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Osipov YA, Posukh OV, Kalashnikova DA, Antoshina PA, Laktionov PP, Skrypnik PA, Belyakin SN, Singh PB. H3K9 and H4K20 methyltransferases are directly involved in the heterochromatinization of the paternal chromosomes in male Planococcus citri embryos. Chromosoma 2023; 132:317-328. [PMID: 37700063 DOI: 10.1007/s00412-023-00809-3] [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: 05/01/2023] [Revised: 08/11/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Using a new method for bulk preparation of early stage embryos, we have investigated the role played by putative Planococcus citri H3K9 and H4K20 histone methyl transferases (HMTases) in regulating heterochromatinization of the imprinted paternal chromosomal set in male embryos. We found that H3K9 and H420 HMTases are required for heterochromatinization of the paternal chromosomes. We present evidence that both HMTases maintain the paternal "imprint" during the cleavage divisions when both parental chromosome sets are euchromatic. A testable model that accommodates our findings is proposed.
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Affiliation(s)
- Yakov A Osipov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Olga V Posukh
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Darya A Kalashnikova
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Polina A Antoshina
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Petr P Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Polina A Skrypnik
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
- Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, 630090, Novosibirsk, Russian Federation
| | - Stepan N Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation.
| | - Prim B Singh
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation.
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, 010000, Nur-Sultan, Kazakhstan.
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2
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Wang Y, Yu Y, Yang W, Wu L, Yang Y, Lu Q, Zhou J. SETD4 Confers Cancer Stem Cell Chemoresistance in Nonsmall Cell Lung Cancer Patients via the Epigenetic Regulation of Cellular Quiescence. Stem Cells Int 2023; 2023:7367854. [PMID: 37274024 PMCID: PMC10239305 DOI: 10.1155/2023/7367854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/23/2023] [Accepted: 05/08/2023] [Indexed: 06/06/2023] Open
Abstract
Increasing evidence indicates that quiescent cancer stem cells (CSCs) are a root cause of chemoresistance. SET domain-containing protein 4 (SETD4) epigenetically regulates cell quiescence in breast cancer stem cells (BCSCs), and SETD4-positive BCSCs are chemoradioresistant. However, the role of SETD4 in chemoresistance, tumor progression, and prognosis in nonsmall cell lung cancer (NSCLC) patients is unclear. Here, SETD4-positive cells were identified as quiescent lung cancer stem cells (qLCSCs) since they expressed high levels of ALDH1 and CD133 and low levels of Ki67. SETD4 expression was significantly higher in advanced-stage NSCLC tissues than in early-stage NSCLC tissues and significantly higher in samples from the chemoresistant group than in those from the chemosensitive group. Patients with high SETD4 expression had shorter progression-free survival (PFS) times than those with low SETD4 expression. SETD4 facilitated heterochromatin formation via H4K20me3, thereby leading to cell quiescence. RNA-seq analysis showed upregulation of genes involved in cell proliferation, glucose metabolism, and PI3K-AKT signaling in activated qLCSCs (A-qLCSCs) compared with qLCSCs. In addition, SETD4 overexpression facilitated PTEN-mediated inhibition of the PI3K-mTOR pathway. In summary, SETD4 confers chemoresistance, tumor progression, and a poor prognosis by regulating CSCs in NSCLC patients.
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Affiliation(s)
- Yuehong Wang
- Department of Respiratory Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yuman Yu
- Department of Geriatrics, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Weijun Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Linying Wu
- Department of Respiratory Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yaoshun Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qianyun Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianying Zhou
- Department of Respiratory Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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3
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Metur SP, Lei Y, Zhang Z, Klionsky DJ. Regulation of autophagy gene expression and its implications in cancer. J Cell Sci 2023; 136:jcs260631. [PMID: 37199330 PMCID: PMC10214848 DOI: 10.1242/jcs.260631] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Autophagy is a catabolic cellular process that targets and eliminates superfluous cytoplasmic components via lysosomal degradation. This evolutionarily conserved process is tightly regulated at multiple levels as it is critical for the maintenance of homeostasis. Research in the past decade has established that dysregulation of autophagy plays a major role in various diseases, such as cancer and neurodegeneration. However, modulation of autophagy as a therapeutic strategy requires identification of key players that can fine tune the induction of autophagy without complete abrogation. In this Review, we summarize the recent discoveries on the mechanism of regulation of ATG (autophagy related) gene expression at the level of transcription, post transcription and translation. Furthermore, we briefly discuss the role of aberrant expression of ATG genes in the context of cancer.
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Affiliation(s)
- Shree Padma Metur
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuchen Lei
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhihai Zhang
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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4
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González-Rodríguez P, Füllgrabe J, Joseph B. The hunger strikes back: an epigenetic memory for autophagy. Cell Death Differ 2023:10.1038/s41418-023-01159-4. [PMID: 37031275 DOI: 10.1038/s41418-023-01159-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Historical and demographical human cohorts of populations exposed to famine, as well as animal studies, revealed that exposure to food deprivation is associated to lasting health-related effects for the exposed individuals, as well as transgenerational effects in their offspring that affect their diseases' risk and overall longevity. Autophagy, an evolutionary conserved catabolic process, serves as cellular response to cope with nutrient starvation, allowing the mobilization of an internal source of stored nutrients and the production of energy. We review the evidence obtained in multiple model organisms that support the idea that autophagy induction, including through dietary regimes based on reduced food intake, is in fact associated to improved health span and extended lifespan. Thereafter, we expose autophagy-induced chromatin remodeling, such as DNA methylation and histone posttranslational modifications that are known heritable epigenetic marks, as a plausible mechanism for transgenerational epigenetic inheritance of hunger.
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Affiliation(s)
- Patricia González-Rodríguez
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jens Füllgrabe
- Cambridge Epigenetix Ltd, The Trinity Building, Chesterford Research Park, Cambridge, UK
| | - Bertrand Joseph
- Institute of Environmental Medicine, Toxicology Unit, Karolinska Institutet, Stockholm, Sweden.
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5
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Goissis MD, Cibelli JB. Early Cell Specification in Mammalian Fertilized and Somatic Cell Nuclear Transfer Embryos. Methods Mol Biol 2023; 2647:59-81. [PMID: 37041329 DOI: 10.1007/978-1-0716-3064-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Early cell specification in mammalian preimplantation embryos is an intricate cellular process that leads to coordinated spatial and temporal expression of specific genes. Proper segregation into the first two cell lineages, the inner cell mass (ICM) and the trophectoderm (TE), is imperative for developing the embryo proper and the placenta, respectively. Somatic cell nuclear transfer (SCNT) allows the formation of a blastocyst containing both ICM and TE from a differentiated cell nucleus, which means that this differentiated genome must be reprogrammed to a totipotent state. Although blastocysts can be generated efficiently through SCNT, the full-term development of SCNT embryos is impaired mostly due to placental defects. In this review, we examine the early cell fate decisions in fertilized embryos and compare them to observations in SCNT-derived embryos, in order to understand if these processes are affected by SCNT and could be responsible for the low success of reproductive cloning.
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Affiliation(s)
- Marcelo D Goissis
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil.
| | - Jose B Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
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6
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Mapook A, Hyde KD, Hassan K, Kemkuignou BM, Čmoková A, Surup F, Kuhnert E, Paomephan P, Cheng T, de Hoog S, Song Y, Jayawardena RS, Al-Hatmi AMS, Mahmoudi T, Ponts N, Studt-Reinhold L, Richard-Forget F, Chethana KWT, Harishchandra DL, Mortimer PE, Li H, Lumyong S, Aiduang W, Kumla J, Suwannarach N, Bhunjun CS, Yu FM, Zhao Q, Schaefer D, Stadler M. Ten decadal advances in fungal biology leading towards human well-being. FUNGAL DIVERS 2022; 116:547-614. [PMID: 36123995 PMCID: PMC9476466 DOI: 10.1007/s13225-022-00510-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/28/2022] [Indexed: 11/04/2022]
Abstract
Fungi are an understudied resource possessing huge potential for developing products that can greatly improve human well-being. In the current paper, we highlight some important discoveries and developments in applied mycology and interdisciplinary Life Science research. These examples concern recently introduced drugs for the treatment of infections and neurological diseases; application of -OMICS techniques and genetic tools in medical mycology and the regulation of mycotoxin production; as well as some highlights of mushroom cultivaton in Asia. Examples for new diagnostic tools in medical mycology and the exploitation of new candidates for therapeutic drugs, are also given. In addition, two entries illustrating the latest developments in the use of fungi for biodegradation and fungal biomaterial production are provided. Some other areas where there have been and/or will be significant developments are also included. It is our hope that this paper will help realise the importance of fungi as a potential industrial resource and see the next two decades bring forward many new fungal and fungus-derived products.
