1
|
León NY, Le TNU, Garvie A, Wong LH, Bagheri-Fam S, Harley VR. Y chromosome damage underlies testicular abnormalities in ATR-X syndrome. iScience 2024; 27:109629. [PMID: 38616920 PMCID: PMC11015497 DOI: 10.1016/j.isci.2024.109629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/27/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
ATR-X (alpha thalassemia, mental retardation, X-linked) syndrome features genital and testicular abnormalities including atypical genitalia and small testes with few seminiferous tubules. Our mouse model recapitulated the testicular defects when Atrx was deleted in Sertoli cells (ScAtrxKO) which displayed G2/M arrest and apoptosis. Here, we investigated the mechanisms underlying these defects. In control mice, Sertoli cells contain a single novel "GATA4 PML nuclear body (NB)" that contained the transcription factor GATA4, ATRX, DAXX, HP1α, and PH3 and co-localized with the Y chromosome short arm (Yp). ScAtrxKO mice contain single giant GATA4 PML-NBs with frequent DNA double-strand breaks (DSBs) in G2/M-arrested apoptotic Sertoli cells. HP1α and PH3 were absent from giant GATA4 PML-NBs indicating a failure in heterochromatin formation and chromosome condensation. Our data suggest that ATRX protects a Yp region from DNA damage, thereby preventing Sertoli cell death. We discuss Y chromosome damage/decondensation as a mechanism for testicular failure.
Collapse
Affiliation(s)
- Nayla Y. León
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Thanh Nha Uyen Le
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Andrew Garvie
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lee H. Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Stefan Bagheri-Fam
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Vincent R. Harley
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| |
Collapse
|
2
|
Choi J, Kim T, Cho EJ. HIRA vs. DAXX: the two axes shaping the histone H3.3 landscape. Exp Mol Med 2024; 56:251-263. [PMID: 38297159 PMCID: PMC10907377 DOI: 10.1038/s12276-023-01145-3] [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: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 02/02/2024] Open
Abstract
H3.3, the most common replacement variant for histone H3, has emerged as an important player in chromatin dynamics for controlling gene expression and genome integrity. While replicative variants H3.1 and H3.2 are primarily incorporated into nucleosomes during DNA synthesis, H3.3 is under the control of H3.3-specific histone chaperones for spatiotemporal incorporation throughout the cell cycle. Over the years, there has been progress in understanding the mechanisms by which H3.3 affects domain structure and function. Furthermore, H3.3 distribution and relative abundance profoundly impact cellular identity and plasticity during normal development and pathogenesis. Recurrent mutations in H3.3 and its chaperones have been identified in neoplastic transformation and developmental disorders, providing new insights into chromatin biology and disease. Here, we review recent findings emphasizing how two distinct histone chaperones, HIRA and DAXX, take part in the spatial and temporal distribution of H3.3 in different chromatin domains and ultimately achieve dynamic control of chromatin organization and function. Elucidating the H3.3 deposition pathways from the available histone pool will open new avenues for understanding the mechanisms by which H3.3 epigenetically regulates gene expression and its impact on cellular integrity and pathogenesis.
Collapse
Affiliation(s)
- Jinmi Choi
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Taewan Kim
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Eun-Jung Cho
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea.
| |
Collapse
|
3
|
Quesnel KM, Martin-Kenny N, Bérubé NG. A mouse model of ATRX deficiency with cognitive deficits and autistic traits. J Neurodev Disord 2023; 15:39. [PMID: 37957569 PMCID: PMC10644498 DOI: 10.1186/s11689-023-09508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND ATRX is an ATP-dependent chromatin remodeling protein with essential roles in safeguarding genome integrity and modulating gene expression. Deficiencies in this protein cause ATR-X syndrome, a condition characterized by intellectual disability and an array of developmental abnormalities, including features of autism. Previous studies demonstrated that deleting ATRX in mouse forebrain excitatory neurons postnatally resulted in male-specific memory deficits, but no apparent autistic-like behaviours. METHODS We generated mice with an earlier embryonic deletion of ATRX in forebrain excitatory neurons and characterized their behaviour using a series of memory and autistic-related paradigms. RESULTS We found that mutant mice displayed a broader spectrum of impairments, including fear memory, decreased anxiety-like behaviour, hyperactivity, as well as self-injurious and repetitive grooming. Sex-specific alterations were also observed, including male-specific aggression, sensory gating impairments, and decreased social memory. CONCLUSIONS Collectively, the findings indicate that early developmental abnormalities arising from ATRX deficiency in forebrain excitatory neurons contribute to the presentation of fear memory deficits as well as autistic-like behaviours.
Collapse
Affiliation(s)
- Katherine M Quesnel
- Department of Anatomy & Cell Biology, Western University, London, Canada
- Department of Paediatrics, Western University, London, Canada
- Division of Genetics & Development, Children's Health Research Institute, London, ON, Canada
| | - Nicole Martin-Kenny
- Department of Anatomy & Cell Biology, Western University, London, Canada
- Department of Paediatrics, Western University, London, Canada
- Division of Genetics & Development, Children's Health Research Institute, London, ON, Canada
| | - Nathalie G Bérubé
- Department of Anatomy & Cell Biology, Western University, London, Canada.
- Department of Paediatrics, Western University, London, Canada.
- Division of Genetics & Development, Children's Health Research Institute, London, ON, Canada.
- Department of Oncology, Western University, London, Canada.
| |
Collapse
|
4
|
Sun C, Qi Y, Fowlkes N, Lazic N, Su X, Lozano G, Wasylishen AR. The histone chaperone function of Daxx is dispensable for embryonic development. Cell Death Dis 2023; 14:565. [PMID: 37633949 PMCID: PMC10460429 DOI: 10.1038/s41419-023-06089-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023]
Abstract
Daxx functions as a histone chaperone for the histone H3 variant, H3.3, and is essential for embryonic development. Daxx interacts with Atrx to form a protein complex that deposits H3.3 into heterochromatic regions of the genome, including centromeres, telomeres, and repeat loci. To advance our understanding of histone chaperone activity in vivo, we developed two Daxx mutant alleles in the mouse germline, which abolish the interactions between Daxx and Atrx (DaxxY130A), and Daxx and H3.3 (DaxxS226A). We found that the interaction between Daxx and Atrx is dispensable for viability; mice are born at the expected Mendelian ratio and are fertile. The loss of Daxx-Atrx interaction, however, does cause dysregulated expression of endogenous retroviruses. In contrast, the interaction between Daxx and H3.3, while not required for embryonic development, is essential for postnatal viability. Transcriptome analysis of embryonic tissues demonstrates that this interaction is important for silencing endogenous retroviruses and for maintaining proper immune cell composition. Overall, these results clearly demonstrate that Daxx has both Atrx-dependent and independent functions in vivo, advancing our understanding of this epigenetic regulatory complex.
Collapse
Affiliation(s)
- Chang Sun
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Yuan Qi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natalie Fowlkes
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Nina Lazic
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
| | - Amanda R Wasylishen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, 45267, USA.
| |
Collapse
|
5
|
Tillotson R, Yan K, Ruston J, DeYoung T, Córdova A, Turcotte-Cardin V, Yee Y, Taylor C, Visuvanathan S, Babbs C, Ivakine EA, Sled JG, Nieman BJ, Picketts DJ, Justice MJ. A new mouse model of ATR-X syndrome carrying a common patient mutation exhibits neurological and morphological defects. Hum Mol Genet 2023; 32:2485-2501. [PMID: 37171606 PMCID: PMC10360390 DOI: 10.1093/hmg/ddad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/18/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
ATRX is a chromatin remodelling ATPase that is involved in transcriptional regulation, DNA damage repair and heterochromatin maintenance. It has been widely studied for its role in ALT-positive cancers, but its role in neurological function remains elusive. Hypomorphic mutations in the X-linked ATRX gene cause a rare form of intellectual disability combined with alpha-thalassemia called ATR-X syndrome in hemizygous males. Clinical features also include facial dysmorphism, microcephaly, short stature, musculoskeletal defects and genital abnormalities. As complete deletion of ATRX in mice results in early embryonic lethality, the field has largely relied on conditional knockout models to assess the role of ATRX in multiple tissues. Given that null alleles are not found in patients, a more patient-relevant model was needed. Here, we have produced and characterized the first patient mutation knock-in model of ATR-X syndrome, carrying the most common causative mutation, R246C. This is one of a cluster of missense mutations located in the chromatin-binding domain and disrupts its function. The knock-in mice recapitulate several aspects of the patient disorder, including craniofacial defects, microcephaly, reduced body size and impaired neurological function. They provide a powerful model for understanding the molecular mechanisms underlying ATR-X syndrome and testing potential therapeutic strategies.
Collapse
Affiliation(s)
- Rebekah Tillotson
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way, Oxford OX3 9DS, UK
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Julie Ruston
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Taylor DeYoung
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
| | - Alex Córdova
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Valérie Turcotte-Cardin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Yohan Yee
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Christine Taylor
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Shagana Visuvanathan
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way, Oxford OX3 9DS, UK
| | - Evgueni A Ivakine
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John G Sled
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Translational Medicine Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Brian J Nieman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Translational Medicine Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Monica J Justice
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
| |
Collapse
|
6
|
Floyd W, Pierpoint M, Su C, Patel R, Luo L, Deland K, Wisdom AJ, Zhu D, Ma Y, DeWitt SB, Williams NT, Lazarides AL, Somarelli JA, Corcoran DL, Eward WC, Cardona DM, Kirsch DG. Atrx deletion impairs CGAS/STING signaling and increases sarcoma response to radiation and oncolytic herpesvirus. J Clin Invest 2023; 133:e149310. [PMID: 37200088 PMCID: PMC10313374 DOI: 10.1172/jci149310] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/16/2023] [Indexed: 05/20/2023] Open
Abstract
ATRX is one of the most frequently altered genes in solid tumors, and mutation is especially frequent in soft tissue sarcomas. However, the role of ATRX in tumor development and response to cancer therapies remains poorly understood. Here, we developed a primary mouse model of soft tissue sarcoma and showed that Atrx-deleted tumors were more sensitive to radiation therapy and to oncolytic herpesvirus. In the absence of Atrx, irradiated sarcomas had increased persistent DNA damage, telomere dysfunction, and mitotic catastrophe. Our work also showed that Atrx deletion resulted in downregulation of the CGAS/STING signaling pathway at multiple points in the pathway and was not driven by mutations or transcriptional downregulation of the CGAS/STING pathway components. We found that both human and mouse models of Atrx-deleted sarcoma had a reduced adaptive immune response, markedly impaired CGAS/STING signaling, and increased sensitivity to TVEC, an oncolytic herpesvirus that is currently FDA approved for the treatment of aggressive melanomas. Translation of these results to patients with ATRX-mutant cancers could enable genomically guided cancer therapy approaches to improve patient outcomes.
