1
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Liu CC, Chen L, Cai YW, Chen YF, Liu YM, Zhou YJ, Shao ZM, Yu KD. Targeting EMSY-mediated methionine metabolism is a potential therapeutic strategy for triple-negative breast cancer. Cell Rep Med 2024; 5:101396. [PMID: 38290515 PMCID: PMC10897545 DOI: 10.1016/j.xcrm.2024.101396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
Cancer stem cells (CSCs) are the most intractable subpopulation of triple-negative breast cancer (TNBC) cells, which have been associated with a high risk of relapse and poor prognosis. However, eradication of CSCs continues to be difficult. Here, we integrate the multiomics data of a TNBC cohort (n = 360) to identify vital markers of CSCs. We discover that EMSY, inducing a BRCAness phenotype, is preferentially expressed in breast CSCs, promotes ALDH+ cells enrichment, and is positively correlated with poor relapse-free survival. Mechanistically, EMSY competitively binds to the Jmjc domain, which is critical for KDM5B enzyme activity, to reshape methionine metabolism, and to promote CSC self-renewal and tumorigenesis in an H3K4 methylation-dependent manner. Moreover, EMSY accumulation in TNBC cells sensitizes them to PARP inhibitors against bulk cells and methionine deprivation against CSCs. These findings indicate that clinically relevant eradication of CSCs could be achieved with a strategy that targets CSC-specific vulnerabilities in amino acid metabolism.
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Affiliation(s)
- Cui-Cui Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Lie Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Wen Cai
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Fei Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yi-Ming Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yu-Jie Zhou
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ke-Da Yu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center and Cancer Institute, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China.
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2
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Sokolova V, Miratsky J, Svetlov V, Brenowitz M, Vant J, Lewis T, Dryden K, Lee G, Sarkar S, Nudler E, Singharoy A, Tan D. Structural mechanism of HP1α-dependent transcriptional repression and chromatin compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569387. [PMID: 38076844 PMCID: PMC10705452 DOI: 10.1101/2023.11.30.569387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Heterochromatin protein 1 (HP1) plays a central role in establishing and maintaining constitutive heterochromatin. However, the mechanisms underlying HP1-nucleosome interactions and their contributions to heterochromatin functions remain elusive. In this study, we employed a multidisciplinary approach to unravel the interactions between human HP1α and nucleosomes. We have elucidated the cryo-EM structure of an HP1α dimer bound to an H2A.Z nucleosome, revealing that the HP1α dimer interfaces with nucleosomes at two distinct sites. The primary binding site is located at the N-terminus of histone H3, specifically at the trimethylated K9 (K9me3) region, while a novel secondary binding site is situated near histone H2B, close to nucleosome superhelical location 4 (SHL4). Our biochemical data further demonstrates that HP1α binding influences the dynamics of DNA on the nucleosome. It promotes DNA unwrapping near the nucleosome entry and exit sites while concurrently restricting DNA accessibility in the vicinity of SHL4. This study offers a model that explains how HP1α functions in heterochromatin maintenance and gene silencing, particularly in the context of H3K9me-dependent mechanisms. Additionally, it sheds light on the H3K9me-independent role of HP1 in responding to DNA damage.
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Affiliation(s)
- Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Jacob Miratsky
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Vladimir Svetlov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael Brenowitz
- Departments of Biochemistry and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John Vant
- School of Molecular Sciences, Arizona State University; Tempe, AZ, USA
| | - Tyler Lewis
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Kelly Dryden
- Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903 USA
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
| | - Shayan Sarkar
- Department of Pathology, Stony Brook University; Stony Brook, New York, 11794 USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University; Stony Brook, NY, USA
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3
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Jin Z, Yu B, Huang Y. Structural insights into the chromodomain of Oxpecker in complex with histone H3 lysine 9 trimethylation reveal a transposon silencing mechanism by heterodimerization. Biochem Biophys Res Commun 2023; 652:95-102. [PMID: 36841100 DOI: 10.1016/j.bbrc.2023.02.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 02/21/2023]
Abstract
Oxpecker, the homolog of Rhino/HP1D, exclusively expressed in Drosophila ovaries, belongs to the Heterochromatin Protein 1 family, as does Rhino. Rhi recognizes piRNA clusters enriched with the heterochromatin marker H3K9me3 via its N-terminal chromodomain and recruits Deadlock via its C-terminal chromoshadow domain, further recruits Moonshiner, a paralog of the TATA box-binding protein-related factor 2 large subunits, to promote transcription of piRNA precursors, thereby protecting the genome. Despite Oxp possessing only the chromodomain, its loss leads to the upregulation of transposons in the female germline. In this study, we solved the crystal structure of the Oxp chromodomain in complex with the histone H3K9me3 peptide. As the Oxp chromodomain dimerizes, two H3K9me3 peptides bind to the Oxp chromodomain in an antiparallel manner. ITC experiments and site-directed mutagenesis experiments showed that E44 determines Oxp's five-fold stronger binding ability to H3K9me3 than that of Rhi. In addition, we found that Oxp and Rhi can form a heterodimer, which may shed light on the molecular mechanism by which Oxp regulates transposon silencing in the absence of CSD.