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Affiliation(s)
- Ausana Mapook
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
- Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou, 510225 China
| | - Khadija Hassan
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
| | - Blondelle Matio Kemkuignou
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
| | - Adéla Čmoková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Frank Surup
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Brunswick, Germany
| | - Eric Kuhnert
- Centre of Biomolecular Drug Research (BMWZ), Institute for Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Pathompong Paomephan
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Department of Biotechnology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400 Thailand
| | - Tian Cheng
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Sybren de Hoog
- Center of Expertise in Mycology, Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Guizhou Medical University, Guiyang, China
- Microbiology, Parasitology and Pathology Graduate Program, Federal University of Paraná, Curitiba, Brazil
| | - Yinggai Song
- Department of Dermatology, Peking University First Hospital, Peking University, Beijing, China
| | - Ruvishika S. Jayawardena
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Abdullah M. S. Al-Hatmi
- Center of Expertise in Mycology, Radboud University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nadia Ponts
- INRAE, UR1264 Mycology and Food Safety (MycSA), 33882 Villenave d’Ornon, France
| | - Lena Studt-Reinhold
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), Tulln an der Donau, Austria
| | | | - K. W. Thilini Chethana
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Dulanjalee L. Harishchandra
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Peter E. Mortimer
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Huili Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Saisamorm Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, 10300 Thailand
| | - Worawoot Aiduang
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200 Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Chitrabhanu S. Bhunjun
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Feng-Ming Yu
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- School of Science, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- Yunnan Key Laboratory of Fungal Diversity and Green Development, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Qi Zhao
- Yunnan Key Laboratory of Fungal Diversity and Green Development, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Doug Schaefer
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Brunswick, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106 Brunswick, Germany
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7
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Bernués J, Izquierdo-Boulstridge A, Reina O, Castejón L, Fernández-Castañer E, Leal N, Guerrero-Pepinosa N, Bonet-Costa C, Vujatovic O, Climent-Cantó P, Azorín F. Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation. Nucleic Acids Res 2022; 50:9212-9225. [PMID: 36039761 PMCID: PMC9458452 DOI: 10.1093/nar/gkac716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 08/01/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Post-translational modifications (PTMs) of core histones are important epigenetic determinants that correlate with functional chromatin states. However, despite multiple linker histone H1s PTMs have been identified, little is known about their genomic distribution and contribution to the epigenetic regulation of chromatin. Here, we address this question in Drosophila that encodes a single somatic linker histone, dH1. We previously reported that dH1 is dimethylated at K27 (dH1K27me2). Here, we show that dH1K27me2 is a major PTM of Drosophila heterochromatin. At mitosis, dH1K27me2 accumulates at pericentromeric heterochromatin, while, in interphase, it is also detected at intercalary heterochromatin. ChIPseq experiments show that >98% of dH1K27me2 enriched regions map to heterochromatic repetitive DNA elements, including transposable elements, simple DNA repeats and satellite DNAs. Moreover, expression of a mutated dH1K27A form, which impairs dH1K27me2, alters heterochromatin organization, upregulates expression of heterochromatic transposable elements and results in the accumulation of RNA:DNA hybrids (R-loops) in heterochromatin, without affecting H3K9 methylation and HP1a binding. The pattern of dH1K27me2 is H3K9 methylation independent, as it is equally detected in flies carrying a H3K9R mutation, and is not affected by depletion of Su(var)3-9, HP1a or Su(var)4-20. Altogether these results suggest that dH1K27me2 contributes to heterochromatin organization independently of H3K9 methylation.
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Affiliation(s)
- Jordi Bernués
- To whom correspondence should be addressed. Tel: +34 934034960;
| | - Andrea Izquierdo-Boulstridge
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lucía Castejón
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elena Fernández-Castañer
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Núria Leal
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Nancy Guerrero-Pepinosa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carles Bonet-Costa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Olivera Vujatovic
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Paula Climent-Cantó
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac 4, 08028 Barcelona, Spain,Institute for Research in Biomedicine of Barcelona, IRB Barcelona. The Barcelona Institute of Science and Technology. Baldiri Reixac 10, 08028 Barcelona, Spain
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8
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Di Stefano L. All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing. Cells 2022; 11:cells11162501. [PMID: 36010577 PMCID: PMC9406493 DOI: 10.3390/cells11162501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute a sizeable portion of many eukaryotic genomes. Through their mobility, they represent a major source of genetic variation, and their activation can cause genetic instability and has been linked to aging, cancer and neurodegenerative diseases. Accordingly, tight regulation of TE transcription is necessary for normal development. Chromatin is at the heart of TE regulation; however, we still lack a comprehensive understanding of the precise role of chromatin marks in TE silencing and how chromatin marks are established and maintained at TE loci. In this review, I discuss evidence documenting the contribution of chromatin-associated proteins and histone marks in TE regulation across different species with an emphasis on Drosophila and mammalian systems.
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Affiliation(s)
- Luisa Di Stefano
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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9
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Gopinathan G, Diekwisch TGH. Epigenetics and Early Development. J Dev Biol 2022; 10:jdb10020026. [PMID: 35735917 PMCID: PMC9225096 DOI: 10.3390/jdb10020026] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
The epigenome controls all aspect of eukaryotic development as the packaging of DNA greatly affects gene expression. Epigenetic changes are reversible and do not affect the DNA sequence itself but rather control levels of gene expression. As a result, the science of epigenetics focuses on the physical configuration of chromatin in the proximity of gene promoters rather than on the mechanistic effects of gene sequences on transcription and translation. In the present review we discuss three prominent epigenetic modifications, DNA methylation, histone methylation/acetylation, and the effects of chromatin remodeling complexes. Specifically, we introduce changes to the methylated state of DNA through DNA methyltransferases and DNA demethylases, discuss the effects of histone tail modifications such as histone acetylation and methylation on gene expression and present the functions of major ATPase subunit containing chromatin remodeling complexes. We also introduce examples of how changes in these epigenetic factors affect early development in humans and mice. In summary, this review provides an overview over the most important epigenetic mechanisms and provides examples of the dramatic effects of epigenetic changes in early mammalian development.
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10
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Lin Y, Qiu T, Wei G, Que Y, Wang W, Kong Y, Xie T, Chen X. Role of Histone Post-Translational Modifications in Inflammatory Diseases. Front Immunol 2022; 13:852272. [PMID: 35280995 PMCID: PMC8908311 DOI: 10.3389/fimmu.2022.852272] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Inflammation is a defensive reaction for external stimuli to the human body and generally accompanied by immune responses, which is associated with multiple diseases such as atherosclerosis, type 2 diabetes, Alzheimer’s disease, psoriasis, asthma, chronic lung diseases, inflammatory bowel disease, and multiple virus-associated diseases. Epigenetic mechanisms have been demonstrated to play a key role in the regulation of inflammation. Common epigenetic regulations are DNA methylation, histone modifications, and non-coding RNA expression; among these, histone modifications embrace various post-modifications including acetylation, methylation, phosphorylation, ubiquitination, and ADP ribosylation. This review focuses on the significant role of histone modifications in the progression of inflammatory diseases, providing the potential target for clinical therapy of inflammation-associated diseases.
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Affiliation(s)
- Yingying Lin
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Ting Qiu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Guifeng Wei
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Yueyue Que
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Wenxin Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yichao Kong
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Xiabin Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
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11
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Nothof SA, Magdinier F, Van-Gils J. Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication. Genes (Basel) 2022; 13:genes13040639. [PMID: 35456445 PMCID: PMC9029427 DOI: 10.3390/genes13040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Chromatin structure is an essential regulator of gene expression. Its state of compaction contributes to the regulation of genetic programs, in particular during differentiation. Epigenetic processes, which include post-translational modifications of histones, DNA methylation and implication of non-coding RNA, are powerful regulators of gene expression. Neurogenesis and neuronal differentiation are spatio-temporally regulated events that allow the formation of the central nervous system components. Here, we review the chromatin structure and post-translational histone modifications associated with neuronal differentiation. Studying the impact of histone modifications on neuronal differentiation improves our understanding of the pathophysiological mechanisms of chromatinopathies and opens up new therapeutic avenues. In addition, we will discuss techniques for the analysis of histone modifications on a genome-wide scale and the pathologies associated with the dysregulation of the epigenetic machinery.
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Affiliation(s)
- Sophie A. Nothof
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Frédérique Magdinier
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Julien Van-Gils
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
- Reference Center AD SOOR, AnDDI-RARE, Inserm U 1211, Medical Genetics Department, Bordeaux University, Center Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France
- Correspondence:
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12
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Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Is There a Histone Code for Cellular Quiescence? Front Cell Dev Biol 2021; 9:739780. [PMID: 34778253 PMCID: PMC8586460 DOI: 10.3389/fcell.2021.739780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022] Open
Abstract
Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
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Affiliation(s)
- Kenya Bonitto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kirthana Sarathy
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kaiser Atai
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mithun Mitra
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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13
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Epigenetic features in regulation of telomeres and telomerase in stem cells. Emerg Top Life Sci 2021; 5:497-505. [PMID: 34486664 DOI: 10.1042/etls20200344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 01/12/2023]
Abstract
The epigenetic nature of telomeres is still controversial and different human cell lines might show diverse histone marks at telomeres. Epigenetic modifications regulate telomere length and telomerase activity that influence telomere structure and maintenance. Telomerase is responsible for telomere elongation and maintenance and is minimally composed of the catalytic protein component, telomerase reverse transcriptase (TERT) and template forming RNA component, telomerase RNA (TERC). TERT promoter mutations may underpin some telomerase activation but regulation of the gene is not completely understood due to the complex interplay of epigenetic, transcriptional, and posttranscriptional modifications. Pluripotent stem cells (PSCs) can maintain an indefinite, immortal, proliferation potential through their endogenous telomerase activity, maintenance of telomere length, and a bypass of replicative senescence in vitro. Differentiation of PSCs results in silencing of the TERT gene and an overall reversion to a mortal, somatic cell phenotype. The precise mechanisms for this controlled transcriptional silencing are complex. Promoter methylation has been suggested to be associated with epigenetic control of telomerase regulation which presents an important prospect for understanding cancer and stem cell biology. Control of down-regulation of telomerase during differentiation of PSCs provides a convenient model for the study of its endogenous regulation. Telomerase reactivation has the potential to reverse tissue degeneration, drive repair, and form a component of future tissue engineering strategies. Taken together it becomes clear that PSCs provide a unique system to understand telomerase regulation fully and drive this knowledge forward into aging and therapeutic application.
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14
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Building Pluripotency Identity in the Early Embryo and Derived Stem Cells. Cells 2021; 10:cells10082049. [PMID: 34440818 PMCID: PMC8391114 DOI: 10.3390/cells10082049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The fusion of two highly differentiated cells, an oocyte with a spermatozoon, gives rise to the zygote, a single totipotent cell, which has the capability to develop into a complete, fully functional organism. Then, as development proceeds, a series of programmed cell divisions occur whereby the arising cells progressively acquire their own cellular and molecular identity, and totipotency narrows until when pluripotency is achieved. The path towards pluripotency involves transcriptome modulation, remodeling of the chromatin epigenetic landscape to which external modulators contribute. Both human and mouse embryos are a source of different types of pluripotent stem cells whose characteristics can be captured and maintained in vitro. The main aim of this review is to address the cellular properties and the molecular signature of the emerging cells during mouse and human early development, highlighting similarities and differences between the two species and between the embryos and their cognate stem cells.
