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Poli A, Pennacchio FA, Ghisleni A, di Gennaro M, Lecacheur M, Nastały P, Crestani M, Pramotton FM, Iannelli F, Beznusenko G, Mironov AA, Panzetta V, Fusco S, Sheth B, Poulikakos D, Ferrari A, Gauthier N, Netti PA, Divecha N, Maiuri P. PIP4K2B is mechanoresponsive and controls heterochromatin-driven nuclear softening through UHRF1. Nat Commun 2023; 14:1432. [PMID: 36918565 PMCID: PMC10015053 DOI: 10.1038/s41467-023-37064-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
Phosphatidylinositol-5-phosphate (PtdIns5P)-4-kinases (PIP4Ks) are stress-regulated phosphoinositide kinases able to phosphorylate PtdIns5P to PtdIns(4,5)P2. In cancer patients their expression is typically associated with bad prognosis. Among the three PIP4K isoforms expressed in mammalian cells, PIP4K2B is the one with more prominent nuclear localisation. Here, we unveil the role of PIP4K2B as a mechanoresponsive enzyme. PIP4K2B protein level strongly decreases in cells growing on soft substrates. Its direct silencing or pharmacological inhibition, mimicking cell response to softness, triggers a concomitant reduction of the epigenetic regulator UHRF1 and induces changes in nuclear polarity, nuclear envelope tension and chromatin compaction. This substantial rewiring of the nucleus mechanical state drives YAP cytoplasmic retention and impairment of its activity as transcriptional regulator, finally leading to defects in cell spreading and motility. Since YAP signalling is essential for initiation and growth of human malignancies, our data suggest that potential therapeutic approaches targeting PIP4K2B could be beneficial in the control of the altered mechanical properties of cancer cells.
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Affiliation(s)
- Alessandro Poli
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
| | | | - Andrea Ghisleni
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Paulina Nastały
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdansk, Poland
| | - Michele Crestani
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Francesca M Pramotton
- EMPA-Materials Science and Technology, Dubenforf, Switzerland
- Institute for Mechanical Systems, ETH, Zurich, Switzerland
| | - Fabio Iannelli
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Valeria Panzetta
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples, Italy
- Centro di Ricerca Interdipartimentale sui Biomateriali CRIB, University of Naples Federico II, Naples, Italy
- Istituto Italiano di Tecnologia, IIT@CRIB, Naples, Italy
| | - Sabato Fusco
- Department of Medicine and Health Sciences "V. Tiberio", University of Molise, Campobasso, Italy
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Aldo Ferrari
- Institute for Mechanical Systems, ETH, Zurich, Switzerland
| | - Nils Gauthier
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo A Netti
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples, Italy
- Centro di Ricerca Interdipartimentale sui Biomateriali CRIB, University of Naples Federico II, Naples, Italy
- Istituto Italiano di Tecnologia, IIT@CRIB, Naples, Italy
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Paolo Maiuri
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.
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2
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Kahl KG, Atalay S, Maudsley AA, Sheriff S, Cummings A, Frieling H, Schmitz B, Lanfermann H, Ding XQ. Altered neurometabolism in major depressive disorder: A whole brain 1H-magnetic resonance spectroscopic imaging study at 3T. Prog Neuropsychopharmacol Biol Psychiatry 2020; 101:109916. [PMID: 32169561 DOI: 10.1016/j.pnpbp.2020.109916] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/25/2020] [Accepted: 03/07/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Major depressive disorder (MDD) is a severe mental disorder with a neurobiological basis that is poorly understood. Several studies demonstrated widespread, functional and neurometabolic alterations in MDD. However, little is known about whole brain neurometabolic alterations in MDD. METHOD Thirty-two patients with MDD and 32 paired on a one-to-one basis healthy controls (CTRL) underwent 1H-whole brain spectroscopic (1H-WBS) imaging. Lobar and cerebellar metabolite concentrations of brain N-acetylaspartate (NAA), total choline (tCho), total creatine (tCr), glutamine (Gln), glutamate (Glu), and myo-Inositol (mI) were assessed in patients and controls. RESULTS Decreased NAA, tCho, and tCr were found in the right frontal and right parietal lobe in MDD compared to CTRL, and to a lesser extent in the left frontal lobe. Furthermore, in MDD increased glutamine was observed in the right frontal lobe and bitemporal lobes, and increased glutamate in the cerebellum. CONCLUSION Altered global neurometabolism examined using 1H-WBS imaging in MDD may be interpreted as signs of neuronal dysfunction, altered energy metabolism, and oligodendrocyte dysfunction. In particular, the parallel decrease in NAA, tCr and tCho in the same brain regions may be indicative of neuronal dysfunction that may be counterbalanced by an increase of the neuroprotective metabolite glutamine. Future prospective investigations are warranted to study the functional importance of these findings.
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Affiliation(s)
- Kai G Kahl
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany.
| | - Sirin Atalay
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Andrew A Maudsley
- Department of Radiology, University of Miami School of Medicine, Miami, FL, USA
| | - Sulaiman Sheriff
- Department of Radiology, University of Miami School of Medicine, Miami, FL, USA
| | - Anna Cummings
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Birte Schmitz
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - Heinrich Lanfermann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - Xiao-Qi Ding
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
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3
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Singh PB, Newman AG. On the relations of phase separation and Hi-C maps to epigenetics. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191976. [PMID: 32257349 PMCID: PMC7062049 DOI: 10.1098/rsos.191976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
The relationship between compartmentalization of the genome and epigenetics is long and hoary. In 1928, Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller's discovery of position-effect variegation in 1930 went on to show that heterochromatin is a cytologically visible state of heritable (epigenetic) gene repression. Current insights into compartmentalization have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalization seen in Hi-C maps is owing to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5 Mb) heterochromatin-like domains and smaller (less than 100 kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes contributes to polymer-polymer phase separation that packages epigenetically heritable chromatin states during interphase. Contacts mediated by HP1 'bridging' are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic subcompartment that emerges from contacts between large KRAB-ZNF heterochromatin-like domains. Further, mutational analyses have revealed a finer, innate, compartmentalization in Hi-C experiments that probably reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres-where the HP1-H3K9me2/3 interaction represents the most evolutionarily conserved paradigm-could drive and generate the fundamental compartmentalization of the interphase nucleus. This has implications for the mechanism(s) that maintains cellular identity, be it a terminally differentiated fibroblast or a pluripotent embryonic stem cell.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Nur-Sultan Z05K4F4, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Street 2, Novosibirsk 630090, Russian Federation
| | - Andrew G. Newman
- Institute of Cell and Neurobiology, Charité—Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
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Du W, Dong Q, Zhang Z, Liu B, Zhou T, Xu RM, Wang H, Zhu B, Li Y. Stella protein facilitates DNA demethylation by disrupting the chromatin association of the RING finger-type E3 ubiquitin ligase UHRF1. J Biol Chem 2019; 294:8907-8917. [PMID: 31018966 DOI: 10.1074/jbc.ra119.008008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/19/2019] [Indexed: 11/06/2022] Open
Abstract
Stella is a maternal gene required for oogenesis and early embryogenesis. Stella overexpression in somatic cells causes global demethylation. As we have recently shown, Stella sequesters nuclear ubiquitin-like with PHD and RING finger domains 1 (UHRF1), a RING finger-type E3 ubiquitin ligase essential for DNA methylation mediated by DNA methyltransferase 1 and triggers global demethylation. Here, we report an overexpressed mutant Stella protein without nuclear export activity surprisingly retained its ability to cause global demethylation. By combining biochemical interaction assays, isothermal titration calorimetry, immunostaining, and live-cell imaging with fluorescence recovery after photobleaching, we found that Stella disrupts UHRF1's association with chromatin by directly binding to the plant homeodomain of UHRF1 and competing for the interaction between UHRF1 and the histone H3 tail. Consistently, overexpression of Stella mutants that do not directly interact with UHRF1 fails to cause genome-wide demethylation. In the presence of nuclear Stella, UHRF1 could not bind to chromatin and exhibited increased dynamics in the nucleus. Our results indicate that Stella employs a multilayered mechanism to achieve robust UHRF1 inhibition, which involves the dissociation from chromatin and cytoplasmic sequestration of UHRF1.
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Affiliation(s)
- Wenlong Du
- From the College of Life Sciences, Beijing Normal University, Beijing 100875.,the National Institute of Biological Sciences, Beijing 102206.,the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101
| | - Qiang Dong
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101
| | - Zhuqiang Zhang
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101
| | - Baodong Liu
- the State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, and
| | - Ting Zhou
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101
| | - Rui-Ming Xu
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101.,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- the State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, and
| | - Bing Zhu
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101.,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingfeng Li
- the National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101,
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Yeasmin Khusbu F, Chen FZ, Chen HC. Targeting ubiquitin specific protease 7 in cancer: A deubiquitinase with great prospects. Cell Biochem Funct 2018; 36:244-254. [PMID: 29781103 DOI: 10.1002/cbf.3336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/21/2018] [Accepted: 04/23/2018] [Indexed: 12/20/2022]
Abstract
Deubiquitinase (DUB)-mediated cleavage of ubiquitin chain balances ubiquitination and deubiquitination for determining protein fate. USP7 is one of the best characterized DUBs and functionally important. Numerous proteins have been identified as potential substrates and binding partners of USP7; those play crucial roles in diverse array of cellular and biological processes including tumour suppression, cell cycle, DNA repair, chromatin remodelling, and epigenetic regulation. This review aims at summarizing the current knowledge of this wide association of USP7 with many cellular processes that enlightens the possibility of abnormal USP7 activity in promoting oncogenesis and the importance of identification of specific inhibitors.