Collapse
Affiliation(s)
- Warren Floyd
- Department of Pharmacology and Cancer Biology, and
| | | | - Chang Su
- Department of Pharmacology and Cancer Biology, and
| | - Rutulkumar Patel
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Katherine Deland
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - Amy J. Wisdom
- Department of Radiation Oncology, Brigham and Women’s Hospital/Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniel Zhu
- Department of Pharmacology and Cancer Biology, and
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Nerissa T. Williams
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Jason A. Somarelli
- Department of Sarcoma, Moffitt Cancer Center, Tampa, Florida, USA
- Duke Cancer Institute, Durham, North Carolina, USA
| | - David L. Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
| | | | - Diana M. Cardona
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - David G. Kirsch
- Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Radiation Oncology and
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
7
|
Gaspar TB, Jesus TT, Azevedo MT, Macedo S, Soares MA, Martins RS, Leite R, Rodrigues L, Rodrigues DF, Cardoso L, Borges I, Canberk S, Gärtner F, Miranda-Alves L, Lopes JM, Soares P, Vinagre J. Generation of an Obese Diabetic Mouse Model upon Conditional Atrx Disruption. Cancers (Basel) 2023; 15:cancers15113018. [PMID: 37296979 DOI: 10.3390/cancers15113018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/15/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Atrx loss was recently ascertained as insufficient to drive pancreatic neuroendocrine tumour (PanNET) formation in mice islets. We have identified a preponderant role of Atrx in the endocrine dysfunction in a Rip-Cre;AtrxKO genetically engineered mouse model (GEMM). To validate the impact of a different Cre-driver line, we used similar methodologies and characterised the Pdx1-Cre;AtrxKO (P.AtrxKO) GEMM to search for PanNET formation and endocrine fitness disruption for a period of up to 24 months. Male and female mice presented different phenotypes. Compared to P.AtrxWT, P.AtrxHOM males were heavier during the entire study period, hyperglycaemic between 3 and 12 mo., and glucose intolerant only from 6 mo.; in contrast, P.AtrxHOM females started exhibiting increased weight gains later (after 6 mo.), but diabetes or glucose intolerance was detected by 3 mo. Overall, all studied mice were overweight or obese from early ages, which challenged the histopathological evaluation of the pancreas and liver, especially after 12 mo. Noteworthily, losing Atrx predisposed mice to an increase in intrapancreatic fatty infiltration (FI), peripancreatic fat deposition, and macrovesicular steatosis. As expected, no animal developed PanNETs. An obese diabetic GEMM of disrupted Atrx is presented as potentially useful for metabolic studies and as a putative candidate for inserting additional tumourigenic genetic events.
Collapse
Affiliation(s)
- Tiago Bordeira Gaspar
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Tito Teles Jesus
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Maria Teresa Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Sofia Macedo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Mariana Alves Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Laboratório de Endocrinologia Experimental (LEEx), Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Programa de Pós-Graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Rui Sousa Martins
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Faculty of Sciences of the University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Rúben Leite
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- School of Health (ESS), Polytechnic Institute of Porto (IPP), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Lia Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Daniela Ferreira Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular and Cell Biology (IBMC), University of Porto, 4200-135 Porto, Portugal
| | - Luís Cardoso
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Department of Endocrinology, Diabetes and Metabolism, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | - Inês Borges
- Centro de Diagnóstico Veterinário (Cedivet), 4200-071 Porto, Portugal
| | - Sule Canberk
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Fátima Gärtner
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
| | - Leandro Miranda-Alves
- Laboratório de Endocrinologia Experimental (LEEx), Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Programa de Pós-Graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - José Manuel Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário de São João (CHUSJ), 4200-319 Porto, Portugal
| | - Paula Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - João Vinagre
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| |
Collapse
|
8
|
Clatterbuck Soper SF, Meltzer PS. ATRX/DAXX: Guarding the Genome against the Hazards of ALT. Genes (Basel) 2023; 14:genes14040790. [PMID: 37107548 PMCID: PMC10137841 DOI: 10.3390/genes14040790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Proliferating cells must enact a telomere maintenance mechanism to ensure genomic stability. In a subset of tumors, telomeres are maintained not by telomerase, but through a homologous recombination-based mechanism termed Alternative Lengthening of Telomeres or ALT. The ALT process is linked to mutations in the ATRX/DAXX/H3.3 histone chaperone complex. This complex is responsible for depositing non-replicative histone variant H3.3 at pericentric and telomeric heterochromatin but has also been found to have roles in ameliorating replication in repeat sequences and in promoting DNA repair. In this review, we will discuss ways in which ATRX/DAXX helps to protect the genome, and how loss of this complex allows ALT to take hold.
Collapse
|
9
|
Zhu J, Chen K, Sun YH, Ye W, Liu J, Zhang D, Su N, Wu L, Kou X, Zhao Y, Wang H, Gao S, Kang L. LSM1-mediated Major Satellite RNA decay is required for nonequilibrium histone H3.3 incorporation into parental pronuclei. Nat Commun 2023; 14:957. [PMID: 36810573 PMCID: PMC9944933 DOI: 10.1038/s41467-023-36584-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Epigenetic reprogramming of the parental genome is essential for zygotic genome activation and subsequent embryo development in mammals. Asymmetric incorporation of histone H3 variants into the parental genome has been observed previously, but the underlying mechanism remains elusive. In this study, we discover that RNA-binding protein LSM1-mediated major satellite RNA decay plays a central role in the preferential incorporation of histone variant H3.3 into the male pronucleus. Knockdown of Lsm1 disrupts nonequilibrium pronucleus histone incorporation and asymmetric H3K9me3 modification. Subsequently, we find that LSM1 mainly targets major satellite repeat RNA (MajSat RNA) for decay and that accumulated MajSat RNA in Lsm1-depleted oocytes leads to abnormal incorporation of H3.1 into the male pronucleus. Knockdown of MajSat RNA reverses the anomalous histone incorporation and modifications in Lsm1-knockdown zygotes. Our study therefore reveals that accurate histone variant incorporation and incidental modifications in parental pronuclei are specified by LSM1-dependent pericentromeric RNA decay.
Collapse
Affiliation(s)
- Jiang Zhu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Kang Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yu H Sun
- Departments of Biology, University of Rochester, 14642, Rochester, NY, USA
| | - Wen Ye
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Juntao Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Dandan Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Nan Su
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Li Wu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Xiaochen Kou
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Yanhong Zhao
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Hong Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China. .,Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
| | - Lan Kang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
| |
Collapse
|
10
|
Guo M, Fang Z, Chen B, Songyang Z, Xiong Y. Distinct dosage compensations of ploidy-sensitive and -insensitive X chromosome genes during development and in diseases. iScience 2023; 26:105997. [PMID: 36798435 PMCID: PMC9926305 DOI: 10.1016/j.isci.2023.105997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/12/2022] [Accepted: 01/12/2023] [Indexed: 01/20/2023] Open
Abstract
The active X chromosome in mammals is upregulated to balance its dosage to autosomes during evolution. However, it is elusive why the known dosage compensation machinery showed uneven and small influence on X genes. Here, based on >20,000 transcriptomes, we identified two X gene groups (ploidy-sensitive [PSX] and ploidy-insensitive [PIX]), showing distinct but evolutionarily conserved dosage compensations (termed XAR). We demonstrated that XAR-PIX was downregulated whereas XAR-PSX upregulated at both RNA and protein levels across cancer types, in contrast with their trends during stem cell differentiation. XAR-PIX, but not XAR-PSX, was lower and correlated with autoantibodies and inflammation in patients of lupus, suggesting that insufficient dosage of PIX genes contribute to lupus pathogenesis. We further identified and experimentally validated two XAR regulators, TP53 and ATRX. Collectively, we provided insights into X dosage compensation in mammals and demonstrated different regulation of PSX and PIX and their pathophysiological roles in human diseases.
Collapse
Affiliation(s)
- Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhengwen Fang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Bohong Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China,Corresponding author
| |
Collapse
|
11
|
Bieluszewska A, Wulfridge P, Doherty J, Ren W, Sarma K. ATRX histone binding and helicase activities have distinct roles in neuronal differentiation. Nucleic Acids Res 2022; 50:9162-9174. [PMID: 35998910 PMCID: PMC9458459 DOI: 10.1093/nar/gkac683] [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: 05/17/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
ATRX is a chromatin remodeler, which is mutated in ATRX syndrome, a neurodevelopmental disorder. ATRX mutations that alter histone binding or chromatin remodeling activities cluster in the PHD finger or the helicase domain respectively. Using engineered mouse embryonic stem cells that exclusively express ATRX protein with mutations in the PHD finger (PHDmut) or helicase domains (K1584R), we examine how specific ATRX mutations affect neurodifferentiation. ATRX PHDmut and K1584R proteins interact with the DAXX histone chaperone but show reduced localization to pericentromeres. Neurodifferentiation is both delayed and compromised in PHDmut and K1584R, and manifest differently from complete ATRX loss. We observe reduced enrichment of PHDmut protein to ATRX targets, while K1584R accumulates at these sites. Interestingly, ATRX mutations have distinct effects on the genome-wide localization of the polycomb repressive complex 2 (PRC2), with PHDmut and ATRX knockout showing reduced PRC2 binding at polycomb targets and K1584R showing loss at some sites and gains at others. Notably, each mutation associated with unique gene signatures, suggesting distinct pathways leading to impaired neurodifferentiation. Our results indicate that the histone binding and chromatin remodeling functions of ATRX play non-redundant roles in neurodevelopment, and when mutated lead to ATRX syndrome through separate regulatory pathways.
Collapse
Affiliation(s)
- Anna Bieluszewska
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA,Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA,Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Doherty
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA,Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenqing Ren
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA,Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kavitha Sarma
- To whom correspondence should be addressed. Tel: +1 215 898 3970;
| |
Collapse
|
12
|
Sun C, Estrella JS, Whitley EM, Chau GP, Lozano G, Wasylishen AR. Mouse modeling provides insights into Daxx and Atrx tumor suppressive mechanisms in the endocrine pancreas. Dis Model Mech 2022; 15:276356. [PMID: 35976056 PMCID: PMC9438929 DOI: 10.1242/dmm.049552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/19/2022] [Indexed: 11/20/2022] Open
Abstract
Genome sequencing has revealed the importance of epigenetic regulators in tumorigenesis. The genes encoding the chromatin remodeling complex DAXX:ATRX are frequently mutated in pancreatic neuroendocrine tumors (PanNETs); however, the underlying mechanisms of how mutations contribute to tumorigenesis are only partially understood, in part because of the lack of relevant pre-clinical models. Here we used genetically engineered mouse models combined with environmental stress to evaluate the tumor suppressor functions of Daxx and Atrx in the mouse pancreas. Daxx or Atrx loss, alone or in combination with Men1 loss, do not drive nor accelerate pancreatic neuroendocrine tumorigenesis. Moreover, Daxx loss does not cooperate with environmental stresses (ionizing radiation or pancreatitis) or with the loss of other tumor suppressors (Pten or p53) to promote pancreatic neuroendocrine tumorigenesis. However, due to promiscuity of the Cre promoter used, hepatocellular carcinomas (HCC) and osteosarcomas were observed in some instances. Overall, our findings suggest that Daxx and Atrx are not robust tumor suppressors in the endocrine pancreas of mice and indicate the context of a human genome is essential for tumorigenesis.
Collapse
Affiliation(s)
- Chang Sun
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Jeannelyn S Estrella
- Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Elizabeth M Whitley
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gilda P Chau
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Amanda R Wasylishen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| |
Collapse
|
13
|
Gaspar TB, Macedo S, Sá A, Soares MA, Rodrigues DF, Sousa M, Mendes N, Martins RS, Cardoso L, Borges I, Canberk S, Gärtner F, Miranda-Alves L, Sobrinho-Simões M, Lopes JM, Soares P, Vinagre J. Characterisation of an Atrx Conditional Knockout Mouse Model: Atrx Loss Causes Endocrine Dysfunction Rather Than Pancreatic Neuroendocrine Tumour. Cancers (Basel) 2022; 14:cancers14163865. [PMID: 36010860 PMCID: PMC9406167 DOI: 10.3390/cancers14163865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 12/22/2022] Open
Abstract
Simple Summary ATRX and DAXX mutations occur in 30–40% of pancreatic neuroendocrine tumours (PanNETs), and there are no reports in the literature of any genetically engineered mouse model (GEMM) evaluating the effect of Atrx disruption as a putative driver event on PanNET initiation. We created a novel GEMM with Atrx conditional disruption in β cells. We observed that this genetic alteration, per se, was not tumourigenic, but we reported novel roles of Atrx on endocrine function, which resulted in dysglycaemia and the exacerbation of inflammageing (increased pancreatic inflammation and hepatic steatosis). Abstract ATRX is a chromatin remodeller that maintains telomere homeostasis. Loss of ATRX is described in approximately 10% of pancreatic neuroendocrine tumours (PanNETs) and associated with poorer prognostic features. Here, we present a genetically engineered mouse model (GEMM) addressing the role of Atrx loss (AtrxKO) in pancreatic β cells, evaluating a large cohort of ageing mice (for up to 24 months (mo.)). Atrx loss did not cause PanNET formation but rather resulted in worsening of ageing-related pancreatic inflammation and endocrine dysfunction in the first year of life. Histopathological evaluation highlighted an exacerbated prevalence and intensity of pancreatic inflammation, ageing features, and hepatic steatosis in AtrxKO mice. Homozygous floxed mice presented hyperglycaemia, increased weights, and glucose intolerance after 6 months, but alterations in insulinaemia were not detected. Floxed individuals presented an improper growth of their pancreatic endocrine fraction that may explain such an endocrine imbalance. A pilot study of BRACO-19 administration to AtrxKO mice resulted in telomere instability, reinforcing the involvement of Atrx in the maintenance of β cell telomere homeostasis. Thereby, a non-obese dysglycaemic GEMM of disrupted Atrx is here presented as potentially useful for metabolic studies and putative candidate for inserting additional tumourigenic genetic events.