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Affiliation(s)
- Zhaohui Jin
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, 200092, China
| | - Bowen Yu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ying Huang
- Department of General Surgery, Shanghai Key Laboratory of Biliary Tract Disease Research, State Key Laboratory of Oncogenes and Related Genes, Xinhua Hospital, Shanghai Jiao Tong University, Shanghai, 200092, China.
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4
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Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast. Biomolecules 2023; 13:biom13020377. [PMID: 36830746 PMCID: PMC9953268 DOI: 10.3390/biom13020377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
DNA is stored in the nucleus of a cell in a folded state; however, only the necessary genetic information is extracted from the required group of genes. The key to extracting genetic information is chromatin ambivalence. Depending on the chromosomal region, chromatin is characterized into low-density "euchromatin" and high-density "heterochromatin", with various factors being involved in its regulation. Here, we focus on chromatin regulation and gene expression by the yeast FACT complex, which functions in both euchromatin and heterochromatin. FACT is known as a histone H2A/H2B chaperone and was initially reported as an elongation factor associated with RNA polymerase II. In budding yeast, FACT activates promoter chromatin by interacting with the transcriptional activators SBF/MBF via the regulation of G1/S cell cycle genes. In fission yeast, FACT plays an important role in the formation of higher-order chromatin structures and transcriptional repression by binding to Swi6, an HP1 family protein, at heterochromatin. This FACT property, which refers to the alternate chromatin-regulation depending on the binding partner, is an interesting phenomenon. Further analysis of nucleosome regulation within heterochromatin is expected in future studies.
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5
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Fraser CJ, Whitehall SK. Heterochromatin in the fungal plant pathogen, Zymoseptoria tritici: Control of transposable elements, genome plasticity and virulence. Front Genet 2022; 13:1058741. [DOI: 10.3389/fgene.2022.1058741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Heterochromatin is a repressive chromatin state that plays key roles in the functional organisation of eukaryotic genomes. In fungal plant pathogens, effector genes that are required for host colonization tend to be associated with heterochromatic regions of the genome that are enriched with transposable elements. It has been proposed that the heterochromatin environment silences effector genes in the absence of host and dynamic chromatin remodelling facilitates their expression during infection. Here we discuss this model in the context of the key wheat pathogen, Zymoseptoria tritici. We cover progress in understanding the deposition and recognition of heterochromatic histone post translational modifications in Z. tritici and the role that heterochromatin plays in control of genome plasticity and virulence.
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6
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Mahood T, Pascoe CD, Karakach TK, Jha A, Basu S, Ezzati P, Spicer V, Mookherjee N, Halayko AJ. Integrating Proteomes for Lung Tissues and Lavage Reveals Pathways That Link Responses in Allergen-Challenged Mice. ACS OMEGA 2021; 6:1171-1189. [PMID: 33490776 PMCID: PMC7818314 DOI: 10.1021/acsomega.0c04269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
To capture interplay between biological pathways, we analyzed the proteome from matched lung tissues and bronchoalveolar lavage fluid (BALF) of individual allergen-naïve and house dust mite (HDM)-challenged BALB/c mice, a model of allergic asthma. Unbiased label-free liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis quantified 2675 proteins from tissues and BALF of allergen-naïve and HDM-exposed mice. In comparing the four datasets, we found significantly greater diversity in proteins between lung tissues and BALF than in the changes induced by HDM challenge. The biological pathways enriched after allergen exposure were compartment-dependent. Lung tissues featured innate immune responses and oxidative stress, while BALF most strongly revealed changes in metabolism. We combined lung tissues and BALF proteomes, which principally highlighted oxidation reduction (redox) pathways, a finding influenced chiefly by the lung tissue dataset. Integrating lung and BALF proteomes also uncovered new proteins and biological pathways that may mediate lung tissue and BALF interactions after allergen challenge, for example, B-cell receptor signaling. We demonstrate that enhanced insight is fostered when different biological compartments from the lung are investigated in parallel. Integration of proteomes from lung tissues and BALF compartments reveals new information about protein networks in response to environmental challenge and interaction between intracellular and extracellular processes.