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Affiliation(s)
- Farjana Yeasmin Khusbu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Fang-Zhi Chen
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Han-Chun Chen
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
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6
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Elia L, Kunderfranco P, Carullo P, Vacchiano M, Farina FM, Hall IF, Mantero S, Panico C, Papait R, Condorelli G, Quintavalle M. UHRF1 epigenetically orchestrates smooth muscle cell plasticity in arterial disease. J Clin Invest 2018; 128:2473-2486. [PMID: 29558369 DOI: 10.1172/jci96121] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 03/13/2018] [Indexed: 12/26/2022] Open
Abstract
Adult vascular smooth muscle cells (VSMCs) dedifferentiate in response to extracellular cues such as vascular damage and inflammation. Dedifferentiated VSMCs are proliferative, migratory, less contractile, and can contribute to vascular repair as well as to cardiovascular pathologies such as intimal hyperplasia/restenosis in coronary artery and arterial aneurysm. We here demonstrate the role of ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) as an epigenetic master regulator of VSMC plasticity. UHRF1 expression correlated with the development of vascular pathologies associated with modulation of noncoding RNAs, such as microRNAs. miR-145 - pivotal in regulating VSMC plasticity, which is reduced in vascular diseases - was found to control Uhrf1 mRNA translation. In turn, UHRF1 triggered VSMC proliferation, directly repressing promoters of cell-cycle inhibitor genes (including p21 and p27) and key prodifferentiation genes via the methylation of DNA and histones. Local vascular viral delivery of Uhrf1 shRNAs or Uhrf1 VSMC-specific deletion prevented intimal hyperplasia in mouse carotid artery and decreased vessel damage in a mouse model of aortic aneurysm. Our study demonstrates the fundamental role of Uhrf1 in regulating VSMC phenotype by promoting proliferation and dedifferentiation. UHRF1 targeting may hold therapeutic potential in vascular pathologies.
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Affiliation(s)
- Leonardo Elia
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.,Institute of Genetic and Biomedical Research, National Research Council, Milan Unit, Rozzano, Milan, Italy
| | | | - Pierluigi Carullo
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Institute of Genetic and Biomedical Research, National Research Council, Milan Unit, Rozzano, Milan, Italy
| | - Marco Vacchiano
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | | | - Ignacio Fernando Hall
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Humanitas University, Rozzano, Milan, Italy
| | - Stefano Mantero
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Institute of Genetic and Biomedical Research, National Research Council, Milan Unit, Rozzano, Milan, Italy
| | - Cristina Panico
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Roberto Papait
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Gianluigi Condorelli
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy.,Institute of Genetic and Biomedical Research, National Research Council, Milan Unit, Rozzano, Milan, Italy.,Humanitas University, Rozzano, Milan, Italy
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7
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Abhishek S, Nivya MA, Nakarakanti NK, Deeksha W, Khosla S, Rajakumara E. Biochemical and dynamic basis for combinatorial recognition of H3R2K9me2 by dual domains of UHRF1. Biochimie 2018; 149:105-114. [PMID: 29656054 DOI: 10.1016/j.biochi.2018.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/10/2018] [Indexed: 01/10/2023]
Abstract
UHRF1 is a multi-domain protein comprising of a tandem tudor (UHRF1 TTD), a PHD finger, and a SET and RING-associated domain. It is required for the maintenance of CG methylation, heterochromatin formation and DNA repair. Isothermal titration calorimetry binding studies of unmodified and methylated lysine histone peptides establish that the UHRF1 TTD binds dimethylated Lys9 on histone H3 (H3K9me2). Further, MD simulation and binding studies reveal that TTD-PHD of UHRF1 (UHRF1 TTD-PHD) preferentially recognizes dimethyl-lysine status. Importantly, we show that Asp145 in the binding pocket determines the preferential recognition of the dimethyl-ammonium group of H3K9me2. Interestingly, PHD finger of the UHRF1 TTD-PHD has a negligible contribution to the binding affinity for recognition of K9me2 by the UHRF1 TTD. Surprisingly, Lys4 methylation on H3 peptide has an insignificant effect on combinatorial recognition of R2 and K9me2 on H3 by the UHRF1 TTD-PHD. We propose that subtle variations of key residues at the binding pocket determine status specific recognition of histone methyl-lysines by the reader domains.
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Affiliation(s)
- Suman Abhishek
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - M Angel Nivya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - Naveen Kumar Nakarakanti
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - Waghela Deeksha
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India
| | - Sanjeev Khosla
- Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, 500001, India.
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India.
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8
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Choudhry H, Zamzami MA, Omran Z, Wu W, Mousli M, Bronner C, Alhosin M. Targeting microRNA/UHRF1 pathways as a novel strategy for cancer therapy. Oncol Lett 2017; 15:3-10. [PMID: 29285183 PMCID: PMC5738699 DOI: 10.3892/ol.2017.7290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin-like containing plant homeodomain and RING finger domains 1 (UHRF1) is an anti-apoptotic protein involved in the silencing of several tumor suppressor genes (TSGs) through epigenetic modifications including DNA methylation and histone post-translational alterations, and also epigenetic-independent mechanisms. UHRF1 overexpression is observed in a number of solid tumors and hematological malignancies, and is considered a primary mechanism in inhibiting apoptosis. UHRF1 exerts its inhibitory activity on TSGs by binding to functional domains and therefore influences several epigenetic actors including DNA methyltransferase, histone deacetylase 1, histone acetyltransferase Tat-interacting protein 60 and histone methyltransferases G9a and Suv39H1. UHRF1 is considered to control a large macromolecular protein complex termed epigenetic code replication machinery, in order to maintain epigenetic silencing of TSGs during cell division, thus enabling cancer cells to escape apoptosis. MicroRNAs (miRNAs) are able to regulate the expression of its target gene by functioning as either an oncogene or a tumor suppressor. In the present review, the role of tumor suppressive miRNAs in the regulation of UHRF1, and the importance of targeting the microRNA/UHRF1 pathways in order to induce the reactivation of silenced TSGs and subsequent apoptosis are discussed.
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Affiliation(s)
- Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ziad Omran
- College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Marc Mousli
- Laboratory of Biophotonics and Pharmacology, Faculty of Pharmacy, University of Strasbourg, 67401 Illkirch Cedex, France
| | - Christian Bronner
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), National Institute of Health and Medical Research U964, National Center for Scientific Research UMR7104, University of Strasbourg, 67404 Illkirch Cedex, France
| | - Mahmoud Alhosin
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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9
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Chen R, Zhang Q, Duan X, York P, Chen GD, Yin P, Zhu H, Xu M, Chen P, Wu Q, Li D, Samarut J, Xu G, Zhang P, Cao X, Li J, Wong J. The 5-Hydroxymethylcytosine (5hmC) Reader UHRF2 Is Required for Normal Levels of 5hmC in Mouse Adult Brain and Spatial Learning and Memory. J Biol Chem 2017; 292:4533-4543. [PMID: 28115522 DOI: 10.1074/jbc.m116.754580] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 12/27/2016] [Indexed: 12/21/2022] Open
Abstract
UHRF2 has been implicated as a novel regulator for both DNA methylation (5mC) and hydroxymethylation (5hmC), but its physiological function and role in DNA methylation/hydroxymethylation are unknown. Here we show that in mice, UHRF2 is more abundantly expressed in the brain and a few other tissues. Uhrf2 knock-out mice are viable and fertile and exhibit no gross defect. Although there is no significant change of DNA methylation, the Uhrf2 null mice exhibit a reduction of 5hmC in the brain, including the cortex and hippocampus. Furthermore, the Uhrf2 null mice exhibit a partial impairment in spatial memory acquisition and retention. Consistent with the phenotype, gene expression profiling uncovers a role for UHRF2 in regulating neuron-related gene expression. Finally, we provide evidence that UHRF2 binds 5hmC in cells but does not appear to affect the TET1 enzymatic activity. Together, our study supports UHRF2 as a bona fide 5hmC reader and further demonstrates a role for 5hmC in neuronal function.
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Affiliation(s)
- Ruoyu Chen
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qiao Zhang
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiaoya Duan
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Philippe York
- the Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030
| | - Guo-Dong Chen
- the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Pengcheng Yin
- the Key Laboratory of Brain Functional Genomics, Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai 200062, China
| | - Haijun Zhu
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Meichen Xu
- the Key Laboratory of Brain Functional Genomics, Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai 200062, China
| | - Peilin Chen
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qihan Wu
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dali Li
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jacques Samarut
- the Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon 69007, France, and
| | - Guoliang Xu
- the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Pumin Zhang
- the Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030
| | - Xiaohua Cao
- the Key Laboratory of Brain Functional Genomics, Ministry of Education, Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai 200062, China
| | - Jiwen Li
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China,
| | - Jiemin Wong
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China, .,the Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China
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10
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Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals. J Biosci 2016; 41:759-786. [DOI: 10.1007/s12038-016-9650-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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11
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Ramesh V, Bayam E, Cernilogar FM, Bonapace IM, Schulze M, Riemenschneider MJ, Schotta G, Götz M. Loss of Uhrf1 in neural stem cells leads to activation of retroviral elements and delayed neurodegeneration. Genes Dev 2016; 30:2199-2212. [PMID: 27798843 PMCID: PMC5088568 DOI: 10.1101/gad.284992.116] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/20/2016] [Indexed: 11/24/2022]
Abstract
In order to understand whether early epigenetic mechanisms instruct the long-term behavior of neural stem cells (NSCs) and their progeny, we examined Uhrf1 (ubiquitin-like PHD ring finger-1; also known as Np95), as it is highly expressed in NSCs of the developing brain and rapidly down-regulated upon differentiation. Conditional deletion of Uhrf1 in the developing cerebral cortex resulted in rather normal proliferation and neurogenesis but severe postnatal neurodegeneration. During development, deletion of Uhrf1 lead to global DNA hypomethylation with a strong activation of the intracisternal A particle (IAP) family of endogenous retroviral elements, accompanied by an increase in 5-hydroxymethylcytosine. Down-regulation of Tet enzymes rescued the IAP activation in Uhrf1 conditional knockout (cKO) cells, suggesting an antagonistic interplay between Uhrf1 and Tet on IAP regulation. As IAP up-regulation persists into postnatal stages in the Uhrf1 cKO mice, our data show the lack of means to repress IAPs in differentiating neurons that normally never express Uhrf1 The high load of viral proteins and other transcriptional deregulation ultimately led to postnatal neurodegeneration. Taken together, these data show that early developmental NSC factors can have long-term effects in neuronal differentiation and survival. Moreover, they highlight how specific the consequences of widespread changes in DNA methylation are for certain classes of retroviral elements.