Collapse
Affiliation(s)
- Tiago Bordeira Gaspar
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Sofia Macedo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Ana Sá
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Mariana Alves Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Laboratório de Endocrinologia Experimental (LEEx), Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil
- Programa de Pós-Graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-905, Brazil
| | - Daniela Ferreira Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute for Molecular and Cell Biology (IBMC), University of Porto, 4200-135 Porto, Portugal
| | - Mafalda Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute for Molecular and Cell Biology (IBMC), University of Porto, 4200-135 Porto, Portugal
| | - Nuno Mendes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Rui Sousa Martins
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Sciences of the University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Luís Cardoso
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Department of Endocrinology, Diabetes and Metabolism, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal
| | - Inês Borges
- Centro de Diagnóstico Veterinário (Cedivet), 4200-071 Porto, Portugal
| | - Sule Canberk
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Fátima Gärtner
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Leandro Miranda-Alves
- Laboratório de Endocrinologia Experimental (LEEx), Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil
- Programa de Pós-Graduação em Endocrinologia, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-905, Brazil
| | - Manuel Sobrinho-Simões
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário de São João (CHUSJ), 4200-319 Porto, Portugal
| | - José Manuel Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário de São João (CHUSJ), 4200-319 Porto, Portugal
| | - Paula Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
| | - João Vinagre
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal
- Correspondence: ; Tel.: +351-225-570-700
| |
Collapse
|
14
|
Rajam SM, Varghese PC, Dutta D. Histone Chaperones as Cardinal Players in Development. Front Cell Dev Biol 2022; 10:767773. [PMID: 35445016 PMCID: PMC9014011 DOI: 10.3389/fcell.2022.767773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
Dynamicity and flexibility of the chromatin landscape are critical for most of the DNA-dependent processes to occur. This higher-order packaging of the eukaryotic genome into the chromatin is mediated by histones and associated non-histone proteins that determine the states of chromatin. Histone chaperones- “the guardian of genome stability and epigenetic information” controls the chromatin accessibility by escorting the nucleosomal and non-nucleosomal histones as well as their variants. This distinct group of molecules is involved in all facets of histone metabolism. The selectivity and specificity of histone chaperones to the histones determine the maintenance of the chromatin in an open or closed state. This review highlights the functional implication of the network of histone chaperones in shaping the chromatin function in the development of an organism. Seminal studies have reported embryonic lethality at different stages of embryogenesis upon perturbation of some of the chaperones, suggesting their essentiality in development. We hereby epitomize facts and functions that emphasize the relevance of histone chaperones in orchestrating different embryonic developmental stages starting from gametogenesis to organogenesis in multicellular organisms.
Collapse
Affiliation(s)
- Sruthy Manuraj Rajam
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Pallavi Chinnu Varghese
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India
| |
Collapse
|
15
|
van Gerven MR, Bozsaky E, Matser YAH, Vosseberg J, Taschner-Mandl S, Koster J, Tytgat GAM, Molenaar JJ, van den Boogaard M. The mutational spectrum of ATRX aberrations in neuroblastoma and the associated patient and tumor characteristics. Cancer Sci 2022; 113:2167-2178. [PMID: 35384159 PMCID: PMC9207354 DOI: 10.1111/cas.15363] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/18/2022] [Accepted: 04/02/2022] [Indexed: 11/30/2022] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. The chromatin remodeler ATRX is frequently mutated in high‐risk patients with a poor prognosis. Although many studies have reported ATRX aberrations and the associated clinical characteristics in neuroblastoma, a comprehensive overview is currently lacking. In this study, we extensively characterize the mutational spectrum of ATRX aberrations in neuroblastoma tumors reported in previous studies and present an overview of patient and tumor characteristics. We collected the data of a total of 127 neuroblastoma patients and three cell lines with ATRX aberrations originating from 20 papers. We subdivide the ATRX aberrations into nonsense, missense, and multiexon deletions (MEDs) and show that 68% of them are MEDs. Of these MEDs, 75% are predicted to be in‐frame. Furthermore, we identify a missense mutational hotspot region in the helicase domain. We also confirm that all three ATRX mutation types are more often identified in patients diagnosed at an older age, but still approximately 40% of the patients are aged 5 years or younger at diagnosis. Surprisingly, we found that 11q deletions are enriched in neuroblastomas with ATRX deletions compared to a reference cohort, but not in neuroblastomas with ATRX point mutations. Taken together, our data emphasizes a distinct ATRX mutation spectrum in neuroblastoma, which should be considered when studying molecular phenotypes and therapeutic strategies.
Collapse
Affiliation(s)
| | - Eva Bozsaky
- Tumor biology group, St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Yvette A H Matser
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | | | - Jan Koster
- Department of Oncogenomics, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | | | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | | |
Collapse
|
16
|
Barreto VM, Kubasova N, Alves-Pereira CF, Gendrel AV. X-Chromosome Inactivation and Autosomal Random Monoallelic Expression as "Faux Amis". Front Cell Dev Biol 2021; 9:740937. [PMID: 34631717 PMCID: PMC8495168 DOI: 10.3389/fcell.2021.740937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 12/23/2022] Open
Abstract
X-chromosome inactivation (XCI) and random monoallelic expression of autosomal genes (RMAE) are two paradigms of gene expression regulation where, at the single cell level, genes can be expressed from either the maternal or paternal alleles. X-chromosome inactivation takes place in female marsupial and placental mammals, while RMAE has been described in mammals and also other species. Although the outcome of both processes results in random monoallelic expression and mosaicism at the cellular level, there are many important differences. We provide here a brief sketch of the history behind the discovery of XCI and RMAE. Moreover, we review some of the distinctive features of these two phenomena, with respect to when in development they are established, their roles in dosage compensation and cellular phenotypic diversity, and the molecular mechanisms underlying their initiation and stability.
Collapse
Affiliation(s)
- Vasco M Barreto
- Chronic Diseases Research Centre, CEDOC, Nova Medical School, Lisbon, Portugal
| | - Nadiya Kubasova
- Chronic Diseases Research Centre, CEDOC, Nova Medical School, Lisbon, Portugal
| | - Clara F Alves-Pereira
- Department of Genetics, Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
17
|
León NY, Harley VR. ATR-X syndrome: genetics, clinical spectrum, and management. Hum Genet 2021; 140:1625-1634. [PMID: 34524523 DOI: 10.1007/s00439-021-02361-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022]
Abstract
ATR-X, an acronym for alpha thalassemia and mental retardation X-linked, syndrome is a congenital condition predominantly affecting males, characterized by mild to severe intellectual disability, facial, skeletal, urogenital, and hematopoietic anomalies. Less common are heart defects, eye anomalies, renal abnormalities, and gastrointestinal dysfunction. ATR-X syndrome is caused by germline variants in the ATRX gene. Until recently, the diagnosis of the ATR-X syndrome had been guided by the classical clinical manifestations and confirmed by molecular techniques. However, our new systematic analysis shows that the only clinical sign shared by all affected individuals is intellectual disability, with the other manifestations varying even within the same family. More than 190 different germline ATRX mutations in some 200 patients have been analyzed. With improved and more frequent analysis by molecular technologies, more subtle deletions and insertions have been detected recently. Moreover, emerging technologies reveal non-classic phenotypes of ATR-X syndrome as well as the description of a new clinical feature, the development of osteosarcoma which suggests an increased cancer risk in ATR-X syndrome. This review will focus on the different types of inherited ATRX mutations and their relation to clinical features in the ATR-X syndrome. We will provide an update of the frequency of clinical manifestations, the affected organs, and the genotype-phenotype correlations. Finally, we propose a shift in the diagnosis of ATR-X patients, from a clinical diagnosis to a molecular-based approach. This may assist clinicians in patient management, risk assessment and genetic counseling.
Collapse
Affiliation(s)
- Nayla Y León
- Sex Development Laboratory, Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, 27-31 Wright Street, Melbourne, VIC, 3168, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
| | - Vincent R Harley
- Sex Development Laboratory, Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, 27-31 Wright Street, Melbourne, VIC, 3168, Australia. .,Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia.
| |
Collapse
|
18
|
Huang TC, Chang KC, Chang JY, Tsai YS, Yang YJ, Chang WC, Mo CF, Yu PH, Chiang CT, Lin SP, Kuo PL. Variants in Maternal Effect Genes and Relaxed Imprinting Control in a Special Placental Mesenchymal Dysplasia Case with Mild Trophoblast Hyperplasia. Biomedicines 2021; 9:biomedicines9050544. [PMID: 34068021 PMCID: PMC8152467 DOI: 10.3390/biomedicines9050544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
Placental mesenchymal dysplasia (PMD) and partial hydatidiform mole (PHM) placentas share similar characteristics, such as placental overgrowth and grape-like placental tissues. Distinguishing PMD from PHM is critical because the former can result in normal birth, while the latter diagnosis will lead to artificial abortion. Aneuploidy and altered dosage of imprinted gene expression are implicated in the pathogenesis of PHM and also some of the PMD cases. Diandric triploidy is the main cause of PHM, whereas mosaic diploid androgenetic cells in the placental tissue have been associated with the formation of PMD. Here, we report a very special PMD case also presenting with trophoblast hyperplasia phenotype, which is a hallmark of PHM. This PMD placenta has a normal biparental diploid karyotype and is functionally sufficient to support normal fetal growth. We took advantage of this unique case to further dissected the potential common etiology between these two diseases. We show that the differentially methylated region (DMR) at NESP55, a secondary DMR residing in the GNAS locus, is significantly hypermethylated in the PMD placenta. Furthermore, we found heterozygous mutations in NLRP2 and homozygous variants in NLRP7 in the mother’s genome. NLRP2 and NLRP7 are known maternal effect genes, and their mutation in pregnant females affects fetal development. The variants/mutations in both genes have been associated with imprinting defects in mole formation and potentially contributed to the mild abnormal imprinting observed in this case. Finally, we identified heterozygous mutations in the X-linked ATRX gene, a known maternal–zygotic imprinting regulator in the patient. Overall, our study demonstrates that PMD and PHM may share overlapping etiologies with the defective/relaxed dosage control of imprinted genes, representing two extreme ends of a spectrum.
Collapse
Affiliation(s)
- Tien-Chi Huang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
| | - Kung-Chao Chang
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan;
| | - Jen-Yun Chang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
| | - Yi-Shan Tsai
- Department of Radiology, National Cheng Kung University Hospital, Tainan 704, Taiwan;
| | - Yao-Jong Yang
- Department of Pediatrics, National Cheng Kung University Hospital, Tainan 704, Taiwan;
| | - Wei-Chun Chang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
| | - Chu-Fan Mo
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
| | - Pei-Hsiu Yu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Department of Obstetrics and Gynecology, Kuo General Hospital, Tainan 700, Taiwan
| | - Chun-Ting Chiang
- Department and Graduated Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei 106, Taiwan;
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan; (T.-C.H.); (J.-Y.C.); (W.-C.C.); (C.-F.M.)
