038/ncomms3889] [Citation(s) in RCA: 288] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 11/07/2013] [Indexed: 01/20/2023] Open
Abstract
Epidemiological studies suggest that a father's diet can influence offspring health. A proposed mechanism for paternal transmission of environmental information is via the sperm epigenome. The epigenome includes heritable information such as DNA methylation. We hypothesize that the dietary supply of methyl donors will alter epigenetic reprogramming in sperm. Here we feed male mice either a folate-deficient or folate-sufficient diet throughout life. Paternal folate deficiency is associated with increased birth defects in the offspring, which include craniofacial and musculoskeletal malformations. Genome-wide DNA methylation analysis and the subsequent functional analysis identify differential methylation in sperm of genes implicated in development, chronic diseases such as cancer, diabetes, autism and schizophrenia. While >300 genes are differentially expressed in offspring placenta, only two correspond to genes with differential methylation in sperm. This model suggests epigenetic transmission may involve sperm histone H3 methylation or DNA methylation and that adequate paternal dietary folate is essential for offspring health.
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Affiliation(s)
- R Lambrot
- 1] Department of Animal Science, McGill University, Ste Anne-de-Bellevue, Québec H9X3V9, Canada [2]
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Magee DA, Spillane C, Berkowicz EW, Sikora KM, MacHugh DE. Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits. Anim Genet 2014; 45 Suppl 1:25-39. [PMID: 24990393 DOI: 10.1111/age.12168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 12/30/2022]
Abstract
The phenomenon of genomic imprinting, whereby a subset of mammalian genes display parent-of-origin-specific monoallelic expression, is one of the most active areas of epigenetics research. Over the past two decades, more than 100 imprinted mammalian genes have been identified, while considerable advances have been made in elucidating the molecular mechanisms governing imprinting. These studies have helped to unravel the epigenome--a separate layer of regulatory information contained in eukaryotic chromosomes that influences gene expression and phenotypes without involving changes to the underlying DNA sequence. Although most studies of genomic imprinting in mammals have focussed on mouse models or human biomedical disorders, there is burgeoning interest in the phenotypic effects of imprinted genes in domestic livestock species. In particular, research has focused on imprinted genes influencing foetal growth and development, which are associated with economically important production traits in cattle, sheep and pigs. These findings, when coupled with the data emerging from the various different livestock genome projects, have major implications for the future of animal breeding, health and management. Here, we review current scientific knowledge regarding genomic imprinting in livestock species and evaluate how this information can be used in modern livestock improvement programmes.
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Affiliation(s)
- D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
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Hammoud SS, Low DHP, Yi C, Carrell DT, Guccione E, Cairns BR. Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis. Cell Stem Cell 2014; 15:239-53. [PMID: 24835570 DOI: 10.1016/j.stem.2014.04.006] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 02/24/2014] [Accepted: 04/07/2014] [Indexed: 01/16/2023]
Abstract
Adult germline stem cells (AGSCs) self-renew (Thy1(+) enriched) or commit to gametogenesis (Kit(+) enriched). To better understand how chromatin regulates AGSC biology and gametogenesis, we derived stage-specific high-resolution profiles of DNA methylation, 5hmC, histone modifications/variants, and RNA-seq in AGSCs and during spermatogenesis. First, we define striking signaling and transcriptional differences between AGSC types, involving key self-renewal and proliferation pathways. Second, key pluripotency factors (e.g., Nanog) are silent in AGSCs and bear particular chromatin/DNAme attributes that may "poise" them for reactivation after fertilization. Third, AGSCs display chromatin "poising/bivalency" of enhancers and promoters for embryonic transcription factors. Remarkably, gametogenesis occurs without significant changes in DNAme and instead involves transcription of DNA-methylated promoters bearing high RNAPol2, H3K9ac, H3K4me3, low CG content, and (often) 5hmC. Furthermore, key findings were confirmed in human sperm. Here, we reveal AGSC signaling asymmetries and chromatin/DNAme strategies in AGSCs to poise key transcription factors and to activate DNA-methylated promoters during gametogenesis.