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Affiliation(s)
- Vidya Ramesh
- Institute for Stem Cell Research, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Physiological Genomics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Efil Bayam
- Institute for Stem Cell Research, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Physiological Genomics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Filippo M Cernilogar
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-University, 82152 Munich, Germany
| | - Ian M Bonapace
- Department of Functional and Structural Biology, University of Insubria, 21052 Busto Arsizio, Italy
| | - Markus Schulze
- Department of Neuropathology, Regensburg University Hospital, 93053 Regensburg, Germany
| | | | - Gunnar Schotta
- Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-University, 82152 Munich, Germany
- Munich Center for Integrated Protein Science (CiPS), 81377 Munich, Germany
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Physiological Genomics, Helmholtz Center Munich, 85764 Neuherberg, Germany
- SyNergy, Excellence Cluster Systems Neurology, University of Munich, 81377 Munich, Germany
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12
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Zhao Q, Zhang J, Chen R, Wang L, Li B, Cheng H, Duan X, Zhu H, Wei W, Li J, Wu Q, Han JDJ, Yu W, Gao S, Li G, Wong J. Dissecting the precise role of H3K9 methylation in crosstalk with DNA maintenance methylation in mammals. Nat Commun 2016; 7:12464. [PMID: 27554592 PMCID: PMC5426519 DOI: 10.1038/ncomms12464] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022] Open
Abstract
In mammals it is unclear if UHRF1-mediated DNA maintenance methylation by DNMT1 is strictly dependent on histone H3K9 methylation. Here we have generated an Uhrf1 knockin (KI) mouse model that specifically abolishes the H3K9me2/3-binding activity of Uhrf1. The homozygous Uhrf1 KI mice are viable and fertile, and exhibit ∼10% reduction of DNA methylation in various tissues. The reduced DNA methylation occurs globally in the genome and does not restrict only to the H3K9me2/3 enriched repetitive sequences. In vitro UHRF1 binds with higher affinity to reconstituted nucleosome with hemi-methylated CpGs than that with H3K9me2/3, although it binds cooperatively to nucleosome with both modifications. We also show that the nucleosome positioning affects the binding of methylated DNA by UHRF1. Thus, while our study supports a role for H3K9 methylation in promoting DNA methylation, it demonstrates for the first time that DNA maintenance methylation in mammals is largely independent of H3K9 methylation.
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Affiliation(s)
- Qian Zhao
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiqin Zhang
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ruoyu Chen
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lina Wang
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Bo Li
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Hao Cheng
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Xiaoya Duan
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Haijun Zhu
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Qihan Wu
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jing-Dong J. Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Wenqiang Yu
- Department of Biochemistry and Molecular Biology, Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity, Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China
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13
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Ludwig AK, Zhang P, Cardoso MC. Modifiers and Readers of DNA Modifications and Their Impact on Genome Structure, Expression, and Stability in Disease. Front Genet 2016; 7:115. [PMID: 27446199 PMCID: PMC4914596 DOI: 10.3389/fgene.2016.00115] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/06/2016] [Indexed: 12/16/2022] Open
Abstract
Cytosine base modifications in mammals underwent a recent expansion with the addition of several naturally occurring further modifications of methylcytosine in the last years. This expansion was accompanied by the identification of the respective enzymes and proteins reading and translating the different modifications into chromatin higher order organization as well as genome activity and stability, leading to the hypothesis of a cytosine code. Here, we summarize the current state-of-the-art on DNA modifications, the enzyme families setting the cytosine modifications and the protein families reading and translating the different modifications with emphasis on the mouse protein homologs. Throughout this review, we focus on functional and mechanistic studies performed on mammalian cells, corresponding mouse models and associated human diseases.
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Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
| | - M C Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Darmstadt Germany
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14
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Chung HR, Xu C, Fuchs A, Mund A, Lange M, Staege H, Schubert T, Bian C, Dunkel I, Eberharter A, Regnard C, Klinker H, Meierhofer D, Cozzuto L, Winterpacht A, Di Croce L, Min J, Will H, Kinkley S. PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3. eLife 2016; 5. [PMID: 27223324 PMCID: PMC4915813 DOI: 10.7554/elife.10607] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 05/19/2016] [Indexed: 02/04/2023] Open
Abstract
PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes. DOI:http://dx.doi.org/10.7554/eLife.10607.001 In human and other eukaryotic cells, DNA is packaged around proteins called histones to form a structure known as chromatin. Chemical tags added to the histones alter how the DNA is packaged and the activity of the genes encoded by that DNA. For example, many active genes are packaged around histone H3 proteins that have “Lysine 4 tri-methyl” tags attached to them. Another protein that is associated with chromatin is called PHF13 and it has several roles, including repairing damaged DNA. However, it was not known whether PHF13 binds to chromatin via the chemical tags, or in another way. Ho-Ryun, Xu, Fuchs et al. used several biochemical techniques in mouse and human cells to explore how PHF13 specifically interacts with chromatin. These experiments showed that PHF13 binds specifically to DNA and to two types of methyl tags (lysine 4-tri-methyl or lysine 4-di-methyl). These chemical tags are predominantly found at active promoters as well as at a small subset of less active promoters known as bivalent promoters. PHF13 interacted with other proteins on the chromatin that are known to either drive or repress gene activity and it’s depletion affected the activity of many genes. Whether PHF13 increased or decreased gene activity depended on whether it was bound to active or bivalent promoters. The active promoters targeted by PHF13 had higher numbers of the tri-methyl tags whereas the di-methyl tags were more common on the bivalent promoters. These findings provide preliminary evidence that a protein binding to different methyl tags in the same place on histone H3 can have opposite effects on gene activity. Ho-Ryun, Xu, Fuchs et al. now intend to find out more about the other proteins that interact with PHF13 on chromatin. DOI:http://dx.doi.org/10.7554/eLife.10607.002
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Affiliation(s)
- Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chao Xu
- Structural Genomics Consortium, Toronto, Canada
| | - Alisa Fuchs
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas Mund
- Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Hannah Staege
- Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Tobias Schubert
- Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Ilona Dunkel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anton Eberharter
- Adolf-Butenandt-Institute and Center for Integrated Protein Science, Ludwig-Maximilians-University, Munich, Germany
| | - Catherine Regnard
- Adolf-Butenandt-Institute and Center for Integrated Protein Science, Ludwig-Maximilians-University, Munich, Germany
| | - Henrike Klinker
- Adolf-Butenandt-Institute and Center for Integrated Protein Science, Ludwig-Maximilians-University, Munich, Germany
| | | | - Luca Cozzuto
- Centre for Genomic Regulation, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andreas Winterpacht
- Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Luciano Di Croce
- Centre for Genomic Regulation, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys, Barcelona, Spain
| | - Jinrong Min
- Structural Genomics Consortium, Toronto, Canada
| | - Hans Will
- Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sarah Kinkley
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Heinrich-Pette-Institute - Leibniz Institute for Experimental Virology, Hamburg, Germany
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15
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Kuznetsova IS, Ostromyshenskii DI, Komissarov AS, Prusov AN, Waisertreiger IS, Gorbunova AV, Trifonov VA, Ferguson-Smith MA, Podgornaya OI. LINE-related component of mouse heterochromatin and complex chromocenters’ composition. Chromosome Res 2016; 24:309-23. [DOI: 10.1007/s10577-016-9525-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/23/2016] [Accepted: 04/17/2016] [Indexed: 10/21/2022]
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16
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Tauber M, Fischle W. Conserved linker regions and their regulation determine multiple chromatin-binding modes of UHRF1. Nucleus 2016; 6:123-32. [PMID: 25891992 PMCID: PMC4615792 DOI: 10.1080/19491034.2015.1026022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin-like with PHD and RING Finger domains 1 (UHRF1) is an important nuclear protein that is mutated and aberrantly expressed in many tumors. The protein integrates different chromatin modifications and is essential for their maintenance throughout the cell cycle. Separate chromatin-binding modules of UHRF1 have been studied on a functional and structural level. The unmodified N-terminus of histone H3 is recognized by a PHD domain, while a TTD domain specifically interacts with histone H3 Lysine 9 trimethylation. A SRA region binds hemimethylatd DNA. Emerging evidence indicates that the modules of UHRF1 do not act independently of each other but establish complex modes of interaction with patterns of chromatin modifications. This multivalent readout is regulated by allosteric binding of phosphatidylinositol 5-phosphate to a region outside the PHD, TTD and SRA domains as well as by phosphorylation of one of the linker regions connecting these modules. Here, we summarize the current knowledge on UHRF1 chromatin interaction and introduce a novel model of conformational transitions of the protein that are directed by the flexible and highly charged linker regions. We propose that these are essential in setting up defined structural states of the protein where different domains or combinations thereof are available for binding chromatin modifications or are prevented from doing so. Lastly, we suggest that controlled tuning of intramolecular linker interactions by ligands and posttranslational modifications establishes a rational framework for comprehending UHRF1 regulation and putatively the working mode of other chromatin factors in different physiological contexts.