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei 106, Taiwan
- Center for Systems Biology, National Taiwan University, Taipei 106, Taiwan
- Correspondence: (S.-P.L.); (P.-L.K.)
| | - Pao-Lin Kuo
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Correspondence: (S.-P.L.); (P.-L.K.)
| |
Collapse
|
19
|
Tamming RJ, Dumeaux V, Jiang Y, Shafiq S, Langlois L, Ellegood J, Qiu LR, Lerch JP, Bérubé NG. Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits. Cell Rep 2021; 31:107838. [PMID: 32610139 PMCID: PMC7326465 DOI: 10.1016/j.celrep.2020.107838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 04/13/2020] [Accepted: 06/08/2020] [Indexed: 12/31/2022] Open
Abstract
ATRX gene mutations have been identified in syndromic and non-syndromic intellectual disabilities in humans. ATRX is known to maintain genomic stability in neuroprogenitor cells, but its function in differentiated neurons and memory processes remains largely unresolved. Here, we show that the deletion of neuronal Atrx in mice leads to distinct hippocampal structural defects, fewer presynaptic vesicles, and an enlarged postsynaptic area at CA1 apical dendrite-axon junctions. We identify male-specific impairments in long-term contextual memory and in synaptic gene expression, linked to altered miR-137 levels. We show that ATRX directly binds to the miR-137 locus and that the enrichment of the suppressive histone mark H3K27me3 is significantly reduced upon the loss of ATRX. We conclude that the ablation of ATRX in excitatory forebrain neurons leads to sexually dimorphic effects on miR-137 expression and on spatial memory, identifying a potential therapeutic target for neurological defects caused by ATRX dysfunction. Loss of ATRX in neurons has sexually dimorphic effects on long-term spatial memory Targeted deletion of neuronal ATRX in mice causes ultrastructural synaptic defects ATRX null neurons show sex-specific changes in miR-137 and target synaptic transcripts ATRX directly binds and suppresses miR-137 in males via enrichment of H3K27me3
Collapse
Affiliation(s)
- Renee J Tamming
- Children's Health Research Institute, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Biochemistry, Western University, London, ON, Canada
| | - Vanessa Dumeaux
- Department of Paediatrics, Western University, London, ON, Canada; PERFORM Centre, Concordia University, Montreal, QC, Canada
| | - Yan Jiang
- Children's Health Research Institute, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada
| | - Sarfraz Shafiq
- Children's Health Research Institute, London, ON, Canada; Department of Paediatrics, Western University, London, ON, Canada; Department of Anatomy & Cell Biology, Western University, London, ON, Canada
| | - Luana Langlois
- Children's Health Research Institute, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Anatomy & Cell Biology, Western University, London, ON, Canada
| | - Jacob Ellegood
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lily R Qiu
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada; Wellcome Centre for Integrative Neuroimaging, The University of Oxford, Oxford, UK
| | - Jason P Lerch
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada; Wellcome Centre for Integrative Neuroimaging, The University of Oxford, Oxford, UK
| | - Nathalie G Bérubé
- Children's Health Research Institute, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Paediatrics, Western University, London, ON, Canada; Department of Anatomy & Cell Biology, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada.
| |
Collapse
|
20
|
Mossink B, Negwer M, Schubert D, Nadif Kasri N. The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective. Cell Mol Life Sci 2021; 78:2517-2563. [PMID: 33263776 PMCID: PMC8004494 DOI: 10.1007/s00018-020-03714-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorders (ASD), are a large group of disorders in which early insults during brain development result in a wide and heterogeneous spectrum of clinical diagnoses. Mutations in genes coding for chromatin remodelers are overrepresented in NDD cohorts, pointing towards epigenetics as a convergent pathogenic pathway between these disorders. In this review we detail the role of NDD-associated chromatin remodelers during the developmental continuum of progenitor expansion, differentiation, cell-type specification, migration and maturation. We discuss how defects in chromatin remodelling during these early developmental time points compound over time and result in impaired brain circuit establishment. In particular, we focus on their role in the three largest cell populations: glutamatergic neurons, GABAergic neurons, and glia cells. An in-depth understanding of the spatiotemporal role of chromatin remodelers during neurodevelopment can contribute to the identification of molecular targets for treatment strategies.
Collapse
Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Moritz Negwer
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
| |
Collapse
|
21
|
Funato K, Smith RC, Saito Y, Tabar V. Dissecting the impact of regional identity and the oncogenic role of human-specific NOTCH2NL in an hESC model of H3.3G34R-mutant glioma. Cell Stem Cell 2021; 28:894-905.e7. [PMID: 33631117 DOI: 10.1016/j.stem.2021.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/04/2020] [Accepted: 01/30/2021] [Indexed: 12/18/2022]
Abstract
H3.3G34R-mutant gliomas are lethal tumors of the cerebral hemispheres with unknown mechanisms of regional specificity and tumorigenicity. We developed a human embryonic stem cell (hESC)-based model of H3.3G34R-mutant glioma that recapitulates the key features of the tumors with cell-type specificity to forebrain interneuronal progenitors but not hindbrain precursors. We show that H3.3G34R, ATRX, and TP53 mutations cooperatively impact alternative RNA splicing events, particularly suppression of intron retention. This leads to increased expression of components of the Notch pathway, notably NOTCH2NL, a human-specific gene family. We also uncover a parallel mechanism of enhanced NOTCH2NL expression via genomic amplification of its locus in some H3.3G34R-mutant tumors. These findings demonstrate a novel mechanism whereby evolutionary pathways that lead to larger brain size in humans are co-opted to drive tumor growth.
Collapse
Affiliation(s)
- Kosuke Funato
- Department of Neurosurgery, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics, Sloan Kettering Institute, New York, NY 10065, USA
| | - Ryan C Smith
- Department of Neurosurgery, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuhki Saito
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY 10065, USA
| | - Viviane Tabar
- Department of Neurosurgery, Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics, Sloan Kettering Institute, New York, NY 10065, USA.
| |
Collapse
|
22
|
Ray-Gallet D, Almouzni G. The Histone H3 Family and Its Deposition Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:17-42. [PMID: 33155135 DOI: 10.1007/978-981-15-8104-5_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the cell nucleus, the organization of the eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. This chromatin organization contributes to the regulation of all DNA template-based reactions impacting genome function, stability, and plasticity. Histones and their variants endow chromatin with unique properties and show a distinct distribution into the genome that is regulated by dedicated deposition machineries. The histone variants have important roles during early development, cell differentiation, and chromosome segregation. Recent progress has also shed light on how mutations and transcriptional deregulation of these variants participate in tumorigenesis. In this chapter we introduce the organization of the genome in chromatin with a focus on the basic unit, the nucleosome, which contains histones as the major protein component. Then we review our current knowledge on the histone H3 family and its variants-in particular H3.3 and CenH3CENP-A-focusing on their deposition pathways and their dedicated histone chaperones that are key players in histone dynamics.
Collapse
Affiliation(s)
- Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.
| |
Collapse
|
23
|
Martire S, Banaszynski LA. The roles of histone variants in fine-tuning chromatin organization and function. Nat Rev Mol Cell Biol 2020; 21:522-541. [PMID: 32665685 PMCID: PMC8245300 DOI: 10.1038/s41580-020-0262-8] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Histones serve to both package and organize DNA within the nucleus. In addition to histone post-translational modification and chromatin remodelling complexes, histone variants contribute to the complexity of epigenetic regulation of the genome. Histone variants are characterized by a distinct protein sequence and a selection of designated chaperone systems and chromatin remodelling complexes that regulate their localization in the genome. In addition, histone variants can be enriched with specific post-translational modifications, which in turn can provide a scaffold for recruitment of variant-specific interacting proteins to chromatin. Thus, through these properties, histone variants have the capacity to endow specific regions of chromatin with unique character and function in a regulated manner. In this Review, we provide an overview of recent advances in our understanding of the contribution of histone variants to chromatin function in mammalian systems. First, we discuss new molecular insights into chaperone-mediated histone variant deposition. Next, we discuss mechanisms by which histone variants influence chromatin properties such as nucleosome stability and the local chromatin environment both through histone variant sequence-specific effects and through their role in recruiting different chromatin-associated complexes. Finally, we focus on histone variant function in the context of both embryonic development and human disease, specifically developmental syndromes and cancer.
Collapse
Affiliation(s)
- Sara Martire
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Laura A Banaszynski
- Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
24
|
Timpano S, Picketts DJ. Neurodevelopmental Disorders Caused by Defective Chromatin Remodeling: Phenotypic Complexity Is Highlighted by a Review of ATRX Function. Front Genet 2020; 11:885. [PMID: 32849845 PMCID: PMC7432156 DOI: 10.3389/fgene.2020.00885] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/20/2020] [Indexed: 12/15/2022] Open
Abstract
The ability to determine the genetic etiology of intellectual disability (ID) and neurodevelopmental disorders (NDD) has improved immensely over the last decade. One prevailing metric from these studies is the large percentage of genes encoding epigenetic regulators, including many members of the ATP-dependent chromatin remodeling enzyme family. Chromatin remodeling proteins can be subdivided into five classes that include SWI/SNF, ISWI, CHD, INO80, and ATRX. These proteins utilize the energy from ATP hydrolysis to alter nucleosome positioning and are implicated in many cellular processes. As such, defining their precise roles and contributions to brain development and disease pathogenesis has proven to be complex. In this review, we illustrate that complexity by reviewing the roles of ATRX on genome stability, replication, and transcriptional regulation and how these mechanisms provide key insight into the phenotype of ATR-X patients.
Collapse
Affiliation(s)
- Sara Timpano
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - David J. Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Medicine, University of Ottawa, Ottawa, ON, Canada
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
| |
Collapse
|
25
|
Wasylishen AR, Sun C, Moyer SM, Qi Y, Chau GP, Aryal NK, McAllister F, Kim MP, Barton MC, Estrella JS, Su X, Lozano G. Daxx maintains endogenous retroviral silencing and restricts cellular plasticity in vivo. SCIENCE ADVANCES 2020; 6:eaba8415. [PMID: 32821827 PMCID: PMC7406367 DOI: 10.1126/sciadv.aba8415] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/18/2020] [Indexed: 05/26/2023]
Abstract
Tumor sequencing studies have emphasized the role of epigenetics and altered chromatin homeostasis in cancer. Mutations in DAXX, which encodes a chaperone for the histone 3.3 variant, occur in 25% of pancreatic neuroendocrine tumors (PanNETs). To advance our understanding of physiological functions of Daxx, we developed a conditional Daxx allele in mice. We demonstrate that Daxx loss is well tolerated in the pancreas but creates a permissive transcriptional state that cooperates with environmental stress (inflammation) and other genetic lesions (Men1 loss) to alter gene expression and cell state, impairing pancreas recovery from inflammatory stress in vivo. The transcriptional changes are associated with dysregulation of endogenous retroviral elements (ERVs), and dysregulation of endogenous genes near ERVs is also observed in human PanNETs with DAXX mutations. Our results reveal a physiologic function of DAXX, provide a mechanism associated with impaired tissue regeneration and tumorigenesis, and expand our understanding of ERV regulation in somatic cells.