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15
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Bachleitner S, Sulyok M, Sørensen JL, Strauss J, Studt L. The H4K20 methyltransferase Kmt5 is involved in secondary metabolism and stress response in phytopathogenic Fusarium species. Fungal Genet Biol 2021; 155:103602. [PMID: 34214671 DOI: 10.1016/j.fgb.2021.103602] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 02/08/2023]
Abstract
Fusarium fujikuroi and Fusarium graminearum are agronomically important plant pathogens, both infecting important staple food plants and thus leading to huge economic losses worldwide. F.fujikuroi belongs to the Fusarium fujikuroi species complex (FFSC) and causes bakanae disease on rice, whereas F.graminearum, a member of the Fusarium graminearum species complex (FGSC), is the causal agent of Fusarium Head Blight (FHB) disease on wheat, barley and maize. In recent years, the importance of chromatin regulation became evident in the plant-pathogen interaction. Several processes, including posttranslational modifications of histones, have been described as regulators of virulence and the biosynthesis of secondary metabolites. In this study, we have functionally characterised methylation of lysine 20 histone 4 (H4K20me) in both Fusarium species. We identified the respective genes solely responsible for H4K20 mono-, di- and trimethylation in F.fujikuroi (FfKMT5) and F.graminearum (FgKMT5). We show that loss of Kmt5 affects colony growth in F.graminearum while this is not the case for F.fujikuroi. Similarly, FgKmt5 is required for full virulence in F.graminearum as Δfgkmt5 is hypovirulent on wheat, whereas the F.fujikuroi Δffkmt5 strain did not deviate from the wild type during rice infection. Lack of Kmt5 had distinct effects on the secondary metabolism in both plant pathogens with the most pronounced effects on fusarin biosynthesis in F.fujikuroi and zearalenone biosynthesis in F.graminearum. Next to this, loss of Kmt5 resulted in an increased tolerance towards oxidative and osmotic stress in both species.
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Affiliation(s)
- Simone Bachleitner
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Michael Sulyok
- Institute of Bioanalytics and Agro-Metabolomics, Department for Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, Tulln 3430, Austria
| | - Jens Laurids Sørensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, DK-9000 Aalborg, Denmark
| | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Lena Studt
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria.
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16
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Garner TB, Hester JM, Carothers A, Diaz FJ. Role of zinc in female reproduction. Biol Reprod 2021; 104:976-994. [PMID: 33598687 PMCID: PMC8599883 DOI: 10.1093/biolre/ioab023] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/09/2021] [Accepted: 02/15/2021] [Indexed: 11/14/2022] Open
Abstract
Zinc is a critical component in a number of conserved processes that regulate female germ cell growth, fertility, and pregnancy. During follicle development, a sufficient intracellular concentration of zinc in the oocyte maintains meiotic arrest at prophase I until the germ cell is ready to undergo maturation. An adequate supply of zinc is necessary for the oocyte to form a fertilization-competent egg as dietary zinc deficiency or chelation of zinc disrupts maturation and reduces the oocyte quality. Following sperm fusion to the egg to initiate the acrosomal reaction, a quick release of zinc, known as the zinc spark, induces egg activation in addition to facilitating zona pellucida hardening and reducing sperm motility to prevent polyspermy. Symmetric division, proliferation, and differentiation of the preimplantation embryo rely on zinc availability, both during the oocyte development and post-fertilization. Further, the fetal contribution to the placenta, fetal limb growth, and neural tube development are hindered in females challenged with zinc deficiency during pregnancy. In this review, we discuss the role of zinc in germ cell development, fertilization, and pregnancy with a focus on recent studies in mammalian females. We further detail the fundamental zinc-mediated reproductive processes that have only been explored in non-mammalian species and speculate on the role of zinc in similar mechanisms of female mammals. The evidence collected over the last decade highlights the necessity of zinc for normal fertility and healthy pregnancy outcomes, which suggests zinc supplementation should be considered for reproductive age women at risk of zinc deficiency.
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Affiliation(s)
- Tyler Bruce Garner
- Huck Institutes of the Life Sciences, Integrative and Biomedical Physiology Program, The Pennsylvania State University, University Park, PA, USA
| | - James Malcolm Hester
- Huck Institutes of the Life Sciences, Integrative and Biomedical Physiology Program, The Pennsylvania State University, University Park, PA, USA
| | - Allison Carothers
- Huck Institutes of the Life Sciences, Integrative and Biomedical Physiology Program, The Pennsylvania State University, University Park, PA, USA
| | - Francisco J Diaz
- Huck Institutes of the Life Sciences, Integrative and Biomedical Physiology Program, The Pennsylvania State University, University Park, PA, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
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17
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Wickramasekara RN, Robertson B, Hulen J, Hallgren J, Stessman HAF. Differential effects by sex with Kmt5b loss. Autism Res 2021; 14:1554-1571. [PMID: 33871180 DOI: 10.1002/aur.2516] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 01/21/2023]
Abstract
Lysine methyl transferase 5B (KMT5B) has been recently highlighted as a risk gene in genetic studies of neurodevelopmental disorders (NDDs), specifically, autism spectrum disorder (ASD) and intellectual disability (ID); yet, its role in the brain is not known. The goal of this work was to neurodevelopmentally characterize the effect(s) of KMT5B haploinsufficiency using a mouse model. A Kmt5b gene-trap mouse line was obtained from the Knockout Mouse Project. Wild type (WT) and heterozygous (HET) mice were subjected to a comprehensive neurodevelopmental test battery to assess reflexes, motor behavior, learning/memory, social behavior, repetitive movement, and common ASD comorbidities (obsessive compulsion, depression, and anxiety). Given the strong sex bias observed in the ASD patient population, we tested both a male and female cohort of animals and compared differences between genotypes and sexes. HET mice were significantly smaller than WT littermates starting at postnatal day 10 through young adulthood which was correlated with smaller brain size (i.e., microcephaly). This was more severe in males than females. HET male neonates also had delayed eye opening and significantly weaker reflexes than WT littermates. In young adults, significant differences between genotypes relative to anxiety, depression, fear, and extinction learning were observed. Interestingly, several sexually dimorphic differences were noted including increased repetitive grooming behavior in HET females and an increased latency to hot plate response in HET females versus a decreased latency in HET males. LAY SUMMARY: Lysine methyl transferase 5B (KMT5B) has been recently highlighted as a risk gene in neurodevelopmental disorders (NDDs), specifically, autism spectrum disorder (ASD) and intellectual disability (ID); yet its role in the brain is not known. Our study indicates that mice lacking one genomic copy of Kmt5b show deficits in neonatal reflexes, sociability, repetitive stress-induced grooming, changes in thermal pain sensing, decreased depression and anxiety, increased fear, slower extinction learning, and lower body weight, length, and brain size. Furthermore, several outcomes differed by sex, perhaps mirroring the sex bias in ASD.
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Affiliation(s)
- Rochelle N Wickramasekara
- Department of Pharmacology & Neuroscience, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Brynn Robertson
- Department of Pharmacology & Neuroscience, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Jason Hulen
- Department of Pharmacology & Neuroscience, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Jodi Hallgren
- Department of Pharmacology & Neuroscience, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Holly A F Stessman
- Department of Pharmacology & Neuroscience, School of Medicine, Creighton University, Omaha, Nebraska, USA
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18
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Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains. Nat Commun 2021; 12:1419. [PMID: 33658503 PMCID: PMC7930052 DOI: 10.1038/s41467-021-21707-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.
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19
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Corvalan AZ, Coller HA. Methylation of histone 4's lysine 20: a critical analysis of the state of the field. Physiol Genomics 2020; 53:22-32. [PMID: 33197229 DOI: 10.1152/physiolgenomics.00128.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chromatin is a highly dynamic structure whose plasticity is achieved through multiple processes including the posttranslational modification of histone tails. Histone modifications function through the recruitment of nonhistone proteins to chromatin and thus have the potential to influence many fundamental biological processes. Here, we focus on the function and regulation of lysine 20 of histone H4 (H4K20) methylation in multiple biological processes including DNA repair, cell cycle regulation, and DNA replication. The purpose of this review is to highlight recent studies that elucidate the functions associated with each of the methylation states of H4K20, their modifying enzymes, and their protein readers. Based on our current knowledge of H4K20 methylation, we critically analyze the data supporting these functions and outline questions for future research.
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Affiliation(s)
- Adriana Z Corvalan
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California.,Department of Biological Chemistry, University of California, Los Angeles, California
| | - Hilary A Coller
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California.,Department of Biological Chemistry, University of California, Los Angeles, California
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20
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Yi SJ, Kim K. New Insights into the Role of Histone Changes in Aging. Int J Mol Sci 2020; 21:ijms21218241. [PMID: 33153221 PMCID: PMC7662996 DOI: 10.3390/ijms21218241] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Aging is the progressive decline or loss of function at the cellular, tissue, and organismal levels that ultimately leads to death. A number of external and internal factors, including diet, exercise, metabolic dysfunction, genome instability, and epigenetic imbalance, affect the lifespan of an organism. These aging factors regulate transcriptome changes related to the aging process through chromatin remodeling. Many epigenetic regulators, such as histone modification, histone variants, and ATP-dependent chromatin remodeling factors, play roles in chromatin reorganization. The key to understanding the role of gene regulatory networks in aging lies in characterizing the epigenetic regulators responsible for reorganizing and potentiating particular chromatin structures. This review covers epigenetic studies on aging, discusses the impact of epigenetic modifications on gene expression, and provides future directions in this area.
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21
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Li M, Tong H, Wang S, Ye W, Li Z, Omar MAA, Ao Y, Ding S, Li Z, Wang Y, Yin C, Zhao X, He K, Liu F, Chen X, Mei Y, Walters JR, Jiang M, Li F. A chromosome-level genome assembly provides new insights into paternal genome elimination in the cotton mealybug Phenacoccus solenopsis. Mol Ecol Resour 2020; 20:1733-1747. [PMID: 33460249 DOI: 10.1111/1755-0998.13232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 11/30/2022]
Abstract
Mealybugs (Hemiptera: Pseudococcidae) are economically important agricultural pests with several compelling biological phenomena including paternal genome elimination (PGE). However, limited high-quality genome assemblies of mealybugs hinder a full understanding of this striking and unusual biological phenomenon. Here, we generated a chromosome-level genome assembly of cotton mealybug, Phenacoccus solenopsis, by combining Illumina short reads, PacBio long reads and Hi-C scaffolding. The assembled genome was 292.54 Mb with a contig N50 of 489.8 kb and a scaffold N50 of 49.0 Mb. Hi-C scaffolding assigned 84.42% of the bases to five chromosomes. A total of 110.75 Mb (37.9%) repeat sequences and 11,880 protein-coding genes were predicted. The completeness of the genome assembly was estimated to be 95.5% based on BUSCO genes. In addition, 27,086 (95.3%) full-length PacBio transcripts were uniquely mapped to the assembled scaffolds, suggesting the high quality of the genome assembly. We showed that cotton mealybugs lack differentiated sex chromosomes by analysing genome resequencing data of males and females. DAPI staining confirmed that one chromosome set in males becomes heterochromatin at an early embryo stage. Chromatin immunoprecipitation assays with sequencing analysis demonstrated that the epigenetic modifications H3K9me3 and H3K27me3 are distributed across the whole genome in males, suggesting that these two modifications might be involved in maintaining heterochromatin status. Both markers were more likely to be distributed in repeat regions, while H3K27me3 had higher overall enrichment. Our results provide a valuable genomic resource and shed new light on the genomic and epigenetic basis of PGE in cotton mealybugs.