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Affiliation(s)
- Maria Tauber
- a Laboratory of Chromatin Biochemistry ; Max Planck Institute for Biophysical Chemistry ; Göttingen , Germany
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17
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Meng H, Harrison DJ, Meehan RR. MBD4 interacts with and recruits USP7 to heterochromatic foci. J Cell Biochem 2015; 116:476-85. [PMID: 25358258 PMCID: PMC4964934 DOI: 10.1002/jcb.25001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/23/2014] [Indexed: 12/19/2022]
Abstract
MBD4 is the only methyl‐CpG binding protein that possesses a C‐terminal glycosylase domain. It has been associated with a number of nuclear pathways including DNA repair, DNA damage response, the initiation of apoptosis, transcriptional repression, and DNA demethylation. However, the precise contribution of MBD4 to these processes in development and relevant diseases remains elusive. We identified UHRF1 and USP7 as two new interaction partners for MBD4. Both UHRF1, a E3 ubiquitin ligase, and USP7, a de‐ubiquinating enzyme, regulate the stability of the DNA maintenance methyltransferase, Dnmt1. The ability of MBD4 to directly interact with and recruit USP7 to chromocenters implicates it as an additional factor that can potentially regulate Dnmt1 activity during cell proliferation. J. Cell. Biochem. 116: 476–485, 2015. © 2014 The Authors. Journal of Cellular Biochemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Huan Meng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK; Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, China
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18
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DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination. Cell Res 2015; 25:911-29. [PMID: 26065575 PMCID: PMC4528052 DOI: 10.1038/cr.2015.72] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/27/2015] [Accepted: 05/07/2015] [Indexed: 12/12/2022] Open
Abstract
DNMT1 is recruited by PCNA and UHRF1 to maintain DNA methylation after replication. UHRF1 recognizes hemimethylated DNA substrates via the SRA domain, but also repressive H3K9me3 histone marks with its TTD. With systematic mutagenesis and functional assays, we could show that chromatin binding further involved UHRF1 PHD binding to unmodified H3R2. These complementation assays clearly demonstrated that the ubiquitin ligase activity of the UHRF1 RING domain is required for maintenance DNA methylation. Mass spectrometry of UHRF1-deficient cells revealed H3K18 as a novel ubiquitination target of UHRF1 in mammalian cells. With bioinformatics and mutational analyses, we identified a ubiquitin interacting motif (UIM) in the N-terminal regulatory domain of DNMT1 that binds to ubiquitinated H3 tails and is essential for DNA methylation in vivo. H3 ubiquitination and subsequent DNA methylation required UHRF1 PHD binding to H3R2. These results show the manifold regulatory mechanisms controlling DNMT1 activity that require the reading and writing of epigenetic marks by UHRF1 and illustrate the multifaceted interplay between DNA and histone modifications. The identification and functional characterization of the DNMT1 UIM suggests a novel regulatory principle and we speculate that histone H2AK119 ubiquitination might also lead to UIM-dependent recruitment of DNMT1 and DNA methylation beyond classic maintenance.
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19
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Jacob V, Chernyavskaya Y, Chen X, Tan PS, Kent B, Hoshida Y, Sadler KC. DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos. Development 2015; 142:510-21. [PMID: 25564650 DOI: 10.1242/dev.115980] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 to hemimethylated DNA during replication and is essential for maintaining DNA methylation. uhrf1 mutant zebrafish have global DNA hypomethylation and display embryonic defects, including a small liver, and they die as larvae. We make the surprising finding that, despite their reduced organ size, uhrf1 mutants express high levels of genes controlling S-phase and have many more cells undergoing DNA replication, as measured by BrdU incorporation. In contrast to wild-type hepatocytes, which are continually dividing during hepatic outgrowth and thus dilute the BrdU label, uhrf1 mutant hepatocytes retain BrdU throughout outgrowth, reflecting cell cycle arrest. Pulse-chase-pulse experiments with BrdU and EdU, and DNA content analysis indicate that uhrf1 mutant cells undergo DNA re-replication and that apoptosis is the fate of many of the re-replicating and arrested hepatocytes. Importantly, the DNA re-replication phenotype and hepatic outgrowth failure are preceded by global loss of DNA methylation. Moreover, uhrf1 mutants are phenocopied by mutation of dnmt1, and Dnmt1 knockdown in uhrf1 mutants enhances their small liver phenotype. Together, these data indicate that unscheduled DNA replication and failed cell cycle progression leading to apoptosis are the mechanisms by which DNA hypomethylation prevents organ expansion in uhrf1 mutants. We propose that cell cycle arrest leading to apoptosis is a strategy that restricts propagation of epigenetically damaged cells during embryogenesis.
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Affiliation(s)
- Vinitha Jacob
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Yelena Chernyavskaya
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Xintong Chen
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Poh Seng Tan
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Health System, Singapore
| | - Brandon Kent
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Yujin Hoshida
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Kirsten C Sadler
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
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20
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Understanding the relationship between DNA methylation and histone lysine methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1362-72. [PMID: 24560929 PMCID: PMC4316174 DOI: 10.1016/j.bbagrm.2014.02.007] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/11/2014] [Indexed: 12/19/2022]
Abstract
DNA methylation acts as an epigenetic modification in vertebrate DNA. Recently it has become clear that the DNA and histone lysine methylation systems are highly interrelated and rely mechanistically on each other for normal chromatin function in vivo. Here we examine some of the functional links between these systems, with a particular focus on several recent discoveries suggesting how lysine methylation may help to target DNA methylation during development, and vice versa. In addition, the emerging role of non-methylated DNA found in CpG islands in defining histone lysine methylation profiles at gene regulatory elements will be discussed in the context of gene regulation. This article is part of a Special Issue entitled: Methylation: A Multifaceted Modification — looking at transcription and beyond. There is an emerging realisation that DNA and histone lysine methylation in mammals are highly interrelated. Targeting of DNA methylation is mechanistically linked to H3K9 methylation. Uhrf1 acts as a link between H3K9 methylation and maintenance methylation during DNA replication. Targeting of Dnmt3a/b is influenced by H3K4 and H3K36 methylation. Non-methylated DNA at CpG islands influences histone methylation through ZF-CxxC proteins.
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21
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Bashtrykov P, Jankevicius G, Jurkowska RZ, Ragozin S, Jeltsch A. The UHRF1 protein stimulates the activity and specificity of the maintenance DNA methyltransferase DNMT1 by an allosteric mechanism. J Biol Chem 2013; 289:4106-15. [PMID: 24368767 DOI: 10.1074/jbc.m113.528893] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-like, containing PHD and RING finger domains protein 1 (UHRF1) is essential for maintenance DNA methylation by DNA methyltransferase 1 (DNMT1). UHRF1 has been shown to recruit DNMT1 to replicated DNA by the ability of its SET and RING-associated (SRA) domain to bind to hemimethylated DNA. Here, we demonstrate that UHRF1 also increases the activity of DNMT1 by almost 5-fold. This stimulation is mediated by a direct interaction of both proteins through the SRA domain of UHRF1 and the replication focus targeting sequence domain of DNMT1, and it does not require DNA binding by the SRA domain. Disruption of the interaction between DNMT1 and UHRF1 by replacement of key residues in the replication focus targeting sequence domain led to a strong reduction of DNMT1 stimulation. Additionally, the interaction with UHRF1 increased the specificity of DNMT1 for methylation of hemimethylated CpG sites. These findings show that apart from the targeting of DNMT1 to the replicated DNA UHRF1 increases the activity and specificity of DNMT1, thus exerting a multifaceted influence on the maintenance of DNA methylation.
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Affiliation(s)
- Pavel Bashtrykov
- From the Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, D-70569 Stuttgart, Germany and
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22
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Rodriguez A, Bjerling P. The links between chromatin spatial organization and biological function. Biochem Soc Trans 2013; 41:1634-9. [PMID: 24256267 PMCID: PMC3836414 DOI: 10.1042/bst20130213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 02/06/2023]
Abstract
During the last few years, there has been a rapid increase in our knowledge of how chromatin is organized inside the nucleus. Techniques such as FISH (fluorescence in situ hybridization) have proved that chromosomes organize themselves in so-called CTs (chromosome territories). In addition, newly developed 3C (chromatin conformation capture) techniques have revealed that certain chromosomal regions tend to interact with adjacent regions on either the same chromosome or adjacent chromosomes, and also that regions in close proximity are replicated simultaneously. Furthermore, transcriptionally repressed or active areas occupy different nuclear compartments. Another new technique, named DamID (DNA adenine methyltransferase identification), has strengthened the notion that transcriptionally repressed genes are often found in close association with the nuclear membrane, whereas transcriptionally active regions are found in the more central regions of the nucleus. However, in response to various stimuli, transcriptionally repressed regions are known to relocalize from the nuclear lamina to the interior of the nucleus, leading to a concomitant up-regulation of otherwise silenced genes. Taken together, these insights are of great interest for the relationship between chromosomal spatial organization and genome function. In the present article, we review recent advances in this field with a focus on mammalian cells and the eukaryotic model organism Schizosaccharomyces pombe.