Collapse
Affiliation(s)
- Amanda R. Wasylishen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chang Sun
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Sydney M. Moyer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yuan Qi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gilda P. Chau
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Neeraj K. Aryal
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael P. Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michelle C. Barton
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeannelyn S. Estrella
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guillermina Lozano
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Genetics and Epigenetics Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| |
Collapse
|
26
|
Burkhart KB, Sando SR, Corrionero A, Horvitz HR. H3.3 Nucleosome Assembly Mutants Display a Late-Onset Maternal Effect. Curr Biol 2020; 30:2343-2352.e3. [PMID: 32470364 DOI: 10.1016/j.cub.2020.04.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/20/2020] [Indexed: 01/03/2023]
Abstract
Maternally inherited RNA and proteins control much of embryonic development. The effect of such maternal information beyond embryonic development is largely unclear. Here, we report that maternal contribution of histone H3.3 assembly complexes can prevent the expression of late-onset anatomical, physiologic, and behavioral abnormalities of C. elegans. We show that mutants lacking hira-1, an evolutionarily conserved H3.3-deposition factor, have severe pleiotropic defects that manifest predominantly at adulthood. These late-onset defects can be maternally rescued, and maternally derived HIRA-1 protein can be detected in hira-1(-/-) progeny. Mitochondrial stress likely contributes to the late-onset defects, given that hira-1 mutants display mitochondrial stress, and the induction of mitochondrial stress results in at least some of the hira-1 late-onset abnormalities. A screen for mutants that mimic the hira-1 mutant phenotype identified PQN-80-a HIRA complex component, known as UBN1 in humans-and XNP-1-a second H3.3 chaperone, known as ATRX in humans. pqn-80 and xnp-1 abnormalities are also maternally rescued. Furthermore, mutants lacking histone H3.3 have a late-onset defect similar to a defect of hira-1, pqn-80, and xnp-1 mutants. These data demonstrate that H3.3 assembly complexes provide non-DNA-based heritable information that can markedly influence adult phenotype. We speculate that similar maternal effects might explain the missing heritability of late-onset human diseases, such as Alzheimer's disease, Parkinson's disease, and type 2 diabetes.
Collapse
Affiliation(s)
- Kirk B Burkhart
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Steven R Sando
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anna Corrionero
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - H Robert Horvitz
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
27
|
Seminal Plasma Induces Overexpression of Genes Associated with Embryo Development and Implantation in Day-6 Porcine Blastocysts. Int J Mol Sci 2020; 21:ijms21103662. [PMID: 32455957 PMCID: PMC7279338 DOI: 10.3390/ijms21103662] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023] Open
Abstract
The infusion of boar seminal plasma (SP) before artificial insemination (AI) positively alters the expression of endometrial genes and pathways involved in embryo development. This study aimed to determine which transcriptome changes occur in preimplantation embryos in response to SP infusions during estrus. Postweaning estrus sows received 40-mL intrauterine infusions of either SP (N = 6) or BTS extender (control group; N = 6) 30 min before each of two post-cervical AIs. On Day 6, embryos were surgically collected and analyzed for differential gene expression. Microarray analysis of embryos revealed 210 annotated genes, differentially expressed (p-value < 0.05 and fold change </> 2) in SP-blastocysts, compared to controls. Most of these genes were associated with biological, cellular, metabolic and developmental processes. The pathways enriched among the upregulated genes related to signal transduction, cellular processes and the endocrine system. Among altered genes involved in these pathways, the SP-group showed a conspicuous overexpression of ApoA-I, CDK1, MAPK1, SMAD2, PRKAA1 and RICTOR, with reported key roles in embryo development, implantation, or progression of pregnancy. In conclusion, the results demonstrate that SP infusions prior to AI upregulates the expression of embryo development related genes in Day 6 pig embryos.
Collapse
|
28
|
Liu Z, Tardat M, Gill ME, Royo H, Thierry R, Ozonov EA, Peters AH. SUMOylated PRC1 controls histone H3.3 deposition and genome integrity of embryonic heterochromatin. EMBO J 2020; 39:e103697. [PMID: 32395866 PMCID: PMC7327501 DOI: 10.15252/embj.2019103697] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Chromatin integrity is essential for cellular homeostasis. Polycomb group proteins modulate chromatin states and transcriptionally repress developmental genes to maintain cell identity. They also repress repetitive sequences such as major satellites and constitute an alternative state of pericentromeric constitutive heterochromatin at paternal chromosomes (pat‐PCH) in mouse pre‐implantation embryos. Remarkably, pat‐PCH contains the histone H3.3 variant, which is absent from canonical PCH at maternal chromosomes, which is marked by histone H3 lysine 9 trimethylation (H3K9me3), HP1, and ATRX proteins. Here, we show that SUMO2‐modified CBX2‐containing Polycomb Repressive Complex 1 (PRC1) recruits the H3.3‐specific chaperone DAXX to pat‐PCH, enabling H3.3 incorporation at these loci. Deficiency of Daxx or PRC1 components Ring1 and Rnf2 abrogates H3.3 incorporation, induces chromatin decompaction and breakage at PCH of exclusively paternal chromosomes, and causes their mis‐segregation. Complementation assays show that DAXX‐mediated H3.3 deposition is required for chromosome stability in early embryos. DAXX also regulates repression of PRC1 target genes during oogenesis and early embryogenesis. The study identifies a novel critical role for Polycomb in ensuring heterochromatin integrity and chromosome stability in mouse early development.
Collapse
Affiliation(s)
- Zichuan Liu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mathieu Tardat
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mark E Gill
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Helene Royo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Raphael Thierry
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Evgeniy A Ozonov
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Antoine Hfm Peters
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| |
Collapse
|
29
|
Straub J, Gregor A, Sauerer T, Fliedner A, Distel L, Suchy C, Ekici AB, Ferrazzi F, Zweier C. Genetic interaction screen for severe neurodevelopmental disorders reveals a functional link between Ube3a and Mef2 in Drosophila melanogaster. Sci Rep 2020; 10:1204. [PMID: 31988313 PMCID: PMC6985129 DOI: 10.1038/s41598-020-58182-5] [Citation(s) in RCA: 4] [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: 09/08/2019] [Accepted: 01/13/2020] [Indexed: 11/09/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically extremely heterogeneous with shared phenotypes often associated with genes from the same networks. Mutations in TCF4, MEF2C, UBE3A, ZEB2 or ATRX cause phenotypically overlapping, syndromic forms of NDDs with severe intellectual disability, epilepsy and microcephaly. To characterize potential functional links between these genes/proteins, we screened for genetic interactions in Drosophila melanogaster. We induced ubiquitous or tissue specific knockdown or overexpression of each single orthologous gene (Da, Mef2, Ube3a, Zfh1, XNP) and in pairwise combinations. Subsequently, we assessed parameters such as lethality, wing and eye morphology, neuromuscular junction morphology, bang sensitivity and climbing behaviour in comparison between single and pairwise dosage manipulations. We found most stringent evidence for genetic interaction between Ube3a and Mef2 as simultaneous dosage manipulation in different tissues including glia, wing and eye resulted in multiple phenotype modifications. We subsequently found evidence for physical interaction between UBE3A and MEF2C also in human cells. Systematic pairwise assessment of the Drosophila orthologues of five genes implicated in clinically overlapping, severe NDDs and subsequent confirmation in a human cell line revealed interactions between UBE3A/Ube3a and MEF2C/Mef2, thus contributing to the characterization of the underlying molecular commonalities.
Collapse
Affiliation(s)
- Jonas Straub
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Tatjana Sauerer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Anna Fliedner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Laila Distel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christine Suchy
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany.
| |
Collapse
|
30
|
Marano D, Fioriniello S, Fiorillo F, Gibbons RJ, D'Esposito M, Della Ragione F. ATRX Contributes to MeCP2-Mediated Pericentric Heterochromatin Organization during Neural Differentiation. Int J Mol Sci 2019; 20:E5371. [PMID: 31671722 PMCID: PMC6862095 DOI: 10.3390/ijms20215371] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/24/2019] [Indexed: 11/16/2022] Open
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a multi-function factor involved in locus-specific transcriptional modulation and the regulation of genome architecture, e.g., pericentric heterochromatin (PCH) organization. MECP2 mutations are responsible for Rett syndrome (RTT), a devastating postnatal neurodevelopmental disorder, the pathogenetic mechanisms of which are still unknown. MeCP2, together with Alpha-thalassemia/mental retardation syndrome X-linked protein (ATRX), accumulates at chromocenters, which are repressive PCH domains. As with MECP2, mutations in ATRX cause ATR-X syndrome which is associated with severe intellectual disability. We exploited two murine embryonic stem cell lines, in which the expression of MeCP2 or ATRX is abolished. Through immunostaining, chromatin immunoprecipitation and western blot, we show that MeCP2 and ATRX are reciprocally dependent both for their expression and targeting to chromocenters. Moreover, ATRX plays a role in the accumulation of members of the heterochromatin protein 1 (HP1) family at PCH and, as MeCP2, modulates their expression. Furthermore, ATRX and HP1 targeting to chromocenters depends on an RNA component. 3D-DNA fluorescence in situ hybridization (FISH) highlighted, for the first time, a contribution of ATRX in MeCP2-mediated chromocenter clustering during neural differentiation. Overall, we provide a detailed dissection of the functional interplay between MeCP2 and ATRX in higher-order PCH organization in neurons. Our findings suggest molecular defects common to RTT and ATR-X syndrome, including an alteration in PCH.
Collapse
Affiliation(s)
- Domenico Marano
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', National Research Council (CNR), 80131 Naples, Italy.
| | - Salvatore Fioriniello
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', National Research Council (CNR), 80131 Naples, Italy.
| | - Francesca Fiorillo
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', National Research Council (CNR), 80131 Naples, Italy.
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Maurizio D'Esposito
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', National Research Council (CNR), 80131 Naples, Italy.
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', National Research Council (CNR), 80131 Naples, Italy.
| |
Collapse
|
31
|
Philip B, Yu DX, Silvis MR, Shin CH, Robinson JP, Robinson GL, Welker AE, Angel SN, Tripp SR, Sonnen JA, VanBrocklin MW, Gibbons RJ, Looper RE, Colman H, Holmen SL. Mutant IDH1 Promotes Glioma Formation In Vivo. Cell Rep 2019; 23:1553-1564. [PMID: 29719265 PMCID: PMC6032974 DOI: 10.1016/j.celrep.2018.03.133] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/23/2018] [Accepted: 03/29/2018] [Indexed: 02/08/2023] Open
Abstract
Isocitrate dehydrogenase 1 (IDH1) is the most commonly mutated gene in grade II–III glioma and secondary glioblastoma (GBM). A causal role for IDH1R132H in gliomagenesis has been proposed, but functional validation in vivo has not been demonstrated. In this study, we assessed the role of IDH1R132H in glioma development in the context of clinically relevant cooperating genetic alterations in vitro and in vivo. Immortal astrocytes expressing IDH1R132H exhibited elevated (R)-2-hydroxyglutarate levels, reduced NADPH, increased proliferation, and anchorage-independent growth. Although not sufficient on its own, IDH1R132H cooperated with PDGFA and loss of Cdkn2a, Atrx, and Pten to promote glioma development in vivo. These tumors resembled pro-neural human mutant IDH1 GBM genetically, histologically, and functionally. Our findings support the hypothesis that IDH1R132H promotes glioma development. This model enhances our understanding of the biology of IDH1R132H-driven gliomas and facilitates testing of therapeutic strategies designed to combat this deadly disease.