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Affiliation(s)
- Meizhen Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haojie Tong
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuping Wang
- Technical Centre for Animal, Plant and Food Inspection and Quarantine, Shanghai Customs, Shanghai, China
| | - Wanyi Ye
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zicheng Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mohamed A A Omar
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.,Department of Plant Protection, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Yan Ao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Simin Ding
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zihao Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ying Wang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chuanlin Yin
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xianxin Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Feiling Liu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xi Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yang Mei
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - James R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - Mingxing Jiang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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22
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Del Corvo M, Bongiorni S, Stefanon B, Sgorlon S, Valentini A, Ajmone Marsan P, Chillemi G. Genome-Wide DNA Methylation and Gene Expression Profiles in Cows Subjected to Different Stress Level as Assessed by Cortisol in Milk. Genes (Basel) 2020; 11:genes11080850. [PMID: 32722461 PMCID: PMC7464205 DOI: 10.3390/genes11080850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022] Open
Abstract
Dairy cattle health, wellbeing and productivity are deeply affected by stress. Its influence on metabolism and immune response is well known, but the underlying epigenetic mechanisms require further investigation. In this study, we compared DNA methylation and gene expression signatures between two dairy cattle populations falling in the high- and low-variant tails of the distribution of milk cortisol concentration (MC), a neuroendocrine marker of stress in dairy cows. Reduced Representation Bisulfite Sequencing was used to obtain a methylation map from blood samples of these animals. The high and low groups exhibited similar amounts of methylated CpGs, while we found differences among non-CpG sites. Significant methylation changes were detected in 248 genes. We also identified significant fold differences in the expression of 324 genes. KEGG and Gene Ontology (GO) analysis showed that genes of both groups act together in several pathways, such as nervous system activity, immune regulatory functions and glucocorticoid metabolism. These preliminary results suggest that, in livestock, cortisol secretion could act as a trigger for epigenetic regulation and that peripheral changes in methylation can provide an insight into central nervous system functions.
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Affiliation(s)
- Marcello Del Corvo
- Department of Animal Science Food and Nutrition—DIANA, Nutrigenomics and Proteomics Research Centre—PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
- Istituto di Biologia e BiotecnologiaAgraria, Consiglio Nazionale delle Ricerche, 20133 Milan, Italy
- Correspondence:
| | - Silvia Bongiorni
- Department of Ecological and Biological sciences DEB, University of Tuscia, 01100 Viterbo, Italy;
| | - Bruno Stefanon
- Department of Agrifood, Environmental and Animal Science–University of Udine, 33100 Udine, Italy; (B.S.); (S.S.)
| | - Sandy Sgorlon
- Department of Agrifood, Environmental and Animal Science–University of Udine, 33100 Udine, Italy; (B.S.); (S.S.)
| | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest systems DIBAF, University of Tuscia, 01100 Viterbo, Italy; (A.V.); (G.C.)
| | - Paolo Ajmone Marsan
- Department of Animal Science Food and Nutrition—DIANA, Nutrigenomics and Proteomics Research Centre—PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy;
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest systems DIBAF, University of Tuscia, 01100 Viterbo, Italy; (A.V.); (G.C.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, 70126 Bari, Italy
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23
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Talebian S, Daghagh H, Yousefi B, Ȍzkul Y, Ilkhani K, Seif F, Alivand MR. The role of epigenetics and non-coding RNAs in autophagy: A new perspective for thorough understanding. Mech Ageing Dev 2020; 190:111309. [PMID: 32634442 DOI: 10.1016/j.mad.2020.111309] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/22/2020] [Accepted: 06/28/2020] [Indexed: 12/18/2022]
Abstract
Autophagy is a major self-degradative intracellular process required for the maintenance of homeostasis and promotion of survival in response to starvation. It plays critical roles in a large variety of physiological and pathological processes. On the other hand, aberrant regulation of autophagy can lead to various cancers and neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Crohn's disease. Emerging evidence strongly supports that epigenetic signatures, related non-coding RNA profiles, and their cross-talking are significantly associated with the control of autophagic responses. Therefore, it may be helpful and promising to manage autophagic processes by finding valuable markers and therapeutic approaches. Although there is a great deal of information on the components of autophagy in the cytoplasm, the molecular basis of the epigenetic regulation of autophagy has not been completely elucidated. In this review, we highlight recent research on epigenetic changes through the expression of autophagy-related genes (ATGs), which regulate autophagy, DNA methylation, histone modifications as well as non-coding RNAs, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and their relationship with human diseases, that play key roles in causing autophagy-related diseases.
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Affiliation(s)
- Shahrzad Talebian
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Daghagh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Aging Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yusuf Ȍzkul
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Khandan Ilkhani
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farhad Seif
- Department of Immunology & Allergy, Academic Center for Education, Culture, and Research, Tehran, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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24
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Sherzai M, Valle A, Perry N, Kalef-Ezra E, Al-Mahdawi S, Pook M, Anjomani Virmouni S. HMTase Inhibitors as a Potential Epigenetic-Based Therapeutic Approach for Friedreich's Ataxia. Front Genet 2020; 11:584. [PMID: 32582297 PMCID: PMC7291394 DOI: 10.3389/fgene.2020.00584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/14/2020] [Indexed: 12/17/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a progressive neurodegenerative disorder caused by a homozygous GAA repeat expansion mutation in intron 1 of the frataxin gene (FXN), which instigates reduced transcription. As a consequence, reduced levels of frataxin protein lead to mitochondrial iron accumulation, oxidative stress, and ultimately cell death; particularly in dorsal root ganglia (DRG) sensory neurons and the dentate nucleus of the cerebellum. In addition to neurological disability, FRDA is associated with cardiomyopathy, diabetes mellitus, and skeletal deformities. Currently there is no effective treatment for FRDA and patients die prematurely. Recent findings suggest that abnormal GAA expansion plays a role in histone modification, subjecting the FXN gene to heterochromatin silencing. Therefore, as an epigenetic-based therapy, we investigated the efficacy and tolerability of two histone methyltransferase (HMTase) inhibitor compounds, BIX0194 (G9a-inhibitor) and GSK126 (EZH2-inhibitor), to specifically target and reduce H3K9me2/3 and H3K27me3 levels, respectively, in FRDA fibroblasts. We show that a combination treatment of BIX0194 and GSK126, significantly increased FXN gene expression levels and reduced the repressive histone marks. However, no increase in frataxin protein levels was observed. Nevertheless, our results are still promising and may encourage to investigate HMTase inhibitors with other synergistic epigenetic-based therapies for further preliminary studies.
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Affiliation(s)
- Mursal Sherzai
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Adamo Valle
- Energy Metabolism and Nutrition, Research Institute of Health Sciences (IUNICS) and Health Research Institute of Balearic Islands (IdISBa), University of Balearic Islands, Palma de Mallorca, Spain.,Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Nicholas Perry
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Ester Kalef-Ezra
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Sahar Al-Mahdawi
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark Pook
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Sara Anjomani Virmouni
- Ataxia Research Group, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom
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25
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Ensuring meiotic DNA break formation in the mouse pseudoautosomal region. Nature 2020; 582:426-431. [PMID: 32461690 PMCID: PMC7337327 DOI: 10.1038/s41586-020-2327-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/24/2020] [Indexed: 11/09/2022]
Abstract
Sex chromosomes in males of most eutherian species share only a diminutive homologous segment, the pseudoautosomal region (PAR), wherein double-strand break (DSB) formation, pairing, and crossing over must occur for correct meiotic segregation1,2. How cells ensure PAR recombination is unknown. Here we delineate an unexpected dynamic ultrastructure of the PAR and identify controlling cis- and trans-acting factors that make this the hottest area of DSB formation in the male mouse genome. Before break formation, multiple DSB-promoting factors hyper-accumulate in the PAR, its chromosome axes elongate, and the sister chromatids separate. These phenomena are linked to heterochromatic mo-2 minisatellite arrays and require MEI4 and ANKRD31 proteins but not axis components REC8 or HORMAD1. We propose that the repetitive PAR sequence confers unique chromatin and higher order structures crucial for recombination. Chromosome synapsis triggers collapse of the elongated PAR structure and, remarkably, oocytes can be reprogrammed to display spermatocyte-like PAR DSB levels simply by delaying or preventing synapsis. Thus, sexually dimorphic behavior of the PAR rests in part on kinetic differences between the sexes for a race between maturation of PAR structure, DSB formation, and completion of pairing and synapsis. Our findings establish a mechanistic paradigm of sex chromosome recombination during meiosis.
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26
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Shue YT, Lee KT, Walters BW, Ong HB, Silvaraju S, Lam WJ, Lim CY. Dynamic shifts in chromatin states differentially mark the proliferative basal cells and terminally differentiated cells of the developing epidermis. Epigenetics 2020; 15:932-948. [PMID: 32175801 DOI: 10.1080/15592294.2020.1738028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications on nucleosomal histones represent a key epigenetic regulatory mechanism to mediate the complex gene expression, DNA replication, and cell cycle changes that occur in embryonic cells undergoing lineage specification, maturation, and differentiation during development. Here, we investigated the dynamics of 13 key histone marks in epidermal cells at three distinct stages of embryonic skin development and identified significant changes that corresponded with the maturation of the proliferative basal epidermal cells and terminally differentiated cells in the stratified layers. In particular, H3K4me3 and H3K27ac were accumulated and became more prominent in the basal cells at later stages of epidermal development, while H3K27me3 was found to be low in the basal cells but highly enriched in the differentiated suprabasal cell types. Constitutive heterochromatin marked by H4K20me3 was also significantly elevated in differentiated epidermal cells at late gestation stages, which exhibited a concomitant loss of H4K16 acetylation. These differential chromatin profiles were established in the embryonic skin by gestation day 15 and further amplified at E18 and in postnatal skin. Our results reveal the dynamic chromatin states that occur as epidermal progenitor cells commit to the lineage and differentiate into the different cells of the stratified epidermis and provide insight to the underlying epigenetic pathways that support normal epidermal development and homoeostasis.