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Affiliation(s)
- Saher Sue Hammoud
- Howard Hughes Medical Institute, Department of Oncological Sciences, and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Diana H P Low
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology, A(∗)STAR (Agency for Science, Technology and Research), Singapore 119074, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
| | - Chongil Yi
- Howard Hughes Medical Institute, Department of Oncological Sciences, and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Douglas T Carrell
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ernesto Guccione
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology, A(∗)STAR (Agency for Science, Technology and Research), Singapore 119074, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore.
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences, and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Leung D, Du T, Wagner U, Xie W, Lee AY, Goyal P, Li Y, Szulwach KE, Jin P, Lorincz MC, Ren B. Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. Proc Natl Acad Sci U S A 2014; 111:6690-5. [PMID: 24757056 PMCID: PMC4020067 DOI: 10.1073/pnas.1322273111] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
During mammalian development, DNA methylation patterns need to be reset in primordial germ cells (PGCs) and preimplantation embryos. However, many LTR retrotransposons and imprinted genes are impervious to such global epigenetic reprogramming via hitherto undefined mechanisms. Here, we report that a subset of such genomic regions are resistant to widespread erasure of DNA methylation in mouse embryonic stem cells (mESCs) lacking the de novo DNA methyltransferases (Dnmts) Dnmt3a and Dnmt3b. Intriguingly, these loci are enriched for H3K9me3 in mESCs, implicating this mark in DNA methylation homeostasis. Indeed, deletion of the H3K9 methyltransferase SET domain bifurcated 1 (Setdb1) results in reduced H3K9me3 and DNA methylation levels at specific loci, concomitant with increased 5-hydroxymethylation (5hmC) and ten-eleven translocation 1 binding. Taken together, these data reveal that Setdb1 promotes the persistence of DNA methylation in mESCs, likely reflecting one mechanism by which DNA methylation is maintained at LTR retrotransposons and imprinted genes during developmental stages when DNA methylation is reprogrammed.
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Affiliation(s)
- Danny Leung
- Ludwig Institute for Cancer Research, and
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093-0653
| | | | | | - Wei Xie
- Tsinghua University–Peking University Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | | | - Preeti Goyal
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and
| | - Yujing Li
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Keith E. Szulwach
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322
| | - Matthew C. Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and
| | - Bing Ren
- Ludwig Institute for Cancer Research, and
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA 92093-0653
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Post-natal imprinting: evidence from marsupials. Heredity (Edinb) 2014; 113:145-55. [PMID: 24595366 DOI: 10.1038/hdy.2014.10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 12/19/2013] [Accepted: 01/09/2014] [Indexed: 12/31/2022] Open
Abstract
Genomic imprinting has been identified in therian (eutherian and marsupial) mammals but not in prototherian (monotreme) mammals. Imprinting has an important role in optimising pre-natal nutrition and growth, and most imprinted genes are expressed and imprinted in the placenta and developing fetus. In marsupials, however, the placental attachment is short-lived, and most growth and development occurs post-natally, supported by a changing milk composition tailor-made for each stage of development. Therefore there is a much greater demand on marsupial females during post-natal lactation than during pre-natal placentation, so there may be greater selection for genomic imprinting in the mammary gland than in the short-lived placenta. Recent studies in the tammar wallaby confirm the presence of genomic imprinting in nutrient-regulatory genes in the adult mammary gland. This suggests that imprinting may influence infant post-natal growth via the mammary gland as it does pre-natally via the placenta. Similarly, an increasing number of imprinted genes have been implicated in regulating feeding and nurturing behaviour in both the adult and the developing neonate/offspring in mice. Together these studies provide evidence that genomic imprinting is critical for regulating growth and subsequently the survival of offspring not only pre-natally but also post-natally.