Collapse
Affiliation(s)
- Beatrice Philip
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Diana X Yu
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Mark R Silvis
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Clifford H Shin
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - James P Robinson
- Hormel Institute, University of Minnesota, 801 16(th) Avenue NE, Austin, MN 55912, USA
| | - Gemma L Robinson
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Adam E Welker
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Stephanie N Angel
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Sheryl R Tripp
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA
| | - Joshua A Sonnen
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA; Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Matthew W VanBrocklin
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ryan E Looper
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Howard Colman
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Neurosurgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA
| | - Sheri L Holmen
- Huntsman Cancer Institute, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
| |
Collapse
|
32
|
Loss of atrx cooperates with p53-deficiency to promote the development of sarcomas and other malignancies. PLoS Genet 2019; 15:e1008039. [PMID: 30970016 PMCID: PMC6476535 DOI: 10.1371/journal.pgen.1008039] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/22/2019] [Accepted: 02/20/2019] [Indexed: 12/24/2022] Open
Abstract
The SWI/SNF-family chromatin remodeling protein ATRX is a tumor suppressor in sarcomas, gliomas and other malignancies. Its loss of function facilitates the alternative lengthening of telomeres (ALT) pathway in tumor cells, while it also affects Polycomb repressive complex 2 (PRC2) silencing of its target genes. To further define the role of inactivating ATRX mutations in carcinogenesis, we knocked out atrx in our previously reported p53/nf1-deficient zebrafish line that develops malignant peripheral nerve sheath tumors and gliomas. Complete inactivation of atrx using CRISPR/Cas9 was lethal in developing fish and resulted in an alpha-thalassemia-like phenotype including reduced alpha-globin expression. In p53/nf1-deficient zebrafish neither peripheral nerve sheath tumors nor gliomas showed accelerated onset in atrx+/- fish, but these fish developed various tumors that were not observed in their atrx+/+ siblings, including epithelioid sarcoma, angiosarcoma, undifferentiated pleomorphic sarcoma and rare types of carcinoma. These cancer types are included in the AACR Genie database of human tumors associated with mutant ATRX, indicating that our zebrafish model reliably mimics a role for ATRX-loss in the early pathogenesis of these human cancer types. RNA-seq of p53/nf1- and p53/nf1/atrx-deficient tumors revealed that down-regulation of telomerase accompanied ALT-mediated lengthening of the telomeres in atrx-mutant samples. Moreover, inactivating mutations in atrx disturbed PRC2-target gene silencing, indicating a connection between ATRX loss and PRC2 dysfunction in cancer development. Somatic mutations in genes coding for epigenetic regulators such as ATRX are found across a diverse group of cancer types, suggesting their broad relevance in tumor induction and progression. However, tumors that have been linked to these chromatin remodelers can arise in many different molecular and cellular contexts, requiring studies with new experimental models to understand the extent and mechanisms of tumor development mediated by these regulatory proteins. Thus, we analyzed the tumor suppressive role of atrx in zebrafish that already harbored inactivating mutations of p53 and nf1. Homozygous deletion of atrx was lethal in developing fish, whereas the partial loss of this gene (atrx+/-) within the p53/nf1-deficient background led to a diverse spectrum of tumors not observed in animals that were wildtype for atrx, including epithelioid sarcoma, angiosarcoma, and rare carcinomas. Most of the cancer types we identified correspond to human tumors in the ATRX-mutant tumor sample cohort within the AACR Genie database, attesting to the relevance of our findings to human cancer. Further analysis revealed downregulation of telomerase during the lengthening of the telomeres through the ALT pathway, and disturbed function of the polycomb repressive complex 2 as key mechanistic components underlying atrx-linked tumorigenesis. These results demonstrate how a p53/nf1 compromised genetic background combined with ATRX haploinsufficiency leads to a broad spectrum of sarcomas and carcinomas associated with loss of this chromatin modulator.
Collapse
|
33
|
Li X, Oh S, Song H, Shin S, Zhang B, Freeman WM, Janknecht R. A potential common role of the Jumonji C domain-containing 1A histone demethylase and chromatin remodeler ATRX in promoting colon cancer. Oncol Lett 2018; 16:6652-6662. [PMID: 30405805 PMCID: PMC6202502 DOI: 10.3892/ol.2018.9487] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/17/2018] [Indexed: 12/14/2022] Open
Abstract
Jumonji C domain-containing 1A (JMJD1A) is a histone demethylase and epigenetic regulator that has been implicated in cancer development. In the current study, its mRNA and protein expression was analyzed in human colorectal tumors. It was demonstrated that JMJD1A levels were increased and correlated with a more aggressive phenotype. Downregulation of JMJD1A in human HCT116 colorectal cancer cells caused negligible growth defects, but robustly decreased clonogenic activity. Transcriptome analysis revealed that JMJD1A downregulation led to multiple changes in HCT116 cells, including inhibition of MYC- and MYCN-regulated pathways and stimulation of the TP53 tumor suppressor response. One gene identified to be stimulated by JMJD1A was α-thalassemia/mental retardation syndrome X-linked (ATRX), which encodes for a chromatin remodeler. The JMJD1A protein, but not a catalytically inactive mutant, activated the ATRX gene promoter and JMJD1A also affected levels of dimethylation on lysine 9 of histone H3. Similar to JMJD1A, ATRX was significantly overexpressed in human colorectal tumors and correlated with increased disease recurrence and lethality. Furthermore, ATRX downregulation in HCT116 cells reduced their growth and clonogenic activity. Accordingly, upregulation of ATRX may represent one mechanism by which JMJD1A promotes colorectal cancer. In addition, the data presented in this study suggest that the current notion of ATRX as a tumor suppressor is incomplete and that ATRX might context dependently also function as a tumor promoter.
Collapse
Affiliation(s)
- Xiaomeng Li
- Department of Endoscopy and Gastrointestinal Medicine, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Hoogeun Song
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Sook Shin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Bin Zhang
- Department of Endoscopy and Gastrointestinal Medicine, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Willard M Freeman
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| |
Collapse
|
34
|
Young CC, Baker RM, Howlett CJ, Hryciw T, Herman JE, Higgs D, Gibbons R, Crawford H, Brown A, Pin CL. The Loss of ATRX Increases Susceptibility to Pancreatic Injury and Oncogenic KRAS in Female But Not Male Mice. Cell Mol Gastroenterol Hepatol 2018; 7:93-113. [PMID: 30510993 PMCID: PMC6260375 DOI: 10.1016/j.jcmgh.2018.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 09/06/2018] [Indexed: 02/09/2023]
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in North America, accounting for >30,000 deaths annually. Although somatic activating mutations in KRAS appear in 97% of PDAC patients, additional factors are required to initiate PDAC. Because mutations in genes encoding chromatin remodelling proteins have been implicated in KRAS-mediated PDAC, we investigated whether loss of chromatin remodeler ɑ-thalassemia, mental-retardation, X-linked (ATRX) affects oncogenic KRAS's ability to promote PDAC. ATRX affects DNA replication, repair, and gene expression and is implicated in other cancers including glioblastomas and pancreatic neuroendocrine tumors. The hypothesis was that deletion of Atrx in pancreatic acinar cells will increase susceptibility to injury and oncogenic KRAS. Methods Mice allowing conditional loss of Atrx within pancreatic acinar cells were examined after induction of recurrent cerulein-induced pancreatitis or oncogenic KRAS (KRASG12D ). Histologic, biochemical, and molecular analysis examined pancreatic pathologies up to 2 months after induction of Atrx deletion. Results Mice lacking Atrx showed more progressive damage, inflammation, and acinar-to-duct cell metaplasia in response to injury relative to wild-type mice. In combination with KRASG12D, Atrx-deficient acinar cells showed increased fibrosis, inflammation, progression to acinar-to-duct cell metaplasia, and pre-cancerous lesions relative to mice expressing only KRASG12D. This sensitivity appears only in female mice, mimicking a significant prevalence of ATRX mutations in human female PDAC patients. Conclusions Our results indicate the absence of ATRX increases sensitivity to injury and oncogenic KRAS only in female mice. This is an instance of a sex-specific mutation that enhances oncogenic KRAS's ability to promote pancreatic intraepithelial lesion formation.
Collapse
Key Words
- ADM, acinar-to-duct cell metaplasia
- ANOVA, analysis of variance
- ATRX, ɑ-thalassemia, mental-retardation, X-linked
- CIP, cerulein induced pancreatitis
- CPA, carboxypeptidase
- DAXX, death associated protein 6
- EZH2, Enhancer of Zeste Homologue 2, MKA, Mist1creERT/+KrasLSL-G12D/+AtrxflΔ18
- Epigenetics
- MIST1
- PDAC, pancreatic ductal adenocarcinoma
- PanIN, pancreatic intraepithelial lesion
- Pancreatic Ductal Adenocarcinoma
- SOX9
- WT, wild-type
- ds, double stranded
Collapse
Affiliation(s)
- Claire C Young
- Department of Paediatrics, University of Western Ontario, London, Ontario, Canada; Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | - Ryan M Baker
- Department of Paediatrics, University of Western Ontario, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Todd Hryciw
- Department of Anatomy and Cell Biology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada; Robarts Research Institute, London, Ontario, Canada
| | | | - Douglas Higgs
- MRC Molecular Haematology Unit, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Richard Gibbons
- MRC Molecular Haematology Unit, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Howard Crawford
- Molecular & Integrative Physiology and Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Arthur Brown
- Department of Anatomy and Cell Biology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada; Robarts Research Institute, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | - Christopher L Pin
- Department of Paediatrics, University of Western Ontario, London, Ontario, Canada; Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada.
| |
Collapse
|
35
|
Haase S, Garcia-Fabiani MB, Carney S, Altshuler D, Núñez FJ, Méndez FM, Núñez F, Lowenstein PR, Castro MG. Mutant ATRX: uncovering a new therapeutic target for glioma. Expert Opin Ther Targets 2018; 22:599-613. [PMID: 29889582 PMCID: PMC6044414 DOI: 10.1080/14728222.2018.1487953] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/08/2018] [Indexed: 12/29/2022]
Abstract
INTRODUCTION ATRX is a chromatin remodeling protein whose main function is the deposition of the histone variant H3.3. ATRX mutations are widely distributed in glioma, and correlate with alternative lengthening of telomeres (ALT) development, but they also affect other cellular functions related to epigenetic regulation. Areas covered: We discuss the main molecular characteristics of ATRX, from its various functions in normal development to the effects of its loss in ATRX syndrome patients and animal models. We focus on the salient consequences of ATRX mutations in cancer, from a clinical to a molecular point of view, focusing on both adult and pediatric glioma. Finally, we will discuss the therapeutic opportunities future research perspectives. Expert opinion: ATRX is a major component of various essential cellular pathways, exceeding its functions as a histone chaperone (e.g. DNA replication and repair, chromatin higher-order structure regulation, gene transcriptional regulation, etc.). However, it is unclear how the loss of these functions in ATRX-null cancer cells affects cancer development and progression. We anticipate new treatments and clinical approaches will emerge for glioma and other cancer types as mechanistic and molecular studies on ATRX are only just beginning to reveal the many critical functions of this protein in cancer.
Collapse
Affiliation(s)
- Santiago Haase
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - María Belén Garcia-Fabiani
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Stephen Carney
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - David Altshuler
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Felipe J Núñez
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Flor M Méndez
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Fernando Núñez
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Pedro R Lowenstein
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| | - Maria G Castro
- a Department of Neurosurgery , The University of Michigan School of Medicine , Ann Arbor , MI , USA
- b Department of Cell & Developmental Biology , The University of Michigan School of Medicine , Ann Arbor , MI , USA
| |
Collapse
|
36
|
Rowland ME, Jiang Y, Beier F, Bérubé NG. Inactivation of hepatic ATRX in Atrx Foxg1cre mice prevents reversal of aging-like phenotypes by thyroxine. Aging (Albany NY) 2018; 10:1223-1238. [PMID: 29883366 PMCID: PMC6046231 DOI: 10.18632/aging.101462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/30/2018] [Indexed: 11/25/2022]
Abstract
ATRX is an ATP-dependent chromatin remodeler required for the maintenance of genomic integrity. We previously reported that conditional Atrx ablation in the mouse embryonic forebrain and anterior pituitary using the Foxg1cre driver causes reduced health and lifespan. In these mice, premature aging-like phenotypes were accompanied by low circulating levels of insulin-like growth factor 1 (IGF-1) and thyroxine (T4), hormones that maintain stem cell pools and normal metabolic profiles, respectively. Based on emerging evidence that T4 stimulates expression of IGF-1 in pre-pubertal mice, we tested whether T4 supplementation in Atrx Foxg1cre mice could restore IGF-1 levels and ameliorate premature aging-like phenotypes. Despite restoration of normal serum T4 levels, we did not observe improvements in circulating IGF-1. In the liver, thyroid hormone target genes were differentially affected upon T4 treatment, with Igf1 and several other thyroid hormone responsive genes failing to recover normal expression levels. These findings hinted at Cre-mediated Atrx inactivation in the liver of Atrx Foxg1cre mice, which we confirmed. We conclude that the phenotypes observed in the Atrx Foxg1cre mice can be explained in part by a role of ATRX in the liver to promote T4-mediated Igf1 expression, thus explaining the inefficacy of T4 therapy observed in this study.