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Affiliation(s)
- Yan Ting Shue
- Epithelial Epigenetics and Development Laboratory, Skin Research Institute of Singapore , Singapore
| | - Kang Ting Lee
- Epithelial Epigenetics and Development Laboratory, Skin Research Institute of Singapore , Singapore
| | - Benjamin William Walters
- Epithelial Epigenetics and Development Laboratory, Skin Research Institute of Singapore , Singapore.,Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester , Manchester, UK
| | - Hui Binn Ong
- Epithelial Epigenetics and Development Laboratory, Skin Research Institute of Singapore , Singapore
| | - Shaktheeshwari Silvaraju
- Epithelial Epigenetics and Development Laboratory, Skin Research Institute of Singapore , Singapore
| | - Wei Jun Lam
- Epithelial Epigenetics and Development Laboratory, Skin Research Institute of Singapore , Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
| | - Chin Yan Lim
- Epithelial Epigenetics and Development Laboratory, Skin Research Institute of Singapore , Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore
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27
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Gil L, Niño SA, Chi-Ahumada E, Rodríguez-Leyva I, Guerrero C, Rebolledo AB, Arias JA, Jiménez-Capdeville ME. Perinuclear Lamin A and Nucleoplasmic Lamin B2 Characterize Two Types of Hippocampal Neurons through Alzheimer's Disease Progression. Int J Mol Sci 2020; 21:E1841. [PMID: 32155994 PMCID: PMC7084765 DOI: 10.3390/ijms21051841] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Recent reports point to a nuclear origin of Alzheimer's disease (AD). Aged postmitotic neurons try to repair their damaged DNA by entering the cell cycle. This aberrant cell cycle re-entry involves chromatin modifications where nuclear Tau and the nuclear lamin are involved. The purpose of this work was to elucidate their participation in the nuclear pathological transformation of neurons at early AD. METHODOLOGY The study was performed in hippocampal paraffin embedded sections of adult, senile, and AD brains at I-VI Braak stages. We analyzed phospho-Tau, lamins A, B1, B2, and C, nucleophosmin (B23) and the epigenetic marker H4K20me3 by immunohistochemistry. RESULTS Two neuronal populations were found across AD stages, one is characterized by a significant increase of Lamin A expression, reinforced perinuclear Lamin B2, elevated expression of H4K20me3 and nuclear Tau loss, while neurons with nucleoplasmic Lamin B2 constitute a second population. CONCLUSIONS The abnormal cell cycle reentry in early AD implies a fundamental neuronal transformation. This implies the reorganization of the nucleo-cytoskeleton through the expression of the highly regulated Lamin A, heterochromatin repression and building of toxic neuronal tangles. This work demonstrates that nuclear Tau and lamin modifications in hippocampal neurons are crucial events in age-related neurodegeneration.
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Affiliation(s)
- Laura Gil
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain; (L.G.)
| | - Sandra A. Niño
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Erika Chi-Ahumada
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | | | - Carmen Guerrero
- Banco de cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - Ana Belén Rebolledo
- Banco de cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - José A. Arias
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain; (L.G.)
| | - María E. Jiménez-Capdeville
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
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28
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Wong SQ, Kumar AV, Mills J, Lapierre LR. Autophagy in aging and longevity. Hum Genet 2020; 139:277-290. [PMID: 31144030 PMCID: PMC6884674 DOI: 10.1007/s00439-019-02031-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023]
Abstract
Our understanding of the process of autophagy and its role in health and diseases has grown remarkably in the last two decades. Early work established autophagy as a general bulk recycling process which involves the sequestration and transport of intracellular material to the lysosome for degradation. Currently, autophagy is viewed as a nexus of metabolic and proteostatic signalling that can determine key physiological decisions from cell fate to organismal lifespan. Here, we review the latest literature on the role of autophagy and lysosomes in stress response and longevity. We highlight the connections between autophagy and metabolic processes, the network associated with its regulation, and the links between autophagic dysfunction, neurodegenerative diseases, and aging.
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Affiliation(s)
- Shi Q Wong
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Anita V Kumar
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Joslyn Mills
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Louis R Lapierre
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA.
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29
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Bhattacharjee P, Das A, Giri AK, Bhattacharjee P. Epigenetic regulations in alternative telomere lengthening: Understanding the mechanistic insight in arsenic-induced skin cancer patients. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135388. [PMID: 31837846 DOI: 10.1016/j.scitotenv.2019.135388] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Telomere integrity is considered to be one of the primary mechanisms during malignant transformation. Arsenic, a group 1 carcinogenic metalloid, has been reported to cause telomere lengthening in a telomerase-independent manner. Recent studies suggest a significant role for epigenetic modifications in regulating telomeric length and integrity. Here, we have explored the role of epigenetic deregulation in alternative lengthening of telomeres (ALT) in arsenic-exposed skin cancer tissues and corresponding non-tumor tissues. The relative telomere length (RTL) was analyzed by qRT-PCR using 2-ΔΔCt method. The subtelomeric methylation pattern of the four chromosomes (7q, 18p, 21q and XpYp) were analysed by Methylation Specific PCR (MSP) in 40 pairs of arsenic exposed skin cancer tissues and its corresponding control. The role of constitutive heterochromatin histone marks in the regulation of telomere length (TL) was analyzed by targeted ELISA. A 2-fold increase of relative telomere length in 85% of the arsenic-induced skin cancer tissues was observed. Among the four chromosomes, subtelomere of XpYp was found to be hypermethylated (p < 0.001) whereas 18p was hypomethylated (p < 0.01). Additionally, the level of H4K20me3, a heterochromatic mark was found to be significantly down-regulated (p < 0.0003), and inversely correlated with telomere length indicating loss of heterochromatinization of telomeric DNA. These observations highlight the novel role of epigenetic regulation in the maintenance of constitutive heterochromatin structure at telomere. Alteration in subtelomeric DNA methylation patterns and depletion of H4K20me3 might lead to loss of heterochromatinization resulting in arsenic-induced telomeric elongation. We provide novel data indicating possible alternative determinants of telomere elongation through epigenetic modifications during arsenic-induced skin carcinogenesis which could be used as early 'epimarkers' in the near future. The findings provide new insights about the mechanism of arsenic-induced carcinogenesis.
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Affiliation(s)
- Pritha Bhattacharjee
- Department of Zoology, University of Calcutta, Kolkata 700019, India; Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | - Ankita Das
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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30
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Guthmann M, Burton A, Torres‐Padilla M. Expression and phase separation potential of heterochromatin proteins during early mouse development. EMBO Rep 2019; 20:e47952. [PMID: 31701657 PMCID: PMC6893284 DOI: 10.15252/embr.201947952] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/03/2019] [Accepted: 10/16/2019] [Indexed: 12/29/2022] Open
Abstract
In most eukaryotes, constitutive heterochromatin is associated with H3K9me3 and HP1α. The latter has been shown to play a role in heterochromatin formation through liquid-liquid phase separation. However, many other proteins are known to regulate and/or interact with constitutive heterochromatic regions in several species. We postulate that some of these heterochromatic proteins may play a role in the regulation of heterochromatin formation by liquid-liquid phase separation. Indeed, an analysis of the constitutive heterochromatin proteome shows that proteins associated with constitutive heterochromatin are significantly more disordered than a random set or a full nucleome set of proteins. Interestingly, their expression begins low and increases during preimplantation development. These observations suggest that the preimplantation embryo is a useful model to address the potential role for phase separation in heterochromatin formation, anticipating exciting research in the years to come.
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Affiliation(s)
- Manuel Guthmann
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
| | - Adam Burton
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
| | - Maria‐Elena Torres‐Padilla
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
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31
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Schultz RM, Stein P, Svoboda P. The oocyte-to-embryo transition in mouse: past, present, and future. Biol Reprod 2019; 99:160-174. [PMID: 29462259 DOI: 10.1093/biolre/ioy013] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/03/2018] [Indexed: 02/06/2023] Open
Abstract
The oocyte-to-embryo transition (OET) arguably initiates with formation of a primordial follicle and culminates with reprogramming of gene expression during the course of zygotic genome activation. This transition results in converting a highly differentiated cell, i.e. oocyte, to undifferentiated cells, i.e. initial blastomeres of a preimplantation embryo. A plethora of changes occur during the OET and include, but are not limited to, changes in transcription, chromatin structure, and protein synthesis; accumulation of macromolecules and organelles that will comprise the oocyte's maternal contribution to the early embryo; sequential acquisition of meiotic and developmental competence to name but a few. This review will focus on transcriptional and post-transcriptional changes that occur during OET in mouse because such changes are likely the major driving force for OET. We often take a historical and personal perspective, and highlight how advances in experimental methods often catalyzed conceptual advances in understanding the molecular bases for OET. We also point out questions that remain open and therefore represent topics of interest for future investigation.
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Affiliation(s)
- Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Anatomy, Physiology, Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Paula Stein
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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32
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Di Malta C, Cinque L, Settembre C. Transcriptional Regulation of Autophagy: Mechanisms and Diseases. Front Cell Dev Biol 2019; 7:114. [PMID: 31312633 PMCID: PMC6614182 DOI: 10.3389/fcell.2019.00114] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/05/2019] [Indexed: 12/18/2022] Open
Abstract
Macro (Autophagy) is a catabolic process that relies on the cooperative function of two organelles: the lysosome and the autophagosome. The recent discovery of a transcriptional gene network that co-regulates the biogenesis and function of these two organelles, and the identification of transcription factors, miRNAs and epigenetic regulators of autophagy, demonstrated that this catabolic process is controlled by both transcriptional and post-transcriptional mechanisms. In this review article, we discuss the nuclear events that control autophagy, focusing particularly on the role of the MiT/TFE transcription factor family. In addition, we will discuss evidence suggesting that the transcriptional regulation of autophagy could be targeted for the treatment of human genetic diseases, such as lysosomal storage disorders (LSDs) and neurodegeneration.