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Abstract
Early follow-up studies of IVF children showed that the frequency of birth anomalies resembled those arising with natural conception. More detailed analyses confirmed these findings, reinforcing the concept of the preimplantation period as teratologically "safe." The use of intracytoplasmic sperm injection (ICSI) to achieve fertilization introduced another variable.ICSI's safety has often been criticized because the fertilizing spermatozoon neither binds to the zona pellucida nor fuses with oolemma. Bypassing these physiologic steps together with the arbitrary selection of the spermatozoon has been reason for concern. Thus far, ICSI offspring undergoing adolescence and beyond has provided sufficient information to reassure these qualms. In fact, the health of the offspring generated through ICSI, once taken into consideration the gestational order, the age and the genetic makeup of the couples are generally reassuring.
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Affiliation(s)
- Gianpiero D Palermo
- The Ronald O. Perelman & Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, 1305 York Avenue, Suite 720, New York, NY, 10021, USA,
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Abstract
Major difficulties exist in the accurate and meaningful diagnosis of male reproductive dysfunction, and our understanding of the epidemiology and etiology of male infertility has proven quite complex.The numerous spermatozoa produced in mammals and other species provides some degree of protection against adverse environmental conditions represented by physical and chemical factors that can reduce reproductive function and increase gonadal damage even resulting in testicular cancer or congenital malformations. The wide fluctuations of sperm production in men, both geographical and temporal, may reflect disparate environmental exposures, occurring on differing genetic backgrounds, in varying psychosocial conditions, and leading to the diversified observed outcomes.Sperm analysis is still the cornerstone in diagnosis of male factor infertility, indeed, individually compromised semen paramaters while adequately address therapeutic practices is progressively flanked by additional tests. Administration of drugs, IUI, correction of varicocele, and, to a certain extent, IVF although they may not be capable of restoring fertility itself often result in childbearing.
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Affiliation(s)
- Gianpiero D Palermo
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, 1305 York Avenue, Suite 720, New York, NY, 10021, USA,
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Genomic Imprinting - der Kampf der Geschlechter auf molekularer Ebene. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Jurkowska RZ, Jeltsch A. Genomic Imprinting-The Struggle of the Genders at the Molecular Level. Angew Chem Int Ed Engl 2013; 52:13524-36. [DOI: 10.1002/anie.201307005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Indexed: 11/10/2022]
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Garner JL, Niles KM, McGraw S, Yeh JR, Cushnie DW, Hermo L, Nagano MC, Trasler JM. Stability of DNA Methylation Patterns in Mouse Spermatogonia Under Conditions of MTHFR Deficiency and Methionine Supplementation1. Biol Reprod 2013; 89:125. [DOI: 10.1095/biolreprod.113.109066] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Girardot M, Hirasawa R, Kacem S, Fritsch L, Pontis J, Kota SK, Filipponi D, Fabbrizio E, Sardet C, Lohmann F, Kadam S, Ait-Si-Ali S, Feil R. PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome. Nucleic Acids Res 2013; 42:235-48. [PMID: 24097435 PMCID: PMC3874197 DOI: 10.1093/nar/gkt884] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Symmetrical dimethylation on arginine-3 of histone H4 (H4R3me2s) has been reported to occur at several repressed genes, but its specific regulation and genomic distribution remained unclear. Here, we show that the type-II protein arginine methyltransferase PRMT5 controls H4R3me2s in mouse embryonic fibroblasts (MEFs). In these differentiated cells, we find that the genome-wide pattern of H4R3me2s is highly similar to that in embryonic stem cells. In both the cell types, H4R3me2s peaks are detected predominantly at G + C-rich regions. Promoters are consistently marked by H4R3me2s, independently of transcriptional activity. Remarkably, H4R3me2s is mono-allelic at imprinting control regions (ICRs), at which it marks the same parental allele as H3K9me3, H4K20me3 and DNA methylation. These repressive chromatin modifications are regulated independently, however, since PRMT5-depletion in MEFs resulted in loss of H4R3me2s, without affecting H3K9me3, H4K20me3 or DNA methylation. Conversely, depletion of ESET (KMT1E) or SUV420H1/H2 (KMT5B/C) affected H3K9me3 and H4K20me3, respectively, without altering H4R3me2s at ICRs. Combined, our data indicate that PRMT5-mediated H4R3me2s uniquely marks the mammalian genome, mostly at G + C-rich regions, and independently from transcriptional activity or chromatin repression. Furthermore, comparative bioinformatics analyses suggest a putative role of PRMT5-mediated H4R3me2s in chromatin configuration in the nucleus.