Collapse
Affiliation(s)
- Megan E Rowland
- Departments of Paediatrics and Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute, London, ON, Canada
| | - Yan Jiang
- Departments of Paediatrics and Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute, London, ON, Canada
| | - Frank Beier
- Children's Health Research Institute, London, ON, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Western Bone and Joint Institute, Western University, London, ON, Canada
| | - Nathalie G Bérubé
- Departments of Paediatrics and Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute, London, ON, Canada
| |
Collapse
|
37
|
Robbez-Masson L, Tie CH, Conde L, Tunbak H, Husovsky C, Tchasovnikarova IA, Timms RT, Herrero J, Lehner PJ, Rowe HM. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Res 2018; 28:836-845. [PMID: 29728366 PMCID: PMC5991525 DOI: 10.1101/gr.228171.117] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/23/2018] [Indexed: 11/24/2022]
Abstract
Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of an SVA retrotransposon reporter. By using naïve versus primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development. Although the HUSH component FAM208A binds to endogenous retroviruses (ERVs) and long interspersed element-1s (LINE-1s or L1s), it is mainly required to repress evolutionarily young L1s (mouse-specific lineages <5 million years old). TRIM28, in contrast, is necessary to repress both ERVs and young L1s. Genes co-repressed by TRIM28 and FAM208A are evolutionarily young, or exhibit tissue-specific expression, are enriched in young L1s, and display evidence for regulation through LTR promoters. Finally, we demonstrate that the HUSH complex is also required to repress L1 elements in human cells. Overall, these data indicate that the HUSH complex and TRIM28 co-repress young retrotransposons and new genes rewired by retrotransposon noncoding DNA.
Collapse
Affiliation(s)
- Luisa Robbez-Masson
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Christopher H.C. Tie
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Hale Tunbak
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Connor Husovsky
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Iva A. Tchasovnikarova
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Richard T. Timms
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Paul J. Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Helen M. Rowe
- Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| |
Collapse
|
38
|
Abstract
ATRX (alpha thalassemia/mental retardation X-linked) complexes with DAXX to deposit histone variant H3.3 into repetitive heterochromatin. Recent genome sequencing studies in cancers have revealed mutations in ATRX and their association with ALT (alternative lengthening of telomeres) activation. Here we report depletion of ATRX in mouse ES cells leads to selective loss in ribosomal RNA gene (rDNA) copy number. Supporting this, ATRX-mutated human ALT-positive tumors also show a substantially lower rDNA copy than ALT-negative tumors. Further investigation shows that the rDNA copy loss and repeat instability are caused by a disruption in H3.3 deposition and thus a failure in heterochromatin formation at rDNA repeats in the absence of ATRX. We also find that ATRX-depleted cells are reduced in ribosomal RNA transcription output and show increased sensitivity to RNA polymerase I (Pol I) transcription inhibitor CX5461. In addition, human ALT-positive cancer cell lines are also more sensitive to CX5461 treatment. Our study provides insights into the contribution of ATRX loss of function to tumorigenesis through the loss of rDNA stability and suggests the therapeutic potential of targeting Pol I transcription in ALT cancers.
Collapse
|
39
|
Tardat M, Déjardin J. Telomere chromatin establishment and its maintenance during mammalian development. Chromosoma 2017; 127:3-18. [PMID: 29250704 PMCID: PMC5818603 DOI: 10.1007/s00412-017-0656-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Telomeres are specialized structures that evolved to protect the end of linear chromosomes from the action of the cell DNA damage machinery. They are composed of tandem arrays of repeated DNA sequences with a specific heterochromatic organization. The length of telomeric repeats is dynamically regulated and can be affected by changes in the telomere chromatin structure. When telomeres are not properly controlled, the resulting chromosomal alterations can induce genomic instability and ultimately the development of human diseases, such as cancer. Therefore, proper establishment, regulation, and maintenance of the telomere chromatin structure are required for cell homeostasis. Here, we review the current knowledge on telomeric chromatin dynamics during cell division and early development in mammals, and how its proper regulation safeguards genome stability.
Collapse
Affiliation(s)
- Mathieu Tardat
- Institute of Human Genetics, CNRS UMR 9002, 141 rue de la Cardonille, 34396, Montpellier, France.
| | - Jérôme Déjardin
- Institute of Human Genetics, CNRS UMR 9002, 141 rue de la Cardonille, 34396, Montpellier, France.
| |
Collapse
|
40
|
Duc C, Benoit M, Détourné G, Simon L, Poulet A, Jung M, Veluchamy A, Latrasse D, Le Goff S, Cotterell S, Tatout C, Benhamed M, Probst AV. Arabidopsis ATRX Modulates H3.3 Occupancy and Fine-Tunes Gene Expression. THE PLANT CELL 2017; 29:1773-1793. [PMID: 28684426 PMCID: PMC5559740 DOI: 10.1105/tpc.16.00877] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 05/24/2017] [Accepted: 06/28/2017] [Indexed: 05/23/2023]
Abstract
Histones are essential components of the nucleosome, the major chromatin subunit that structures linear DNA molecules and regulates access of other proteins to DNA. Specific histone chaperone complexes control the correct deposition of canonical histones and their variants to modulate nucleosome structure and stability. In this study, we characterize the Arabidopsis thaliana Alpha Thalassemia-mental Retardation X-linked (ATRX) ortholog and show that ATRX is involved in histone H3 deposition. Arabidopsis ATRX mutant alleles are viable, but show developmental defects and reduced fertility. Their combination with mutants of the histone H3.3 chaperone HIRA (Histone Regulator A) results in impaired plant survival, suggesting that HIRA and ATRX function in complementary histone deposition pathways. Indeed, ATRX loss of function alters cellular histone H3.3 pools and in consequence modulates the H3.1/H3.3 balance in the cell. H3.3 levels are affected especially at genes characterized by elevated H3.3 occupancy, including the 45S ribosomal DNA (45S rDNA) loci, where loss of ATRX results in altered expression of specific 45S rDNA sequence variants. At the genome-wide scale, our data indicate that ATRX modifies gene expression concomitantly to H3.3 deposition at a set of genes characterized both by elevated H3.3 occupancy and high expression. Together, our results show that ATRX is involved in H3.3 deposition and emphasize the role of histone chaperones in adjusting genome expression.
Collapse
Affiliation(s)
- Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Matthias Benoit
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Gwénaëlle Détourné
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Matthieu Jung
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 67404 Illkirch, France
| | - Alaguraj Veluchamy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405 Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001 Clermont-Ferrand, France
| |
Collapse
|
41
|
Postlmayr A, Wutz A. Insights into the Establishment of Chromatin States in Pluripotent Cells from Studies of X Inactivation. J Mol Biol 2017; 429:1521-1531. [PMID: 28315662 DOI: 10.1016/j.jmb.2017.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 11/20/2022]
Abstract
Animal development entails the sequential and coordinated specialization of cells. During cell differentiation, transcription factors, cell signaling pathways, and chromatin-associated protein complexes cooperate in regulating the expression of a large number of genes. Here, we review the present understanding of the establishment of chromatin states by focusing on X chromosome inactivation (XCI) as a model for facultative heterochromatin formation in female embryonic cells. The inactive X chromosome is large enough to be investigated by biochemical and microscopy techniques. In addition, the ability to compare the inactivated chromatin to the active X in male cells enables us to differentiate events specific to gene silencing during XCI from gene regulatory effects from changing pathways in the same cell. Findings in XCI are useful as blueprints for investigation of the action of epigenetic pathways in differentiation and lineage commitment. We summarize recent studies that have identified factors that are critical for chromosome-wide gene repression in XCI, and we discuss their implications for epigenetic regulation in pluripotent cells of the early embryo.
Collapse
Affiliation(s)
- Andreas Postlmayr
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland; Life Science Zurich Graduate School, Molecular Life Sciences Program, University of Zurich, 8049 Zurich, Switzerland
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich, Otto-Stern-Weg 7, 8093 Zurich, Switzerland.
| |
Collapse
|
42
|
Dyer MA, Qadeer ZA, Valle-Garcia D, Bernstein E. ATRX and DAXX: Mechanisms and Mutations. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026567. [PMID: 28062559 DOI: 10.1101/cshperspect.a026567] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent genome sequencing efforts in a variety of cancers have revealed mutations and/or structural alterations in ATRX and DAXX, which together encode a complex that deposits histone variant H3.3 into repetitive heterochromatin. These regions include retrotransposons, pericentric heterochromatin, and telomeres, the latter of which show deregulation in ATRX/DAXX-mutant tumors. Interestingly, ATRX and DAXX mutations are often found in pediatric tumors, suggesting a particular developmental context in which these mutations drive disease. Here we review the functions of ATRX and DAXX in chromatin regulation as well as their potential contributions to tumorigenesis. We place emphasis on the chromatin remodeler ATRX, which is mutated in the developmental disorder for which it is named, α-thalassemia, mental retardation, X-linked syndrome, and at high frequency in a number of adult and pediatric tumors.
Collapse
Affiliation(s)
- Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Zulekha A Qadeer
- Departments of Oncological Sciences and Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - David Valle-Garcia
- Departments of Oncological Sciences and Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Emily Bernstein
- Departments of Oncological Sciences and Dermatology, Icahn School of Medicine at Mount Sinai, New York, New York 10029.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| |
Collapse
|
43
|
Tamming RJ, Siu JR, Jiang Y, Prado MAM, Beier F, Bérubé NG. Mosaic expression of Atrx in the mouse central nervous system causes memory deficits. Dis Model Mech 2017; 10:119-126. [PMID: 28093507 PMCID: PMC5312007 DOI: 10.1242/dmm.027482] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
The rapid modulation of chromatin organization is thought to play a crucial role in cognitive processes such as memory consolidation. This is supported in part by the dysregulation of many chromatin-remodelling proteins in neurodevelopmental and psychiatric disorders. A key example is ATRX, an X-linked gene commonly mutated in individuals with syndromic and nonsyndromic intellectual disability. The consequences of Atrx inactivation for learning and memory have been difficult to evaluate because of the early lethality of hemizygous-null animals. In this study, we evaluated the outcome of brain-specific Atrx deletion in heterozygous female mice. These mice exhibit a mosaic pattern of ATRX protein expression in the central nervous system attributable to the location of the gene on the X chromosome. Although the hemizygous male mice die soon after birth, heterozygous females survive to adulthood. Body growth is stunted in these animals, and they have low circulating concentrations of insulin growth factor 1. In addition, they are impaired in spatial, contextual fear and novel object recognition memory. Our findings demonstrate that mosaic loss of ATRX expression in the central nervous system leads to endocrine defects and decreased body size and has a negative impact on learning and memory.