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Key Words
- chromatin
- fission yeast
- heterochromatin
- nuclear organization
- transcriptional regulation
- 3c, chromosome conformation capture
- 4c, circularized chromosome conformation capture
- 5c, carbon copy chromosome conformation capture
- cenp, centromere protein
- chip, chromatin immunoprecipitation
- ct, chromosome territory
- dam, dna adenine methyltansferase
- damid, dna adenine methyltransferase identification
- fish, fluorescence in situ hybridization
- hic, genome-wide chromosome conformation capture
- inm, inner nuclear membrane
- lad, lamina-associated domain
- lem, lap2/emerin/man1
- mps, massive parallel sequencing
- nad, nucleoli-associated domain
- nm, nuclear membrane
- onm, outer nuclear membrane
- tfiiic, transcription factor iiic
- tor, time of replication
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Affiliation(s)
- Alejandro Rodriguez
- *Department of Medical Biochemistry and Microbiology (IMBIM), Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
| | - Pernilla Bjerling
- *Department of Medical Biochemistry and Microbiology (IMBIM), Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
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Shirakawa T, Yaman-Deveci R, Tomizawa SI, Kamizato Y, Nakajima K, Sone H, Sato Y, Sharif J, Yamashita A, Takada-Horisawa Y, Yoshida S, Ura K, Muto M, Koseki H, Suda T, Ohbo K. An epigenetic switch is crucial for spermatogonia to exit the undifferentiated state toward a Kit-positive identity. Development 2013; 140:3565-76. [PMID: 23903187 DOI: 10.1242/dev.094045] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetic modifications influence gene expression and chromatin remodeling. In embryonic pluripotent stem cells, these epigenetic modifications have been extensively characterized; by contrast, the epigenetic events of tissue-specific stem cells are poorly understood. Here, we define a new epigenetic shift that is crucial for differentiation of murine spermatogonia toward meiosis. We have exploited a property of incomplete cytokinesis, which causes male germ cells to form aligned chains of characteristic lengths, as they divide and differentiate. These chains revealed the stage of spermatogenesis, so the epigenetic differences of various stages could be characterized. Single, paired and medium chain-length spermatogonia not expressing Kit (a marker of differentiating spermatogonia) showed no expression of Dnmt3a2 and Dnmt3b (two de novo DNA methyltransferases); they also lacked the transcriptionally repressive histone modification H3K9me2. By contrast, spermatogonia consisting of ~8-16 chained cells with Kit expression dramatically upregulated Dnmt3a2/3b expression and also displayed increased H3K9me2 modification. To explore the function of these epigenetic changes in spermatogonia in vivo, the DNA methylation machinery was destabilized by ectopic Dnmt3b expression or Np95 ablation. Forced Dnmt3b expression induced expression of Kit; whereas ablation of Np95, which is essential for maintaining DNA methylation, interfered with differentiation and viability only after spermatogonia become Kit positive. These data suggest that the epigenetic status of spermatogonia shifts dramatically during the Kit-negative to Kit-positive transition. This shift might serve as a switch that determines whether spermatogonia self-renew or differentiate.
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Affiliation(s)
- Takayuki Shirakawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, Japan
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24
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Taylor EM, Bonsu NM, Price RJ, Lindsay HD. Depletion of Uhrf1 inhibits chromosomal DNA replication in Xenopus egg extracts. Nucleic Acids Res 2013; 41:7725-37. [PMID: 23788677 PMCID: PMC3763540 DOI: 10.1093/nar/gkt549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 05/22/2013] [Accepted: 05/25/2013] [Indexed: 12/31/2022] Open
Abstract
UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) has a well-established role in epigenetic regulation through the recognition of various histone marks and interaction with chromatin-modifying proteins. However, its function in regulating cell cycle progression remains poorly understood and has been largely attributed to a role in transcriptional regulation. In this study we have used Xenopus laevis egg extracts to analyse Uhrf1 function in DNA replication in the absence of transcriptional influences. We demonstrate that removal of Uhrf1 inhibits chromosomal replication in this system. We further show that this requirement for Uhrf1, or an associated factor, occurs at an early stage of DNA replication and that the consequences of Uhrf1 depletion are not solely due to its role in loading Dnmt1 onto newly replicated DNA. We describe the pattern of Uhrf1 chromatin association before the initiation of DNA replication and show that this reflects functional requirements both before and after origin licensing. Our data demonstrate that the removal of Xenopus Uhrf1 influences the chromatin association of key replication proteins and reveal Uhrf1 as an important new factor required for metazoan DNA replication.
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Affiliation(s)
- Elaine M. Taylor
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Nicola M. Bonsu
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - R. Jordan Price
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Howard D. Lindsay
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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25
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Snapp RR, Goveia E, Peet L, Bouffard NA, Badger GJ, Langevin HM. Spatial organization of fibroblast nuclear chromocenters: component tree analysis. J Anat 2013; 223:255-61. [PMID: 23848307 DOI: 10.1111/joa.12082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2013] [Indexed: 01/09/2023] Open
Abstract
The nuclei of mouse connective tissue fibroblasts contain chromocenters which are well-defined zones of heterochromatin that can be used as positional landmarks to examine nuclear remodeling in response to a mechanical perturbation. This study used component tree analysis, an image segmentation algorithm that detects high intensity voxels that are topologically connected, to quantify the spatial organization of chromocenters in fibroblasts within whole mouse connective tissue fixed and stained with 4',6-diamidino-2-phenylindole (DAPI). The component tree analysis method was applied to confocal microscopy images of whole mouse areolar connective tissue incubated for 30 min ex vivo with or without static stretch. In stretched tissue, the mean distance between chromocenters within fibroblast nuclei was significantly greater (vs. non-stretched, P < 0.001), corresponding to an average of a 500-nm increase in chromocenter separation (~10% strain). There was no significant difference in chromocenter number or average size between stretch and no stretch. Average chromocenter distance was positively correlated with nuclear cross-sectional area (r = 0.78, P < 0.0001), and nuclear volume (r = 0.42, P < 0.0001), and negatively correlated with nuclear aspect ratio (r = -0.65, P < 0.0001) and nuclear concavity index (r = -0.44, P < 0.0001). These results demonstrate that component trees can be successfully applied to the morphometric analysis of nuclear chromocenters in fibroblasts within whole connective tissue. Static stretching of mouse areolar connective tissue for 30 min resulted in substantially increased separation of nuclear chromocenters in connective tissue fibroblasts. This interior remodeling of the nucleus induced by tissue stretch may impact transcriptionally active euchromatin within the inter-chromocenter space.
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Affiliation(s)
- Robert R Snapp
- Department of Computer Science, University of Vermont College of Medicine, Burlington, VT, USA
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26
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Cao K, Lailler N, Zhang Y, Kumar A, Uppal K, Liu Z, Lee EK, Wu H, Medrzycki M, Pan C, Ho PY, Cooper GP, Dong X, Bock C, Bouhassira EE, Fan Y. High-resolution mapping of h1 linker histone variants in embryonic stem cells. PLoS Genet 2013; 9:e1003417. [PMID: 23633960 PMCID: PMC3636266 DOI: 10.1371/journal.pgen.1003417] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 02/13/2013] [Indexed: 02/07/2023] Open
Abstract
H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H10 displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d, and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark. Embryonic stem cells (ESCs) possess unique chromatin and epigenetic signatures, which are important in defining the identity and genome plasticity of pluripotent stem cells. Although ESC epigenomes have been extensively characterized, the genome localization of histone H1 variants, the chromatin structural proteins facilitating higher-order chromatin folding, remains elusive. Linker histone H1 is essential for mammalian development and regulates the expression of specific genes in ESCs. Here, by using a knock-in system coupled with ChIP–seq, we first achieve the high resolution mapping of two H1 variants on a genome-wide scale in mouse ESCs. Our study reveals the correlations of this underexplored histone family with other epigenetic marks and genome attributes. Surprisingly, we identify a dramatic enrichment of H1d and H1c at major satellite sequences. H10, mapped using an overexpressing ESC line, shows similar features at active promoters but differential binding at repetitive sequences compared with H1d and H1c. Furthermore, using mutant ESCs that are deficient for multiple H1 variants, we demonstrate the role of H1 in chromocenter clustering and transcriptional repression of major satellites. Thus, these results connect this important repressive mark with the well understood ESC epigenome and identify novel functions of H1 in mammalian genome organization.
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Affiliation(s)
- Kaixiang Cao
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nathalie Lailler
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yunzhe Zhang
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Ashwath Kumar
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Karan Uppal
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Zheng Liu
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Eva K. Lee
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Hongwei Wu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Magdalena Medrzycki
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chenyi Pan
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Po-Yi Ho
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Guy P. Cooper
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Xiao Dong
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Eric E. Bouhassira
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yuhong Fan
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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27
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Identification of survival factors in LPS-stimulated anthrax lethal toxin tolerant RAW 264.7 cells through proteomic approach. BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7112-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9. Nat Commun 2013; 4:1563. [DOI: 10.1038/ncomms2562] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 01/29/2013] [Indexed: 12/13/2022] Open
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29
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Abstract
UHRF1 (ubiquitin-like, with PHD and RING finger domains 1) is a critical epigenetic player involved in the maintenance of DNA methylation patterns during DNA replication. Dysregulation of the UHRF1 level is implicated in cancer onset, metastasis, and tumor recurrence. Previous studies demonstrated that UHRF1 can be stabilized through USP7-mediated deubiquitylation, but the mechanism through which UHRF1 is ubiquitylated is still unknown. Here we show that proteasomal degradation of UHRF1 is mediated by the SCF(β-TrCP) E3 ligase. Through bioinformatic and mutagenesis studies, we identified a functional DSG degron in the UHRF1 N terminus that is necessary for UHRF1 stability regulation. We further show that UHRF1 physically interacts with β-TrCP1 in a manner dependent on phosphorylation of serine 108 (S108(UHRF1)) within the DSG degron. Furthermore, we demonstrate that S108(UHRF1) phosphorylation is catalyzed by casein kinase 1 delta (CK1δ) and is important for the recognition of UHRF1 by SCF(β-TrCP). Importantly, we demonstrate that UHRF1 degradation is accelerated in response to DNA damage, coincident with enhanced S108(UHRF1) phosphorylation. Taken together, our data identify SCF(β-TrCP) as a bona fide UHRF1 E3 ligase important for regulating UHRF1 steady-state levels both under normal conditions and in response to DNA damage.
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30
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Cheng J, Yang Y, Fang J, Xiao J, Zhu T, Chen F, Wang P, Li Z, Yang H, Xu Y. Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein. J Biol Chem 2012; 288:1329-39. [PMID: 23161542 DOI: 10.1074/jbc.m112.415398] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
UHRF1 is an important epigenetic regulator connecting DNA methylation and histone methylations. UHRF1 is required for maintenance of DNA methylation through recruiting DNMT1 to DNA replication forks. Recent studies have shown that the plant homeodomain (PHD) of UHRF1 recognizes the N terminus of unmodified histone H3, and the interaction is inhibited by methylation of H3R2, whereas the tandem tudor domain (TTD) of UHRF1 recognizes trimethylated histone H3 lysine 9 (H3K9me3). However, how the two domains of UHRF1 coordinately recognize histone methylations remains elusive. In this report, we identified that PHD largely enhances the interaction between TTD and H3K9me3. We present the crystal structure of UHRF1 containing both TTD and PHD (TTD-PHD) in complex with H3K9m3 peptide at 3.0 Å resolution. The structure shows that TTD-PHD binds to the H3K9me3 peptide with 1:1 stoichiometry with the two domains connected by the H3K9me3 peptide and a linker region. The TTD interacts with residues Arg-8 and trimethylated Lys-9, and the PHD interacts with residues Ala-1, Arg-2, and Lys-4 of the H3K9me3 peptide. The biochemical experiments indicate that PHD-mediated recognition of unmodified H3 is independent of the TTD, whereas TTD-mediated recognition of H3K9me3 PHD. Thus, both TTD and PHD are essential for specific recognition of H3K9me3 by UHRF1. Interestingly, the H3K9me3 peptide induces conformational changes of TTD-PHD, which do not affect the autoubiquitination activity or hemimethylated DNA binding affinity of UHRF1 in vitro. Taken together, our studies provide structural insight into the coordinated recognition of H3K9me3 by the TTD and PHD of UHRF1.