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, 1919 route de Mende, 34293 Montpellier, Laboratoire Epigénétique et Destin Cellulaire, UMR7216, CNRS, Université Paris Diderot, 35 rue Hélène Brion, 75013 Paris, France and Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
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The chicken HS4 insulator element does not protect the H19 ICR from differential DNA methylation in yeast artificial chromosome transgenic mouse. PLoS One 2013; 8:e73925. [PMID: 24023912 PMCID: PMC3762768 DOI: 10.1371/journal.pone.0073925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 07/25/2013] [Indexed: 12/15/2022] Open
Abstract
Mono-allelic expression at the mouse IGF2/H19 locus is controlled by differential allelic DNA methylation of the imprinting control region (ICR). Because a randomly integrated H19 ICR fragment, when incorporated into the genome of transgenic mice (TgM), was allele-specifically methylated in somatic, but not in germ cells, it was suggested that allele-discriminating epigenetic signature, set within or somewhere outside of the Tg H19 ICR fragment in germ cells, was later translated into a differential DNA methylation pattern. To test if the chicken β-globin HS4 (cHS4) chromatin insulator might interfere with methylation imprinting establishment at the H19 ICR, we inserted the H19 ICR fragment, flanked by a set of floxed cHS4 core sequences, into a human β-globin locus YAC and generated TgM (insulated ICR' TgM). As controls, the cHS4 sequences were removed from one side (5'HS4-deleted ICR') or both sides (pseudo-WT ICR') of the insulated ICR' by in vivo cre-loxP recombination. The data show that while maternally inherited transgenic H19 ICR was not methylated in insulated ICR' TgM, it was significantly methylated upon paternal transmission, though the level was lower than in the pseudo-WT ICR' control. Because this reduced level of methylation was also observed in the 5'HS4-deleted ICR' TgM, we speculate that the phenotype is due to VEZF1-dependent demethylation activity, rather than the insulator function, borne in cHS4. Collectively, although we cannot rule out the possibility that cHS4 is incapable of blocking an allele-discriminating signal from outside of the transgene, the epigenetic signature appears to be marked intrinsically within the H19 ICR.
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Erkek S, Hisano M, Liang CY, Gill M, Murr R, Dieker J, Schübeler D, van der Vlag J, Stadler MB, Peters AHFM. Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa. Nat Struct Mol Biol 2013; 20:868-75. [PMID: 23770822 DOI: 10.1038/nsmb.2599] [Citation(s) in RCA: 245] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/29/2013] [Indexed: 12/21/2022]
Abstract
In mammalian spermatozoa, most but not all of the genome is densely packaged by protamines. Here we reveal the molecular logic underlying the retention of nucleosomes in mouse spermatozoa, which contain only 1% residual histones. We observe high enrichment throughout the genome of nucleosomes at CpG-rich sequences that lack DNA methylation. Residual nucleosomes are largely composed of the histone H3.3 variant and are trimethylated at Lys4 of histone H3 (H3K4me3). Canonical H3.1 and H3.2 histones are also enriched at CpG-rich promoters marked by Polycomb-mediated H3K27me3, a modification predictive of gene repression in preimplantation embryos. Histone variant-specific nucleosome retention in sperm is strongly associated with nucleosome turnover in round spermatids. Our data show evolutionary conservation of the basic principles of nucleosome retention in mouse and human sperm, supporting a model of epigenetic inheritance by nucleosomes between generations.
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Affiliation(s)
- Serap Erkek
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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