Collapse
Affiliation(s)
- Renee J Tamming
- Division of Genetics and Development, Children's Health Research Institute, London, Ontario N6C 2V5, Canada.,Departments of Paediatrics, Biochemistry and Oncology, Schulich School of Medicine and Dentistry, the University of Western Ontario, Victoria Research Laboratories, London, Ontario N6A 3K7, Canada
| | - Jennifer R Siu
- Division of Genetics and Development, Children's Health Research Institute, London, Ontario N6C 2V5, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Yan Jiang
- Division of Genetics and Development, Children's Health Research Institute, London, Ontario N6C 2V5, Canada.,Departments of Paediatrics, Biochemistry and Oncology, Schulich School of Medicine and Dentistry, the University of Western Ontario, Victoria Research Laboratories, London, Ontario N6A 3K7, Canada
| | - Marco A M Prado
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, Ontario N6A 3K7, Canada.,Department of Anatomy and Cell Biology and Robarts Research Institute, the University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Frank Beier
- Division of Genetics and Development, Children's Health Research Institute, London, Ontario N6C 2V5, Canada.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, the University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Nathalie G Bérubé
- Division of Genetics and Development, Children's Health Research Institute, London, Ontario N6C 2V5, Canada .,Departments of Paediatrics, Biochemistry and Oncology, Schulich School of Medicine and Dentistry, the University of Western Ontario, Victoria Research Laboratories, London, Ontario N6A 3K7, Canada
| |
Collapse
|
44
|
Kalisch-Smith JI, Simmons DG, Dickinson H, Moritz KM. Review: Sexual dimorphism in the formation, function and adaptation of the placenta. Placenta 2016; 54:10-16. [PMID: 27979377 DOI: 10.1016/j.placenta.2016.12.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/08/2023]
Abstract
Exposure of the embryo or fetus to perturbations in utero can result in intrauterine growth restriction, a primary risk factor for the development of adult disease. However, despite similar exposures, males and females often have altered disease susceptibility or progression from different stages of life. Fetal growth is largely mediated by the placenta, which, like the fetus is genetically XX or XY. The placenta and its associated trophoblast lineages originate from the trophectoderm (TE) of the early embryo. Rodent models (rat, mouse, spiny mouse), have been used extensively to examine placenta development and these have demonstrated the growth trajectory of the placenta in females is generally slower compared to males, and also shows altered adaptive responses to stressful environments. These placental adaptations are likely to depend on the type of stressor, duration, severity and the window of exposure during development. Here we describe the divergent developmental pathways between the male and female placenta contributing to altered differentiation of the TE derived trophoblast subtypes, placental growth, and formation of the placental architecture. Our focus is primarily genetic or environmental perturbations in rodent models which show altered placental responsiveness between sexes. We suggest that perturbations during early placental development may have greater impact on viability and growth of the female fetus whilst those occurring later in gestation may preferentially affect the male fetus. This may be of great relevance to human pregnancies which result from assisted reproductive technologies or complications such as pre-eclampsia and diabetes.
Collapse
Affiliation(s)
- J I Kalisch-Smith
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - D G Simmons
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - H Dickinson
- The Ritchie Centre, Hudson Institute of Medical Research and Department of Obstetrics and Gynaecology, Monash University, Australia
| | - K M Moritz
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia; Centre for Children's Health Research, The University of Queensland, South Brisbane, QLD, 4101, Australia.
| |
Collapse
|
45
|
He Q, Kim H, Huang R, Lu W, Tang M, Shi F, Yang D, Zhang X, Huang J, Liu D, Songyang Z. The Daxx/Atrx Complex Protects Tandem Repetitive Elements during DNA Hypomethylation by Promoting H3K9 Trimethylation. Cell Stem Cell 2016; 17:273-86. [PMID: 26340527 DOI: 10.1016/j.stem.2015.07.022] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 06/14/2015] [Accepted: 07/28/2015] [Indexed: 01/02/2023]
Abstract
In mammals, DNA methylation is essential for protecting repetitive sequences from aberrant transcription and recombination. In some developmental contexts (e.g., preimplantation embryos) DNA is hypomethylated but repetitive elements are not dysregulated, suggesting that alternative protection mechanisms exist. Here we explore the processes involved by investigating the role of the chromatin factors Daxx and Atrx. Using genome-wide binding and transcriptome analysis, we found that Daxx and Atrx have distinct chromatin-binding profiles and are co-enriched at tandem repetitive elements in wild-type mouse ESCs. Global DNA hypomethylation further promoted recruitment of the Daxx/Atrx complex to tandem repeat sequences, including retrotransposons and telomeres. Knockdown of Daxx/Atrx in cells with hypomethylated genomes exacerbated aberrant transcriptional de-repression of repeat elements and telomere dysfunction. Mechanistically, Daxx/Atrx-mediated repression seems to involve Suv39h recruitment and H3K9 trimethylation. Our data therefore suggest that Daxx and Atrx safeguard the genome by silencing repetitive elements when DNA methylation levels are low.
Collapse
Affiliation(s)
- Quanyuan He
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Hyeung Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Rui Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Weisi Lu
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mengfan Tang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fengtao Shi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Dong Yang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Xiya Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China
| | - Dan Liu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, SYSU-BCM Joint Center for Biomedical Sciences and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
46
|
Gendrel AV, Marion-Poll L, Katoh K, Heard E. Random monoallelic expression of genes on autosomes: Parallels with X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:100-110. [PMID: 27101886 DOI: 10.1016/j.semcdb.2016.04.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/08/2016] [Accepted: 04/15/2016] [Indexed: 01/04/2023]
Abstract
Genes are generally expressed from their two alleles, except in some particular cases such as random inactivation of one of the two X chromosomes in female mammals or imprinted genes which are expressed only from the maternal or the paternal allele. A lesser-known phenomenon is random monoallelic expression (RME) of autosomal genes, where genes can be stably expressed in a monoallelic manner, from either one of the parental alleles. Studies on autosomal RME face several challenges. First, RME that is based on epigenetic mechanisms has to be distinguished from biased expression of one allele caused by a DNA sequence polymorphism in a regulatory element. Second, RME should not be confused with transient monoallelic expression often observed in single cell analyses, and that often corresponds to dynamic bursting of expression. Thanks to analyses on clonal cell populations, the existence of RME in cultured cells is now well established. Future studies of RME in vivo will have to overcome tissue heterogeneity and certain technical limitations. Here, we discuss current knowledge on autosomal RME, as well as possible mechanisms controlling these expression patterns and potential implications for development and disease, drawing parallels with what is known for X-chromosome inactivation, a paradigm of random monoallelic expression.
Collapse
Affiliation(s)
- Anne-Valerie Gendrel
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 6, F-75005 Paris, France.
| | - Lucile Marion-Poll
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 6, F-75005 Paris, France
| | - Kimiko Katoh
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 6, F-75005 Paris, France
| | - Edith Heard
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005 Paris, France; Sorbonne Universités, UPMC Univ Paris 6, F-75005 Paris, France.
| |
Collapse
|
47
|
Histone Variant H3.3: A versatile H3 variant in health and in disease. SCIENCE CHINA-LIFE SCIENCES 2016; 59:245-56. [DOI: 10.1007/s11427-016-5006-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/26/2015] [Indexed: 01/24/2023]
|
48
|
Udugama M, M Chang FT, Chan FL, Tang MC, Pickett HA, R McGhie JD, Mayne L, Collas P, Mann JR, Wong LH. Histone variant H3.3 provides the heterochromatic H3 lysine 9 tri-methylation mark at telomeres. Nucleic Acids Res 2015; 43:10227-37. [PMID: 26304540 PMCID: PMC4666390 DOI: 10.1093/nar/gkv847] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 08/11/2015] [Indexed: 11/15/2022] Open
Abstract
In addition to being a hallmark at active genes, histone variant H3.3 is deposited by ATRX at repressive chromatin regions, including the telomeres. It is unclear how H3.3 promotes heterochromatin assembly. We show that H3.3 is targeted for K9 trimethylation to establish a heterochromatic state enriched in trimethylated H3.3K9 at telomeres. In H3f3a−/− and H3f3b−/− mouse embryonic stem cells (ESCs), H3.3 deficiency results in reduced levels of H3K9me3, H4K20me3 and ATRX at telomeres. The H3f3b−/− cells show increased levels of telomeric damage and sister chromatid exchange (t-SCE) activity when telomeres are compromised by treatment with a G-quadruplex (G4) DNA binding ligand or by ASF1 depletion. Overexpression of wild-type H3.3 (but not a H3.3K9 mutant) in H3f3b−/− cells increases H3K9 trimethylation level at telomeres and represses t-SCE activity induced by a G4 ligand. This study demonstrates the importance of H3.3K9 trimethylation in heterochromatin formation at telomeres. It provides insights into H3.3 function in maintaining integrity of mammalian constitutive heterochromatin, adding to its role in mediating transcription memory in the genome.
Collapse
Affiliation(s)
- Maheshi Udugama
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Fiona T M Chang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - F Lyn Chan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Michelle C Tang
- Department of Zoology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - James D R McGhie
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Lynne Mayne
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway
| | - Jeffrey R Mann
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Lee H Wong
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
49
|
Jang CW, Shibata Y, Starmer J, Yee D, Magnuson T. Histone H3.3 maintains genome integrity during mammalian development. Genes Dev 2015; 29:1377-92. [PMID: 26159997 PMCID: PMC4511213 DOI: 10.1101/gad.264150.115] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/16/2015] [Indexed: 12/19/2022]
Abstract
Histone H3.3 is a highly conserved histone H3 replacement variant in metazoans and has been implicated in many important biological processes, including cell differentiation and reprogramming. Germline and somatic mutations in H3.3 genomic incorporation pathway components or in H3.3 encoding genes have been associated with human congenital diseases and cancers, respectively. However, the role of H3.3 in mammalian development remains unclear. To address this question, we generated H3.3-null mouse models through classical genetic approaches. We found that H3.3 plays an essential role in mouse development. Complete depletion of H3.3 leads to developmental retardation and early embryonic lethality. At the cellular level, H3.3 loss triggers cell cycle suppression and cell death. Surprisingly, H3.3 depletion does not dramatically disrupt gene regulation in the developing embryo. Instead, H3.3 depletion causes dysfunction of heterochromatin structures at telomeres, centromeres, and pericentromeric regions of chromosomes, leading to mitotic defects. The resulting karyotypical abnormalities and DNA damage lead to p53 pathway activation. In summary, our results reveal that an important function of H3.3 is to support chromosomal heterochromatic structures, thus maintaining genome integrity during mammalian development.
Collapse
Affiliation(s)
- Chuan-Wei Jang
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Yoichiro Shibata
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Joshua Starmer
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Della Yee
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Terry Magnuson
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| |
Collapse
|
50
|
Sadic D, Schmidt K, Groh S, Kondofersky I, Ellwart J, Fuchs C, Theis FJ, Schotta G. Atrx promotes heterochromatin formation at retrotransposons. EMBO Rep 2015; 16:836-50. [PMID: 26012739 DOI: 10.15252/embr.201439937] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/17/2015] [Indexed: 12/29/2022] Open
Abstract
More than 50% of mammalian genomes consist of retrotransposon sequences. Silencing of retrotransposons by heterochromatin is essential to ensure genomic stability and transcriptional integrity. Here, we identified a short sequence element in intracisternal A particle (IAP) retrotransposons that is sufficient to trigger heterochromatin formation. We used this sequence in a genome-wide shRNA screen and identified the chromatin remodeler Atrx as a novel regulator of IAP silencing. Atrx binds to IAP elements and is necessary for efficient heterochromatin formation. In addition, Atrx facilitates a robust and largely inaccessible heterochromatin structure as Atrx knockout cells display increased chromatin accessibility at retrotransposons and non-repetitive heterochromatic loci. In summary, we demonstrate a direct role of Atrx in the establishment and robust maintenance of heterochromatin.
Collapse
Affiliation(s)
- Dennis Sadic
- Adolf-Butenandt-Institute, Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPS), Munich, Germany
| | - Katharina Schmidt
- Adolf-Butenandt-Institute, Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPS), Munich, Germany
| | - Sophia Groh
- Adolf-Butenandt-Institute, Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPS), Munich, Germany
| | - Ivan Kondofersky
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany
| | - Joachim Ellwart
- Helmholtz Zentrum München, Institute of Molecular Immunology, Munich, Germany
| | - Christiane Fuchs
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany
| | - Fabian J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Garching, Germany
| | - Gunnar Schotta
- Adolf-Butenandt-Institute, Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPS), Munich, Germany
| |
Collapse
|