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Affiliation(s)
- Jingdong Cheng
- Cancer Institute, Shanghai Cancer Center, Fudan University, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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31
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Abstract
DNA hypomethylation was the initial epigenetic abnormality recognized in human tumors. However, for several decades after its independent discovery by two laboratories in 1983, it was often ignored as an unwelcome complication, with almost all of the attention on the hypermethylation of promoters of genes that are silenced in cancers (e.g., tumor-suppressor genes). Because it was subsequently shown that global hypomethylation of DNA in cancer was most closely associated with repeated DNA elements, cancer linked-DNA hypomethylation continued to receive rather little attention. DNA hypomethylation in cancer can no longer be considered an oddity, because recent high-resolution genome-wide studies confirm that DNA hypomethylation is the almost constant companion to hypermethylation of the genome in cancer, just usually (but not always) in different sequences. Methylation changes at individual CpG dyads in cancer can have a high degree of dependence not only on the regional context, but also on neighboring sites. DNA demethylation during carcinogenesis may involve hemimethylated dyads as intermediates, followed by spreading of the loss of methylation on both strands. In this review, active demethylation of DNA and the relationship of cancer-associated DNA hypomethylation to cancer stem cells are discussed. Evidence is accumulating for the biological significance and clinical relevance of DNA hypomethylation in cancer, and for cancer-linked demethylation and de novo methylation being highly dynamic processes.
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Affiliation(s)
- Melanie Ehrlich
- Hayward Genetics Program, Department of Biochemistry, Tulane Cancer Center, Tulane Medical School, 1430 TulaneAvenue, New Orleans, LA 70112, USA.
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32
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The SRA protein UHRF1 promotes epigenetic crosstalks and is involved in prostate cancer progression. Oncogene 2012; 31:4878-87. [PMID: 22330138 DOI: 10.1038/onc.2011.641] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Epigenetic silencing of tumour suppressor genes is an important mechanism involved in cell transformation and tumour progression. The Set and RING-finger-associated domain-containing protein UHRF1 might be an important link between different epigenetic pathways. Here, we report that UHRF1 is frequently overexpressed in human prostate tumours and has an important role in prostate cancer pathogenesis and progression. Analysis of human prostate cancer samples by microarrays and immunohistochemistry showed increased expression of UHRF1 in about half of the cases. Moreover, UHRF1 expression was associated with reduced overall survival after prostatectomy in patients with organ-confined prostate tumours (P < 0.0001). UHRF1 expression was negatively correlated with several tumour suppressor genes and positively with the histone methyltransferase (HMT) EZH2 both in prostate tumours and cell lines. UHRF1 knockdown reduced proliferation, clonogenic capability and anchorage-independent growth of prostate cancer cells. Depletion of UHRF1 resulted in reactivation of several tumour suppressor genes. Gene reactivation upon UHRF1 depletion was associated with changes in histone H3K9 methylation, acetylation and DNA methylation, and impaired binding of the H3K9 HMT Suv39H1 to the promoter of silenced genes. Co-immunoprecipitation experiments showed direct interaction between UHRF1 and Suv39H1. Our data support the notion that UHRF1, along with Suv39H1 and DNA methyltransferases, contributes to epigenetic gene silencing in prostate tumours. This could represent a parallel and convergent pathway to the H3K27 methylation catalyzed by EZH2 to synergistically promote inactivation of tumour suppressor genes. Deregulated expression of UHRF1 is involved in the prostate cancer pathogenesis and might represent a useful marker to distinguish indolent cancer from those at high risk of lethal progression.
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Rajakumara E, Wang Z, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y. PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol Cell 2012; 43:275-284. [PMID: 21777816 DOI: 10.1016/j.molcel.2011.07.006] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/06/2011] [Accepted: 07/07/2011] [Indexed: 01/20/2023]
Abstract
Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD finger (PHD(UHRF1)), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHD(UHRF1) bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHD(UHRF1) binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.
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Affiliation(s)
- Eerappa Rajakumara
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Zhentian Wang
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Honghui Ma
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lulu Hu
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hao Chen
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yan Lin
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Rui Guo
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Feizhen Wu
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Haitao Li
- Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fei Lan
- Constellation Pharmaceuticals, Cambridge, MA 02140, USA
| | - Yujiang Geno Shi
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Xu
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Yang Shi
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Department of Biochemistry, Fudan University Medical School, Shanghai 200032, China.,Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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34
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Fournier A, Sasai N, Nakao M, Defossez PA. The role of methyl-binding proteins in chromatin organization and epigenome maintenance. Brief Funct Genomics 2011; 11:251-64. [PMID: 22184333 DOI: 10.1093/bfgp/elr040] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Methylated DNA can be specifically recognized by a set of proteins called methyl-CpG-binding proteins (MBPs), which belong to three different structural families in mammals: the MBD family, the Kaiso and Kaiso-like proteins and the SRA domain proteins. A current view is that, once bound to methylated DNA, MBPs translate the DNA methylation signal into appropriate functional states, through interactions with diverse partners. However, if some of the biological functions of MBPs have been widely described--notably transcriptional repression--others are poorly understood, and more generally the extent of MBP activities remains unclear. Here we propose to discuss the role of MBPs in two crucial nuclear events: chromatin organization and epigenome maintenance. Finally, important challenges for future research as well as for biomedical applications in pathologies such as cancers--in which DNA methylation patterns are widely altered--will be mentioned.
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Affiliation(s)
- Alexandra Fournier
- Institut National du Cancer (INCa), CNRS UMR7216/Université Paris Diderot, Paris, France
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35
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Pichler G, Wolf P, Schmidt CS, Meilinger D, Schneider K, Frauer C, Fellinger K, Rottach A, Leonhardt H. Cooperative DNA and histone binding by Uhrf2 links the two major repressive epigenetic pathways. J Cell Biochem 2011; 112:2585-93. [PMID: 21598301 PMCID: PMC3569875 DOI: 10.1002/jcb.23185] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Gene expression is regulated by DNA as well as histone modifications but the crosstalk and mechanistic link between these epigenetic signals are still poorly understood. Here we investigate the multi-domain protein Uhrf2 that is similar to Uhrf1, an essential cofactor of maintenance DNA methylation. Binding assays demonstrate a cooperative interplay of Uhrf2 domains that induces preference for hemimethylated DNA, the substrate of maintenance methylation, and enhances binding to H3K9me3 heterochromatin marks. FRAP analyses revealed that localization and binding dynamics of Uhrf2 in vivo require an intact tandem Tudor domain and depend on H3K9 trimethylation but not on DNA methylation. Besides the cooperative DNA and histone binding that is characteristic for Uhrf2, we also found an opposite expression pattern of uhrf1 and uhrf2 during differentiation. While uhrf1 is mainly expressed in pluripotent stem cells, uhrf2 is upregulated during differentiation and highly expressed in differentiated mouse tissues. Ectopic expression of Uhrf2 in uhrf1−/− embryonic stem cells did not restore DNA methylation at major satellites indicating functional differences. We propose that the cooperative interplay of Uhrf2 domains may contribute to a tighter epigenetic control of gene expression in differentiated cells.
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Affiliation(s)
- Garwin Pichler
- Ludwig Maximilians University Munich, Department of Biology II and Center for Integrated Protein Science Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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Xie S, Jakoncic J, Qian C. UHRF1 double tudor domain and the adjacent PHD finger act together to recognize K9me3-containing histone H3 tail. J Mol Biol 2011; 415:318-28. [PMID: 22100450 DOI: 10.1016/j.jmb.2011.11.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 10/03/2011] [Accepted: 11/07/2011] [Indexed: 11/19/2022]
Abstract
Human multi-domain-containing protein UHRF1 has recently been extensively characterized as a key epigenetic regulator for maintaining DNA methylation patterns. UHRF1 SRA domain preferentially binds to hemimethylated CpG sites, and double Tudor domain has been implicated in recognizing H3K9me3 mark, but the role of the adjacent PHD finger remains unclear. Here, we report the high-resolution crystal structure of UHRF1 PHD finger in complex with N-terminal tail of histone H3. We found that the preceding zinc-Cys4 knuckle is indispensable for the PHD finger of UHRF1 to recognize the first four unmodified residues of histone H3 N-terminal tail. Quantitative binding studies indicated that UHRF1 PHD finger (including the preceding zinc-Cys4 knuckle) acts together with the adjacent double Tudor domain to specifically recognize the H3K9me3 mark. Combinatorial recognition of H3K9me3-containing histone H3 tail by UHRF1 PHD finger and double Tudor domain may play a role in establishing and maintaining histone H3K9 methylation patterns during the cell cycle.