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Affiliation(s)
- Chiara Di Malta
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Medical and Translational Sciences, University of Naples Federico II, Naples, Italy
| | - Laura Cinque
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Medical and Translational Sciences, University of Naples Federico II, Naples, Italy
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33
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Yandım C, Karakülah G. Expression dynamics of repetitive DNA in early human embryonic development. BMC Genomics 2019; 20:439. [PMID: 31151386 PMCID: PMC6545021 DOI: 10.1186/s12864-019-5803-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The last decade witnessed a number of genome-wide studies on human pre-implantation, which mostly focused on genes and provided only limited information on repeats, excluding the satellites. Considering the fact that repeats constitute a large portion of our genome with reported links to human physiology and disease, a thorough understanding of their spatiotemporal regulation during human embryogenesis will give invaluable clues on chromatin dynamics across time and space. Therefore, we performed a detailed expression analysis of all repetitive DNA elements including the satellites across stages of human pre-implantation and embryonic stem cells. RESULTS We uncovered stage-specific expressions of more than a thousand repeat elements whose expressions fluctuated with a mild global decrease at the blastocyst stage. Most satellites were highly expressed at the 4-cell level and expressions of ACRO1 and D20S16 specifically peaked at this point. Whereas all members of the SVA elements were highly upregulated at 8-cell and morula stages, other transposons and small RNA repeats exhibited a high level of variation among their specific subtypes. Our repeat enrichment analysis in gene promoters coupled with expression correlations highlighted potential links between repeat expressions and nearby genes, emphasising mostly 8-cell and morula specific genes together with SVA_D, LTR5_Hs and LTR70 transposons. The DNA methylation analysis further complemented the understanding on the mechanistic aspects of the repeatome's regulation per se and revealed critical stages where DNA methylation levels are negatively correlating with repeat expression. CONCLUSIONS Taken together, our study shows that specific expression patterns are not exclusive to genes and long non-coding RNAs but the repeatome also exhibits an intriguingly dynamic pattern at the global scale. Repeats identified in this study; particularly satellites, which were historically associated with heterochromatin, and those with potential links to nearby gene expression provide valuable insights into the understanding of key events in genomic regulation and warrant further research in epigenetics, genomics and developmental biology.
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Affiliation(s)
- Cihangir Yandım
- İzmir Biomedicine and Genome Center (IBG), 35340, İnciraltı, İzmir, Turkey.,Department of Genetics and Bioengineering, İzmir University of Economics, Faculty of Engineering, 35330, Balçova, İzmir, Turkey.,Department of Medicine, Division of Brain Sciences, Hammersmith Hospital, Imperial College London, Faculty of Medicine, W12 0NN, London, UK
| | - Gökhan Karakülah
- İzmir Biomedicine and Genome Center (IBG), 35340, İnciraltı, İzmir, Turkey. .,İzmir International Biomedicine and Genome Institute (iBG-İzmir), Dokuz Eylül University, 35340, İnciraltı, İzmir, Turkey.
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Wu Y, Shi W, Tang T, Wang Y, Yin X, Chen Y, Zhang Y, Xing Y, Shen Y, Xia T, Guo C, Pan Y, Jin L. miR-29a contributes to breast cancer cells epithelial-mesenchymal transition, migration, and invasion via down-regulating histone H4K20 trimethylation through directly targeting SUV420H2. Cell Death Dis 2019; 10:176. [PMID: 30792382 PMCID: PMC6385178 DOI: 10.1038/s41419-019-1437-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/01/2019] [Accepted: 01/08/2019] [Indexed: 12/31/2022]
Abstract
Breast cancer is the most prevalent cancer in women worldwide, which remains incurable once metastatic. Breast cancer stem cells (BCSCs) are a small subset of breast cancer cells which are essential in tumor formation, metastasis, and drug resistance. microRNAs (miRNAs) play important roles in the breast cancer cells and BCSCs by regulating specific genes. In this study, we found that miR-29a was up-regulated in BCSCs, in aggressive breast cancer cell line and in breast cancer tissues. We also confirmed suppressor of variegation 4–20 homolog 2 (SUV420H2), which is a histone methyltransferase that specifically trimethylates Lys-20 of histone H4 (H4K20), as the target of miR-29a. Both miR-29a overexpression and SUV420H2 knockdown in breast cancer cells promoted their migration and invasion in vitro and in vivo. Furthermore, we discovered that SUV420H2-targeting miR-29a attenuated the repression of connective tissue growth factor (CTGF) and growth response protein-1 (EGR1) by H4K20 trimethylation and promoted the EMT progress of breast cancer cells. Taken together, our findings reveal that miR-29a plays critical roles in the EMT and metastasis of breast cancer cells through targeting SUV420H2. These findings may provide new insights into novel molecular therapeutic targets for breast cancer.
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Affiliation(s)
- You Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Wanyue Shi
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Tingting Tang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Yidong Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Xin Yin
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Yanlin Chen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Yanfeng Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Yun Xing
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Yumeng Shen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Tiansong Xia
- Department of Breast Surgery, Breast Disease Center of Jiangsu Province, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu province, China
| | - Changying Guo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China
| | - Yi Pan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China.
| | - Liang Jin
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, School of life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu province, China.
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Singh PB, Shloma VV, Belyakin SN. Maternal regulation of chromosomal imprinting in animals. Chromosoma 2019; 128:69-80. [PMID: 30719566 PMCID: PMC6536480 DOI: 10.1007/s00412-018-00690-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/24/2018] [Accepted: 12/28/2018] [Indexed: 11/29/2022]
Abstract
Chromosomal imprinting requires an epigenetic system that "imprints" one of the two parental chromosomes such that it results in a heritable (cell-to-cell) change in behavior of the "imprinted" chromosome. Imprinting takes place when the parental genomes are separate, which occurs during gamete formation in the respective germ-lines and post-fertilization during the period when the parental pro-nuclei lie separately within the ooplasm of the zygote. In the mouse, chromosomal imprinting is regulated by germ-line specific DNA methylation. But the methylation machinery in the respective germ-lines does not discriminate between imprinted and non-imprinted regions. As a consequence, the mouse oocyte nucleus contains over a thousand oocyte-specific germ-line differentially methylated regions (gDMRs). Upon fertilization, the sperm provides a few hundred sperm-specific gDMRs of its own. Combined, there are around 1600 imprinted and non-imprinted gDMRs in the pro-nuclei of the newly fertilized zygote. It is a remarkable fact that beginning in the maternal ooplasm, there are mechanisms that manage to preserve DNA methylation at ~ 26 known imprinted gDMRs in the face of the ongoing genome-wide DNA de-methylation that characterizes pre-implantation development. Specificity is achieved through the binding of KRAB-zinc finger proteins to their cognate recognition sequences within the gDMRs of imprinted genes. This in turn nucleates the assembly of localized heterochromatin-like complexes that preserve methylation at imprinted gDMRs through recruitment of the maintenance methyl transferase Dnmt1. These studies have shown that a germ-line imprint may cause parent-of-origin-specific behavior only if "licensed" by mechanisms that operate post-fertilization. Study of the germ-line and post-fertilization contributions to the imprinting of chromosomes in classical insect systems (Coccidae and Sciaridae) show that the ooplasm is the likely site where imprinting takes place. By comparing molecular and genetic studies across these three species, we suggest that mechanisms which operate post-fertilization play a key role in chromosomal imprinting phenomena in animals and conserved components of heterochromatin are shared by these mechanisms.
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Affiliation(s)
- Prim B Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Astana, Z05K4F4, Kazakhstan.
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation.
| | - Victor V Shloma
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation
- Genomics Laboratory, Institute of Molecular and Cellular Biology SD RAS, Lavrentyev ave, 8/2, Novosibirsk, 630090, Russian Federation
| | - Stepan N Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov str. 2, Novosibirsk, 630090, Russian Federation
- Genomics Laboratory, Institute of Molecular and Cellular Biology SD RAS, Lavrentyev ave, 8/2, Novosibirsk, 630090, Russian Federation
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Weaver TM, Liu J, Connelly KE, Coble C, Varzavand K, Dykhuizen EC, Musselman CA. The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail. Sci Rep 2019; 9:987. [PMID: 30700785 PMCID: PMC6353875 DOI: 10.1038/s41598-018-37699-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 12/12/2018] [Indexed: 01/09/2023] Open
Abstract
SANT domains are found in a number of chromatin regulators. They contain approximately 50 amino acids and have high similarity to the DNA binding domain of Myb related proteins. Though some SANT domains associate with DNA others have been found to bind unmodified histone tails. There are two SANT domains in Enhancer of Zeste 2 (EZH2), the catalytic subunit of the Polycomb Repressive Complex 2 (PRC2), of unknown function. Here we show that the first SANT domain (SANT1) of EZH2 is a histone binding domain with specificity for the histone H4 N-terminal tail. Using NMR spectroscopy, mutagenesis, and molecular modeling we structurally characterize the SANT1 domain and determine the molecular mechanism of binding to the H4 tail. Though not important for histone binding, we find that the adjacent stimulation response motif (SRM) stabilizes SANT1 and transiently samples its active form in solution. Acetylation of H4K16 (H4K16ac) or acetylation or methylation of H4K20 (H4K20ac and H4K20me3) are seen to abrogate binding of SANT1 to H4, which is consistent with these modifications being anti-correlated with H3K27me3 in-vivo. Our results provide significant insight into this important regulatory region of EZH2 and the first characterization of the molecular mechanism of SANT domain histone binding.
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Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Jiachen Liu
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Katelyn E Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, 47907, USA
| | - Chris Coble
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Katayoun Varzavand
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, 47907, USA
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA.