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Affiliation(s)
- Si Xie
- Department of Biochemistry, The University of Hong Kong, Hong Kong, China
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The PHD finger of human UHRF1 reveals a new subgroup of unmethylated histone H3 tail readers. PLoS One 2011; 6:e27599. [PMID: 22096602 PMCID: PMC3214078 DOI: 10.1371/journal.pone.0027599] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/20/2011] [Indexed: 11/20/2022] Open
Abstract
The human UHRF1 protein (ubiquitin-like containing PHD and RING finger domains 1) has emerged as a potential cancer target due to its implication in cell cycle regulation, maintenance of DNA methylation after replication and heterochromatin formation. UHRF1 functions as an adaptor protein that binds to histones and recruits histone modifying enzymes, like HDAC1 or G9a, which exert their action on chromatin. In this work, we show the binding specificity of the PHD finger of human UHRF1 (huUHRF1-PHD) towards unmodified histone H3 N-terminal tail using native gel electrophoresis and isothermal titration calorimetry. We report the molecular basis of this interaction by determining the crystal structure of huUHRF1-PHD in complex with the histone H3 N-terminal tail. The structure reveals a new mode of histone recognition involving an extra conserved zinc finger preceding the conventional PHD finger region. This additional zinc finger forms part of a large surface cavity that accommodates the side chain of the histone H3 lysine K4 (H3K4) regardless of its methylation state. Mutation of Q330, which specifically interacts with H3K4, to alanine has no effect on the binding, suggesting a loose interaction between huUHRF1-PHD and H3K4. On the other hand, the recognition appears to rely on histone H3R2, which fits snugly into a groove on the protein and makes tight interactions with the conserved aspartates D334 and D337. Indeed, a mutation of the former aspartate disrupts the formation of the complex, while mutating the latter decreases the binding affinity nine-fold.
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Chu J, Loughlin EA, Gaur NA, SenBanerjee S, Jacob V, Monson C, Kent B, Oranu A, Ding Y, Ukomadu C, Sadler KC. UHRF1 phosphorylation by cyclin A2/cyclin-dependent kinase 2 is required for zebrafish embryogenesis. Mol Biol Cell 2011; 23:59-70. [PMID: 22072796 PMCID: PMC3248904 DOI: 10.1091/mbc.e11-06-0487] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Although UHRF1 is essential for many epigenetic marks, the mechanism that regulates UHRF1 is not understood. This study shows that a key component of the cell cycle machinery—cyclin-dependent kinase 2/cyclin A2—phosphorylates UHRF1 and that this phosphorylation is essential for early zebrafish development. Ubiquitin-like, containing PHD and RING finger domains 1 (uhrf1) is regulated at the transcriptional level during the cell cycle and in developing zebrafish embryos. We identify phosphorylation as a novel means of regulating UHRF1 and demonstrate that Uhrf1 phosphorylation is required for gastrulation in zebrafish. Human UHRF1 contains a conserved cyclin-dependent kinase 2 (CDK2) phosphorylation site at Ser-661 that is phosphorylated in vitro by CDK2 partnered with cyclin A2 (CCNA2), but not cyclin E. An antibody specific for phospho-Ser-661 recognizes UHRF1 in both mammalian cancer cells and in nontransformed zebrafish cells, but not in zebrafish bearing a mutation in ccna2. Depleting Uhrf1 from zebrafish embryos by morpholino injection causes arrest before gastrulation and early embryonic death. This phenotype is rescued by wild-type UHRF1, but not by UHRF1 in which the phospho-acceptor site is mutated, demonstrating that UHRF1 phosphorylation is essential for embryogenesis. UHRF1 was detected in the nucleus and cytoplasm, whereas nonphosphorylatable UHRF1 is unable to localize to the cytoplasm, suggesting the importance of localization in UHRF1 function. Together, these data point to an essential role for UHRF1 phosphorylation by CDK/CCNA2 during early vertebrate development.
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Affiliation(s)
- Jaime Chu
- Division of Pediatric Hepatology, Department of Pediatrics, Mount Sinai School of Medicine, New York, NY 10029, USA
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S phase-dependent interaction with DNMT1 dictates the role of UHRF1 but not UHRF2 in DNA methylation maintenance. Cell Res 2011; 21:1723-39. [PMID: 22064703 DOI: 10.1038/cr.2011.176] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent studies demonstrate that UHRF1 is required for DNA methylation maintenance by targeting DNMT1 to DNA replication foci, presumably through its unique hemi-methylated DNA-binding activity and interaction with DNMT1. UHRF2, another member of the UHRF family proteins, is highly similar to UHRF1 in both sequence and structure, raising questions about its role in DNA methylation. In this study, we demonstrate that, like UHRF1, UHRF2 also binds preferentially to methylated histone H3 lysine 9 (H3K9) through its conserved tudor domain and hemi-methylated DNA through the SET and Ring associated domain. Like UHRF1, UHRF2 is enriched in pericentric heterochromatin. The heterochromatin localization depends to large extent on its methylated H3K9-binding activity and to less extent on its methylated DNA-binding activity. Coimmunoprecipitation experiments demonstrate that both UHRF1 and UHRF2 interact with DNMT1, DNMT3a, DNMT3b and G9a. Despite all these conserved functions, we find that UHRF2 is not able to rescue the DNA methylation defect in Uhrf1 null mouse embryonic stem cells. This can be attributed to the inability for UHRF2 to recruit DNMT1 to replication foci during S phase of the cell cycle. Indeed, we find that while UHRF1 interacts with DNMT1 in an S phase-dependent manner in cells, UHRF2 does not. Thus, our study demonstrates that UHRF2 and UHRF1 are not functionally redundant in DNA methylation maintenance and reveals the cell-cycle-dependent interaction between UHRF1 and DNMT1 as a key regulatory mechanism targeting DNMT1 for DNA methylation.
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Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood 2011; 118:3559-69. [PMID: 21828137 PMCID: PMC3186332 DOI: 10.1182/blood-2011-06-357996] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 07/29/2011] [Indexed: 11/20/2022] Open
Abstract
The phenotype of germinal center (GC) B cells includes the unique ability to tolerate rapid proliferation and the mutagenic actions of activation induced cytosine deaminase (AICDA). Given the importance of epigenetic patterning in determining cellular phenotypes, we examined DNA methylation and the role of DNA methyltransferases in the formation of GCs. DNA methylation profiling revealed a marked shift in DNA methylation patterning in GC B cells versus resting/naive B cells. This shift included significant differential methylation of 235 genes, with concordant inverse changes in gene expression affecting most notably genes of the NFkB and MAP kinase signaling pathways. GC B cells were predominantly hypomethylated compared with naive B cells and AICDA binding sites were highly overrepresented among hypomethylated loci. GC B cells also exhibited greater DNA methylation heterogeneity than naive B cells. Among DNA methyltransferases (DNMTs), only DNMT1 was significantly up-regulated in GC B cells. Dnmt1 hypomorphic mice displayed deficient GC formation and treatment of mice with the DNA methyltransferase inhibitor decitabine resulted in failure to form GCs after immune stimulation. Notably, the GC B cells of Dnmt1 hypomorphic animals showed evidence of increased DNA damage, suggesting dual roles for DNMT1 in DNA methylation and double strand DNA break repair.
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Affiliation(s)
- Rita Shaknovich
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
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Defossez PA, Stancheva I. Biological functions of methyl-CpG-binding proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:377-98. [PMID: 21507359 DOI: 10.1016/b978-0-12-387685-0.00012-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA methylation is a stable epigenetic mark in plant and vertebrate genomes; it is implicated in regulation of higher order chromatin structure, maintenance of genome integrity, and stable patterns of gene expression. Biological effects of DNA methylation are, at least in part, mediated by proteins that preferentially bind to methylated DNA. It is now recognized that several structurally unrelated protein folds have the ability to recognize methylated CpGs in vitro and in vivo. In this chapter, we focus on the three major families of methyl-CpG-binding proteins: the MBD protein family, Kaiso and Kaiso-like proteins, and SRA domain proteins. We discuss the structural bases of methyl-CpG recognition, the function and specific properties of individual proteins, and their role in human disease such as Rett syndrome and cancer.
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Crystal structure of PHD domain of UHRF1 and insights into recognition of unmodified histone H3 arginine residue 2. Cell Res 2011; 21:1374-8. [PMID: 21808300 DOI: 10.1038/cr.2011.124] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, Achour M, Xue S, Duan S, Allali-Hassani A, Zuo X, Wang YX, Bronner C, Chédin F, Arrowsmith CH, Dhe-Paganon S. Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J Biol Chem 2011; 286:24300-11. [PMID: 21489993 PMCID: PMC3129210 DOI: 10.1074/jbc.m111.234104] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 03/27/2011] [Indexed: 11/06/2022] Open
Abstract
Histone modifications and DNA methylation represent two layers of heritable epigenetic information that regulate eukaryotic chromatin structure and gene activity. UHRF1 is a unique factor that bridges these two layers; it is required for maintenance DNA methylation at hemimethylated CpG sites, which are specifically recognized through its SRA domain and also interacts with histone H3 trimethylated on lysine 9 (H3K9me3) in an unspecified manner. Here we show that UHRF1 contains a tandem Tudor domain (TTD) that recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). Solution NMR and crystallographic data reveal the TTD simultaneously recognizes H3K9me3 through a conserved aromatic cage in the first Tudor subdomain and unmodified H3K4 within a groove between the tandem subdomains. The subdomains undergo a conformational adjustment upon peptide binding, distinct from previously reported mechanisms for dual histone mark recognition. Mutant UHRF1 protein deficient for H3K4me0/K9me3 binding shows altered localization to heterochromatic chromocenters and fails to reduce expression of a target gene, p16(INK4A), when overexpressed. Our results demonstrate a novel recognition mechanism for the combinatorial readout of histone modification states associated with gene silencing and add to the growing evidence for coordination of, and cross-talk between, the modification states of H3K4 and H3K9 in regulation of gene expression.