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Peeters JGC, Picavet LW, Coenen SGJM, Mauthe M, Vervoort SJ, Mocholi E, de Heus C, Klumperman J, Vastert SJ, Reggiori F, Coffer PJ, Mokry M, van Loosdregt J. Transcriptional and epigenetic profiling of nutrient-deprived cells to identify novel regulators of autophagy. Autophagy 2018; 15:98-112. [PMID: 30153076 PMCID: PMC6287694 DOI: 10.1080/15548627.2018.1509608] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Macroautophagy (hereafter autophagy) is a lysosomal degradation pathway critical for maintaining cellular homeostasis and viability, and is predominantly regarded as a rapid and dynamic cytoplasmic process. To increase our understanding of the transcriptional and epigenetic events associated with autophagy, we performed extensive genome-wide transcriptomic and epigenomic profiling after nutrient deprivation in human autophagy-proficient and autophagy-deficient cells. We observed that nutrient deprivation leads to the transcriptional induction of numerous autophagy-associated genes. These transcriptional changes are reflected at the epigenetic level (H3K4me3, H3K27ac, and H3K56ac) and are independent of autophagic flux. As a proof of principle that this resource can be used to identify novel autophagy regulators, we followed up on one identified target: EGR1 (early growth response 1), which indeed appears to be a central transcriptional regulator of autophagy by affecting autophagy-associated gene expression and autophagic flux. Taken together, these data stress the relevance of transcriptional and epigenetic regulation of autophagy and can be used as a resource to identify (novel) factors involved in autophagy regulation.
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Affiliation(s)
- J G C Peeters
- a Center for Molecular Medicine , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,b Laboratory of Translational Immunology , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,c Division of Pediatrics , Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,e Regenerative Medicine Center , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - L W Picavet
- b Laboratory of Translational Immunology , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,c Division of Pediatrics , Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,e Regenerative Medicine Center , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - S G J M Coenen
- b Laboratory of Translational Immunology , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,c Division of Pediatrics , Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,e Regenerative Medicine Center , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - M Mauthe
- d Department of Cell Biology , University Medical Center Groningen, University of Groningen , Groningen , The Netherlands
| | - S J Vervoort
- a Center for Molecular Medicine , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - E Mocholi
- a Center for Molecular Medicine , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,e Regenerative Medicine Center , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - C de Heus
- a Center for Molecular Medicine , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,f Department of Cell Biology , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - J Klumperman
- a Center for Molecular Medicine , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,f Department of Cell Biology , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - S J Vastert
- b Laboratory of Translational Immunology , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,c Division of Pediatrics , Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - F Reggiori
- d Department of Cell Biology , University Medical Center Groningen, University of Groningen , Groningen , The Netherlands
| | - P J Coffer
- a Center for Molecular Medicine , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,c Division of Pediatrics , Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,e Regenerative Medicine Center , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
| | - M Mokry
- c Division of Pediatrics , Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,e Regenerative Medicine Center , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,g Epigenomics facility , University Medical Center Utrecht , Utrecht , The Netherlands
| | - J van Loosdregt
- a Center for Molecular Medicine , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,b Laboratory of Translational Immunology , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,c Division of Pediatrics , Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands.,e Regenerative Medicine Center , University Medical Center Utrecht, Utrecht University , Utrecht , The Netherlands
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Can Reprogramming of Overall Epigenetic Memory and Specific Parental Genomic Imprinting Memory within Donor Cell-Inherited Nuclear Genome be a Major Hindrance for the Somatic Cell Cloning of Mammals? – A Review. ANNALS OF ANIMAL SCIENCE 2018. [DOI: 10.2478/aoas-2018-0015] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Abstract
Successful cloning of animals by somatic cell nuclear transfer (SCNT) requires epigenetic transcriptional reprogramming of the differentiated state of the donor cell nucleus to a totipotent embryonic ground state. It means that the donor nuclei must cease its own program of gene expression and restore a particular program of the embryonic genome expression regulation that is necessary for normal development. Transcriptional activity of somatic cell-derived nuclear genome during embryo pre- and postimplantation development as well as foetogenesis is correlated with the frequencies for spatial remodeling of chromatin architecture and reprogramming of cellular epigenetic memory. This former and this latter process include such covalent modifications as demethylation/re-methylation of DNA cytosine residues and acetylation/deacetylation as well as demethylation/re-methylation of lysine residues of nucleosomal core-derived histones H3 and H4. The main cause of low SCNT efficiency in mammals turns out to be an incomplete reprogramming of transcriptional activity for donor cell-descended genes. It has been ascertained that somatic cell nuclei should undergo the wide DNA cytosine residue demethylation changes throughout the early development of cloned embryos to reset their own overall epigenetic and parental genomic imprinting memories that have been established by re-methylation of the nuclear donor cell-inherited genome during specific pathways of somatic and germ cell lineage differentiation. A more extensive understanding of the molecular mechanisms and recognition of determinants for epigenetic transcriptional reprogrammability of somatic cell nuclear genome will be helpful to solve the problems resulting from unsatisfactory SCNT effectiveness and open new possibilities for common application of this technology in transgenic research focused on human biomedicine.
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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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Bonnet-Garnier A, Kiêu K, Aguirre-Lavin T, Tar K, Flores P, Liu Z, Peynot N, Chebrout M, Dinnyés A, Duranthon V, Beaujean N. Three-dimensional analysis of nuclear heterochromatin distribution during early development in the rabbit. Chromosoma 2018; 127:387-403. [PMID: 29666907 PMCID: PMC6096579 DOI: 10.1007/s00412-018-0671-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/06/2018] [Accepted: 04/03/2018] [Indexed: 01/29/2023]
Abstract
Changes to the spatial organization of specific chromatin domains such as constitutive heterochromatin have been studied extensively in somatic cells. During early embryonic development, drastic epigenetic reprogramming of both the maternal and paternal genomes, followed by chromatin remodeling at the time of embryonic genome activation (EGA), have been observed in the mouse. Very few studies have been performed in other mammalian species (human, bovine, or rabbit) and the data are far from complete. During this work, we studied the three-dimensional organization of pericentromeric regions during the preimplantation period in the rabbit using specific techniques (3D-FISH) and tools (semi-automated image analysis). We observed that the pericentromeric regions (identified with specific probes for Rsat I and Rsat II genomic sequences) changed their shapes (from pearl necklaces to clusters), their nuclear localizations (from central to peripheral), as from the 4-cell stage. This reorganization goes along with histone modification changes and reduced amount of interactions with nucleolar precursor body surface. Altogether, our results suggest that the 4-cell stage may be a crucial window for events necessary before major EGA, which occurs during the 8-cell stage in the rabbit.
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Affiliation(s)
| | - Kiên Kiêu
- UR341 MaIAGE, INRA, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | | | - Krisztina Tar
- Present Address: Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- BioTalentum Ltd., Aulich Lajos str. 26, Gödöllő, 2100 Hungary
| | - Pierre Flores
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - Zichuan Liu
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
- Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Nathalie Peynot
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - Martine Chebrout
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - András Dinnyés
- BioTalentum Ltd., Aulich Lajos str. 26, Gödöllő, 2100 Hungary
| | | | - Nathalie Beaujean
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
- Present Address: Univ Lyon, Université Claude Bernard Lyon 1, Inserm, INRA, Stem Cell and Brain Research Institute U1208, USC1361, 69500 Bron, France
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Abstract
Autophagy is a catabolic program that is responsible for the degradation of dysfunctional or unnecessary proteins and organelles to maintain cellular homeostasis. Mechanistically, it involves the formation of double-membrane autophagosomes that sequester cytoplasmic material and deliver it to lysosomes for degradation. Eventually, the material is recycled back to the cytoplasm. Abnormalities of autophagy often lead to human diseases, such as neurodegeneration and cancer. In the case of cancer, increasing evidence has revealed the paradoxical roles of autophagy in both tumor inhibition and tumor promotion. Here, we summarize the context-dependent role of autophagy and its complicated molecular mechanisms in the hallmarks of cancer. Moreover, we discuss how therapeutics targeting autophagy can counter malignant transformation and tumor progression. Overall, the findings of studies discussed here shed new light on exploiting the complicated mechanisms of the autophagic machinery and relevant small-molecule modulators as potential antitumor agents to improve therapeutic outcomes.
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Affiliation(s)
- Tianzhi Huang
- Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Xiao Song
- Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Yongyong Yang
- Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Xuechao Wan
- Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Angel A. Alvarez
- Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Namratha Sastry
- Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Haizhong Feng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Hu
- Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Shi-Yuan Cheng
- Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
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44
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Viotti M, Wilson C, McCleland M, Koeppen H, Haley B, Jhunjhunwala S, Klijn C, Modrusan Z, Arnott D, Classon M, Stephan JP, Mellman I. SUV420H2 is an epigenetic regulator of epithelial/mesenchymal states in pancreatic cancer. J Cell Biol 2017; 217:763-777. [PMID: 29229751 PMCID: PMC5800801 DOI: 10.1083/jcb.201705031] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 10/13/2017] [Accepted: 11/13/2017] [Indexed: 12/23/2022] Open
Abstract
Epithelial-to-mesenchymal transition is implicated in metastasis. Viotti et al. show that the histone methyltransferase SUV420H2 favors the mesenchymal identity in pancreatic tumor cells by silencing key drivers of the epithelial state. High levels of SUV420H2 also correlate with a loss of epithelial characteristics in invasive cancer. Epithelial-to-mesenchymal transition is implicated in metastasis, where carcinoma cells lose sessile epithelial traits and acquire mesenchymal migratory potential. The mesenchymal state is also associated with cancer stem cells and resistance to chemotherapy. It might therefore be therapeutically beneficial to promote epithelial identity in cancer. Because large-scale cell identity shifts are often orchestrated on an epigenetic level, we screened for candidate epigenetic factors and identified the histone methyltransferase SUV420H2 (KMT5C) as favoring the mesenchymal identity in pancreatic cancer cell lines. Through its repressive mark H4K20me3, SUV420H2 silences several key drivers of the epithelial state. Its knockdown elicited mesenchymal-to-epithelial transition on a molecular and functional level, and cells displayed decreased stemness and increased drug sensitivity. An analysis of human pancreatic cancer biopsies was concordant with these findings, because high levels of SUV420H2 correlated with a loss of epithelial characteristics in progressively invasive cancer. Together, these data indicate that SUV420H2 is an upstream epigenetic regulator of epithelial/mesenchymal state control.
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Svoboda P. Mammalian zygotic genome activation. Semin Cell Dev Biol 2017; 84:118-126. [PMID: 29233752 DOI: 10.1016/j.semcdb.2017.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/22/2017] [Accepted: 12/08/2017] [Indexed: 12/14/2022]
Abstract
Zygotic genome activation (ZGA) denotes the initiation of gene expression after fertilization. It is part of the complex oocyte-to-embryo transition (OET) in which a highly specialized cell - the oocyte - is fertilized and transformed into a zygote that gives rise to an embryo that will develop into a newborn. From the perspective of gene expression, the OET reflects reprogramming of germ cell gene expression into the new developmental program of the zygote. This reprogramming occurs at transcriptional and post-transcriptional levels. This review will discuss selected aspects of mammalian ZGA, highlighting shared features and evolved differences observed in commonly investigated mammals and non-mammalian model animals.
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Affiliation(s)
- Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20, Prague 4, Czech Republic.
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46
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Seah MKY, Messerschmidt DM. From Germline to Soma: Epigenetic Dynamics in the Mouse Preimplantation Embryo. Curr Top Dev Biol 2017; 128:203-235. [PMID: 29477164 DOI: 10.1016/bs.ctdb.2017.10.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
When reflecting about cell fate commitment we think of differentiation. Be it during embryonic development or in an adult stem cell niche, where cells of a higher potency specialize and cell fate decisions are taken. Under normal circumstances this process is definitive and irreversible. Cell fate commitment is achieved by the establishment of cell-type-specific transcriptional programmes, which in turn are guided, reinforced, and ultimately locked-in by epigenetic mechanisms. Yet, this plunging drift in cellular potency linked to epigenetically restricted access to genomic information is problematic for reproduction. Particularly in mammals where germ cells are not set aside early on like in other species. Instead they are rederived from the embryonic ectoderm, a differentiating embryonic tissue with somatic epigenetic features. The epigenomes of germ cell precursors are efficiently reprogrammed against the differentiation trend, only to specialize once more into highly differentiated, sex-specific gametes: oocyte and sperm. Their differentiation state is reflected in their specialized epigenomes, and erasure of these features is required to enable the acquisition of the totipotent cell fate to kick start embryonic development of the next generation. Recent technological advances have enabled unprecedented insights into the epigenetic dynamics, first of DNA methylation and then of histone modifications, greatly expanding the historically technically limited understanding of this processes. In this chapter we will focus on the details of embryonic epigenetic reprogramming, a cell fate determination process against the tide to a higher potency.
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Affiliation(s)
- Michelle K Y Seah
- Developmental Epigenetics and Disease Group, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daniel M Messerschmidt
- Developmental Epigenetics and Disease Group, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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47
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Funaya S, Aoki F. Regulation of zygotic gene activation by chromatin structure and epigenetic factors. J Reprod Dev 2017; 63:359-363. [PMID: 28579579 PMCID: PMC5593087 DOI: 10.1262/jrd.2017-058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
After fertilization, the genomes derived from an oocyte and spermatozoon are in a transcriptionally silent state before becoming activated at a species-specific time. In mice, the initiation of transcription occurs at the
mid-one-cell stage, which represents the start of the gene expression program. A recent RNA sequencing analysis revealed that the gene expression pattern of one-cell embryos is unique and changes dramatically at the two-cell
stage. However, the mechanism regulating this alteration has not yet been elucidated. It has been shown that chromatin structure and epigenetic factors change dynamically between the one- and two-cell stages. In this article, we
review the characteristics of transcription, chromatin structure, and epigenetic factors in one- and two-cell mouse embryos and discuss the involvement of chromatin structure and epigenetic factors in the alteration of
transcription that occurs between these stages.
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Affiliation(s)
- Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8562, Japan
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Okada Y, Yamaguchi K. Epigenetic modifications and reprogramming in paternal pronucleus: sperm, preimplantation embryo, and beyond. Cell Mol Life Sci 2017; 74:1957-1967. [PMID: 28050628 PMCID: PMC11107594 DOI: 10.1007/s00018-016-2447-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 12/13/2022]
Abstract
Pronuclear/zygotic stage is the very first stage of life. In this period, paternal pronucleus undergoes massive chromatin remodeling called "paternal reprogramming" including protamine-histone replacement and subsequent acquisition of epigenetic modifications. Although these consecutive events are required for the initiation of maternal-zygotic transition, the precise role of paternal reprogramming and its effect on subsequent embryonic development has been largely unknown to date. Recently, various new techniques, especially next-generation sequencing (NGS) and RNAi microinjection contribute to unveil the epigenetic transition from both paternal and maternal to early preimplantation embryos, suggesting not only the simple transcriptional regulation by transcription factors but also dynamic structural alteration of chromatin to initiate the wave of zygotic gene transcription. This review summarizes such recent progress for understanding the epigenetic transition in sperm and preimplantation embryos, and further argue about its transgenerational effect.
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Affiliation(s)
- Yuki Okada
- Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Kosuke Yamaguchi
- Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
- Graduate School of Art and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
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49
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Magaraki A, van der Heijden G, Sleddens-Linkels E, Magarakis L, van Cappellen WA, Peters AHFM, Gribnau J, Baarends WM, Eijpe M. Silencing markers are retained on pericentric heterochromatin during murine primordial germ cell development. Epigenetics Chromatin 2017; 10:11. [PMID: 28293300 PMCID: PMC5346203 DOI: 10.1186/s13072-017-0119-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/02/2017] [Indexed: 12/14/2022] Open
Abstract
Background In the nuclei of most mammalian cells, pericentric heterochromatin is characterized by DNA methylation, histone modifications such as H3K9me3 and H4K20me3, and specific binding proteins like heterochromatin-binding protein 1 isoforms (HP1 isoforms). Maintenance of this specialized chromatin structure is of great importance for genome integrity and for the controlled repression of the repetitive elements within the pericentric DNA sequence. Here we have studied histone modifications at pericentric heterochromatin during primordial germ cell (PGC) development using different fixation conditions and fluorescent immunohistochemical and immunocytochemical protocols. Results We observed that pericentric heterochromatin marks, such as H3K9me3, H4K20me3, and HP1 isoforms, were retained on pericentric heterochromatin throughout PGC development. However, the observed immunostaining patterns varied, depending on the fixation method, explaining previous findings of a general loss of pericentric heterochromatic features in PGCs. Also, in contrast to the general clustering of multiple pericentric regions and associated centromeres in DAPI-dense regions in somatic cells, the pericentric regions of PGCs were more frequently organized as individual entities. We also observed a transient enrichment of the chromatin remodeler ATRX in pericentric regions in embryonic day 11.5 (E11.5) PGCs. At this stage, a similar and low level of major satellite repeat RNA transcription was detected in both PGCs and somatic cells. Conclusions These results indicate that in pericentric heterochromatin of mouse PGCs, only minor reductions in levels of some chromatin-associated proteins occur, in association with a transient increase in ATRX, between E11.5 and E13.5. These pericentric heterochromatin regions more frequently contain only a single centromere in PGCs compared to the surrounding soma, indicating a difference in overall organization, but there is no de-repression of major satellite transcription. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0119-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aristea Magaraki
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Godfried van der Heijden
- Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Erasmus MC, Rotterdam, The Netherlands
| | - Esther Sleddens-Linkels
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Leonidas Magarakis
- Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Central Hospital of Karlstad, Karlstad, Värmland Sweden
| | | | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maureen Eijpe
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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50
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Raurell-Vila H, Bosch-Presegue L, Gonzalez J, Kane-Goldsmith N, Casal C, Brown JP, Marazuela-Duque A, Singh PB, Serrano L, Vaquero A. An HP1 isoform-specific feedback mechanism regulates Suv39h1 activity under stress conditions. Epigenetics 2017; 12:166-175. [PMID: 28059589 DOI: 10.1080/15592294.2016.1278096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The presence of H3K9me3 and heterochromatin protein 1 (HP1) are hallmarks of heterochromatin conserved in eukaryotes. The spreading and maintenance of H3K9me3 is effected by the functional interplay between the H3K9me3-specific histone methyltransferase Suv39h1 and HP1. This interplay is complex in mammals because the three HP1 isoforms, HP1α, β, and γ, are thought to play a redundant role in Suv39h1-dependent deposition of H3K9me3 in pericentric heterochromatin (PCH). Here, we demonstrate that despite this redundancy, HP1α and, to a lesser extent, HP1γ have a closer functional link to Suv39h1, compared to HP1β. HP1α and γ preferentially interact in vivo with Suv39h1, regulate its dynamics in heterochromatin, and increase Suv39h1 protein stability through an inhibition of MDM2-dependent Suv39h1-K87 polyubiquitination. The reverse is also observed, where Suv39h1 increases HP1α stability compared HP1β and γ. The interplay between Suv39h1 and HP1 isoforms appears to be relevant under genotoxic stress. Specifically, loss of HP1α and γ isoforms inhibits the upregulation of Suv39h1 and H3K9me3 that is observed under stress conditions. Reciprocally, Suv39h1 deficiency abrogates stress-dependent upregulation of HP1α and γ, and enhances HP1β levels. Our work defines a specific role for HP1 isoforms in regulating Suv39h1 function under stress via a feedback mechanism that likely regulates heterochromatin formation.
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Affiliation(s)
- Helena Raurell-Vila
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Laia Bosch-Presegue
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain.,b Tissue Repair and Regeneration Group , Department of Systems Biology , Universitat de Vic, Universitat Central de Catalunya , Vic , Spain
| | - Jessica Gonzalez
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Noriko Kane-Goldsmith
- c Department of Genetics , Human Genetics Institute, Rutgers University , Piscataway , NJ , USA
| | - Carmen Casal
- d Microcopy Unit, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Jeremy P Brown
- e Fächerverbund Anatomie, Institut für Zell- und Neurobiologie, Charite - Universitätsmedizin , Berlin , Germany
| | - Anna Marazuela-Duque
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
| | - Prim B Singh
- e Fächerverbund Anatomie, Institut für Zell- und Neurobiologie, Charite - Universitätsmedizin , Berlin , Germany.,f Natural Sciences and Psychology, John Moores University , Liverpool , UK
| | - Lourdes Serrano
- c Department of Genetics , Human Genetics Institute, Rutgers University , Piscataway , NJ , USA
| | - Alejandro Vaquero
- a Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) , L'Hospitalet de Llobregat, Barcelona , Spain
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