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Affiliation(s)
- Nataliya Nady
- From the Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alexander Lemak
- From the Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - John R. Walker
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - George V. Avvakumov
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Michael S. Kareta
- the Department of Molecular & Cellular Biology, University of California, Davis, California 95616
| | - Mayada Achour
- CNRS UMR7213, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, 74 route du rhin, 67401 Illkirch cedex, France
| | - Sheng Xue
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Shili Duan
- From the Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | | | - Xiaobing Zuo
- the Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, and
| | - Yun-Xing Wang
- the Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, and
| | - Christian Bronner
- CNRS UMR7213, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, 74 route du rhin, 67401 Illkirch cedex, France
| | - Frédéric Chédin
- the Department of Molecular & Cellular Biology, University of California, Davis, California 95616
| | - Cheryl H. Arrowsmith
- From the Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Sirano Dhe-Paganon
- the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- the Department of Physiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada
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Hsieh CL, Lin CL, Liu H, Chang YJ, Shih CJ, Zhong CZ, Lee SC, Tan BCM. WDHD1 modulates the post-transcriptional step of the centromeric silencing pathway. Nucleic Acids Res 2011; 39:4048-62. [PMID: 21266480 PMCID: PMC3105424 DOI: 10.1093/nar/gkq1338] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The centromere is a highly specialized chromosomal element that is essential for chromosome segregation during mitosis. Centromere integrity must therefore be properly preserved and is strictly dependent upon the establishment and maintenance of surrounding chromatin structure. Here we identify WDHD1, a WD40-domain and HMG-domain containing protein, as a key regulator of centromere function. We show that WDHD1 associates with centromeres in a cell cycle-dependent manner, coinciding with mid-to-late S phase. WDHD1 down-regulation compromises HP1α localization to pericentric heterochromatin and leads to altered expression of epigenetic markers associated with this chromatin region. As a consequence, such reduced epigenetic silencing is manifested in disrupted heterochromatic state of the centromere and a defective mitosis. Moreover, we demonstrate that a possible underlying mechanism of WDHD1's involvement lies in the proper generation of the small non-coding RNAs encoded by the centromeric satellite repeats. This role is mediated at the post-transcriptional level and likely through stabilizing Dicer association with centromeric RNA. Collectively, these findings suggest that WDHD1 may be a critical component of the RNA-dependent epigenetic control mechanism that sustains centromere integrity and genomic stability.
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Affiliation(s)
- Chia-Ling Hsieh
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
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Murr R. Interplay between different epigenetic modifications and mechanisms. ADVANCES IN GENETICS 2010; 70:101-41. [PMID: 20920747 DOI: 10.1016/b978-0-12-380866-0.60005-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cellular functions including transcription regulation, DNA repair, and DNA replication need to be tightly regulated. DNA sequence can contribute to the regulation of these mechanisms. This is exemplified by the consensus sequences that allow the binding of specific transcription factors, thus regulating transcription rates. Another layer of regulation resides in modifications that do not affect the DNA sequence itself but still results in the modification of chromatin structure and properties, thus affecting the readout of the underlying DNA sequence. These modifications are dubbed as "epigenetic modifications" and include, among others, histone modifications, DNA methylation, and small RNAs. While these events can independently regulate cellular mechanisms, recent studies indicate that joint activities of different epigenetic modifications could result in a common outcome. In this chapter, I will attempt to recapitulate the best known examples of collaborative activities between epigenetic modifications. I will emphasize mostly on the effect of crosstalks between epigenetic modifications on transcription regulation, simply because it is the most exposed and studied aspect of epigenetic interactions. I will also summarize the effect of epigenetic interactions on DNA damage response and DNA repair. The involvement of epigenetic crosstalks in cancer formation, progression, and treatment will be emphasized throughout the manuscript. Due to space restrictions, additional aspects involving histone replacements [Park, Y. J., and Luger, K. (2008). Histone chaperones in nucleosome eviction and histone exchange. Curr. Opin. Struct. Biol.18, 282-289.], histone variants [Boulard, M., Bouvet, P., Kundu, T. K., and Dimitrov, S. (2007). Histone variant nucleosomes: Structure, function and implication in disease. Subcell. Biochem. 41, 71-89; Talbert, P. B., and Henikoff, S. (2010). Histone variants-Ancient wrap artists of the epigenome. Nat. Rev. Mol. Cell Biol.11, 264-275.], and histone modification readers [de la Cruz, X., Lois, S., Sanchez-Molina, S., and Martinez-Balbas, M. A. (2005). Do protein motifs read the histone code? Bioessays27, 164-175; Grewal, S. I., and Jia, S. (2007). Heterochromatin revisited. Nat. Rev. Genet.8, 35-46.] will not be addressed in depth in this chapter, and the reader is referred to the reviews cited here.
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Affiliation(s)
- Rabih Murr
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66,4058 Basel, Switzerland
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47
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Yap KL, Zhou MM. Keeping it in the family: diverse histone recognition by conserved structural folds. Crit Rev Biochem Mol Biol 2010; 45:488-505. [PMID: 20923397 DOI: 10.3109/10409238.2010.512001] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epigenetic regulation of gene transcription relies on an array of recurring structural domains that have evolved to recognize post-translational modifications on histones. The roles of bromodomains, PHD fingers, and the Royal family domains in the recognition of histone modifications to direct transcription have been well characterized. However, only through recent structural studies has it been realized that these basic folds are capable of interacting with increasingly more complex histone modification landscapes, illuminating how nature has concocted a way to accomplish more with less. Here we review the recent biochemical and structural studies of several conserved folds that recognize modified as well as unmodified histone sequences, and discuss their implications on gene expression.
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Affiliation(s)
- Kyoko L Yap
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY, USA
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Mistry H, Tamblyn L, Butt H, Sisgoreo D, Gracias A, Larin M, Gopalakrishnan K, Hande MP, McPherson JP. UHRF1 is a genome caretaker that facilitates the DNA damage response to gamma-irradiation. Genome Integr 2010; 1:7. [PMID: 20678257 PMCID: PMC2914011 DOI: 10.1186/2041-9414-1-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 06/08/2010] [Indexed: 11/10/2022] Open
Abstract
Background DNA double-strand breaks (DSBs) caused by ionizing radiation or by the stalling of DNA replication forks are among the most deleterious forms of DNA damage. The ability of cells to recognize and repair DSBs requires post-translational modifications to histones and other proteins that facilitate access to lesions in compacted chromatin, however our understanding of these processes remains incomplete. UHRF1 is an E3 ubiquitin ligase that has previously been linked to events that regulate chromatin remodeling and epigenetic maintenance. Previous studies have demonstrated that loss of UHRF1 increases the sensitivity of cells to DNA damage however the role of UHRF1 in this response is unclear. Results We demonstrate that UHRF1 plays a critical role for facilitating the response to DSB damage caused by γ-irradiation. UHRF1-depleted cells exhibit increased sensitivity to γ-irradiation, suggesting a compromised cellular response to DSBs. UHRF1-depleted cells show impaired cell cycle arrest and an impaired accumulation of histone H2AX phosphorylation (γH2AX) in response to γ-irradiation compared to control cells. We also demonstrate that UHRF1 is required for genome integrity, in that UHRF1-depleted cells displayed an increased frequency of chromosomal aberrations compared to control cells. Conclusions Our findings indicate a critical role for UHRF1 in maintenance of chromosome integrity and an optimal response to DSB damage.
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Affiliation(s)
- Helena Mistry
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Laura Tamblyn
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Hussein Butt
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Daniel Sisgoreo
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Aileen Gracias
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Meghan Larin
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
| | - Kalpana Gopalakrishnan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - John Peter McPherson
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5 S 1A8, Canada
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Siaud N, Dubois E, Massot S, Richaud A, Dray E, Collier J, Doutriaux MP. The SOS screen in Arabidopsis: a search for functions involved in DNA metabolism. DNA Repair (Amst) 2010; 9:567-78. [PMID: 20227352 DOI: 10.1016/j.dnarep.2010.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/08/2010] [Accepted: 02/10/2010] [Indexed: 11/19/2022]
Abstract
The SOS screen, as originally described by Perkins et al. (1999) [7], was setup with the aim of identifying Arabidopsis functions that might potentially be involved in the DNA metabolism. Such functions, when expressed in bacteria, are prone to disturb replication and thus trigger the SOS response. Consistently, expression of AtRAD51 and AtDMC1 induced the SOS response in bacteria, even affecting E. coli viability. 100 SOS-inducing cDNAs were isolated from a cDNA library constructed from an Arabidopsis cell suspension that was found to highly express meiotic genes. A large proportion of these SOS(+) candidates are clearly related to the DNA metabolism, others could be involved in the RNA metabolism, while the remaining cDNAs encode either totally unknown proteins or proteins that were considered as irrelevant. Seven SOS(+) candidate genes are induced following gamma irradiation. The in planta function of several of the SOS-inducing clones was investigated using T-DNA insertional mutants or RNA interference. Only one SOS(+) candidate, among those examined, exhibited a defined phenotype: silenced plants for DUT1 were sensitive to 5-fluoro-uracil (5FU), as is the case of the leaky dut-1 mutant in E. coli that are affected in dUTPase activity. dUTPase is essential to prevent uracil incorporation in the course of DNA replication.
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Affiliation(s)
- Nicolas Siaud
- Institut de Biologie des Plantes, CNRS UMR8618, Bâtiment 630, Université Paris Sud 11, 91405 Orsay Cedex, France.
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Musselman CA, Kutateladze TG. PHD fingers: epigenetic effectors and potential drug targets. Mol Interv 2010; 9:314-23. [PMID: 20048137 DOI: 10.1124/mi.9.6.7] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The plant homeodomain (PHD) finger is found in many chromatin-remodeling proteins. This small approximately 65-residue domain functions as an "effector" that binds specific epigenetic marks on histone tails, recruiting transcription factors and nucleosome-associated complexes to chromatin. Mutations in the PHD finger or deletion of this domain are linked to a number of human diseases, including cancer, mental retardation, and immunodeficiency. PHD finger-containing proteins may become valuable diagnostic markers and targets to prevent and treat these disorders. In this review, we highlight the progress recently made in understanding the functional significance of chromatin targeting by mammalian PHD fingers, detail the molecular mechanisms and structural features of "histone code" recognition, and discuss the therapeutic potential of PHD fingers.
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