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Affiliation(s)
- Thomas
H. Mahood
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Christopher D. Pascoe
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Tobias K. Karakach
- Bioinformatics
Core Laboratory, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E
3P4, Canada
| | - Aruni Jha
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Sujata Basu
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Peyman Ezzati
- Manitoba
Centre for Proteomics and Systems Biology, Department of Internal
Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Victor Spicer
- Manitoba
Centre for Proteomics and Systems Biology, Department of Internal
Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
| | - Neeloffer Mookherjee
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Manitoba
Centre for Proteomics and Systems Biology, Department of Internal
Medicine, University of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Department
of Immunology, University of Manitoba, Winnipeg, Manitoba R3E 0T5, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
| | - Andrew J. Halayko
- Department
of Physiology & Pathophysiology, University
of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- DEVOTION
Network, Winnipeg, Manitoba R3E 3P4, Canada
- Biology
of Breathing Group, Children’s Hospital
Research Institute of Manitoba, Winnipeg, Manitoba R3E 3P4, Canada
- Canadian
Respiratory Research Network, Ottawa, Ontario K2E 7V7, Canada
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7
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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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8
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Pokorná P, Krepl M, Bártová E, Šponer J. Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network. J Chem Theory Comput 2019; 15:5659-5673. [DOI: 10.1021/acs.jctc.9b00434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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9
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Fonti G, Marcaida MJ, Bryan LC, Träger S, Kalantzi AS, Helleboid PYJ, Demurtas D, Tully MD, Grudinin S, Trono D, Fierz B, Dal Peraro M. KAP1 is an antiparallel dimer with a functional asymmetry. Life Sci Alliance 2019; 2:2/4/e201900349. [PMID: 31427381 PMCID: PMC6701479 DOI: 10.26508/lsa.201900349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 01/10/2023] Open
Abstract
This study reveals the architecture of human KAP1 by integrating molecular modeling with small-angle X-ray scattering and single-molecule experiments. KAP1 dimers feature a structural asymmetry at the C-terminal domains that has functional implications for recruitment of HP1. KAP1 (KRAB domain–associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular interactions and as an E3 small ubiquitin modifier ligase. This work sheds light on the overall organization of the full-length protein combining solution scattering data, integrative modeling, and single-molecule experiments. We show that KAP1 is an elongated antiparallel dimer with an asymmetry at the C-terminal domains. This conformation is consistent with the finding that the Really Interesting New Gene (RING) domain contributes to KAP1 auto-SUMOylation. Importantly, this intrinsic asymmetry has key functional implications for the KAP1 network of interactions, as the heterochromatin protein 1 (HP1) occupies only one of the two putative HP1 binding sites on the KAP1 dimer, resulting in an unexpected stoichiometry, even in the context of chromatin fibers.
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Affiliation(s)
- Giulia Fonti
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Louise C Bryan
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sylvain Träger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra S Kalantzi
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pierre-Yves Jl Helleboid
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Davide Demurtas
- Interdisciplinary Centre for Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mark D Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Sergei Grudinin
- University Grenoble Alpes, Centre National de la Recherche Scientifique, Inria, Grenoble Institut Polytechnique de Grenoble, Laboratoire Jean Kuntzmann, Grenoble, France
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Beat Fierz
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland .,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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10
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Mi J, Yang X, Zhang J, Zhang X, Xu C, Liao S, Tu X. Crystal structure of an ENT domain from Trypanosoma brucei. Biochem Biophys Res Commun 2018; 505:755-760. [PMID: 30293681 DOI: 10.1016/j.bbrc.2018.09.167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 09/26/2018] [Indexed: 11/18/2022]
Abstract
Trypanosoma brucei (T. brucei) is a parasitic protozoan causing human sleeping sickness and related animal diseases. ENT (EMSY N-terminal) domain was first found in EMSY protein which has been proved to be involved in multiple biological processes such as DNA repair, tumorigenesis, and transcriptional regulation. So far, little is known about the function and structure of ENT domains from protozoan. Q385P5 from T. brucei, containing an ENT domain at its N-terminus, is a conserved protein in related kinetoplastid parasites. In this work, the crystal structure of ENT domain of Q385P5 (TbENT) was solved at a resolution of 2.3 Å. TbENT adopts a club-like shape consisting of five helixes, which is similar to the structure of human EMSY ENT domain (HsENT). Interestingly, TbENT shows significantly different orientation on the fifth α-helix compared with HsENT. Meanwhile, human HP1 interacts with a conserved motif adjacent to EMSY ENT domain. However, this conserved binding motif is absent in Q385P5. These differences may imply the different protein interactions and roles of Q385P5 and its ENT domain in T. brucei.
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Affiliation(s)
- Juan Mi
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Xiao Yang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Jiahai Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Xuecheng Zhang
- School of Life Science, Anhui University, Hefei, Anhui, 230027, PR China
| | - Chao Xu
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Shanhui Liao
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, PR China.
| | - Xiaoming Tu
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, PR China.
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11
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Yu B, Lin YA, Parhad SS, Jin Z, Ma J, Theurkauf WE, Zhang ZZ, Huang Y. Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification. EMBO Rep 2018; 19:embr.201745418. [PMID: 29858487 DOI: 10.15252/embr.201745418] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/28/2018] [Accepted: 05/14/2018] [Indexed: 11/09/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) silence transposons in germ cells to maintain genome stability and animal fertility. Rhino, a rapidly evolving heterochromatin protein 1 (HP1) family protein, binds Deadlock in a species-specific manner and so defines the piRNA-producing loci in the Drosophila genome. Here, we determine the crystal structures of Rhino-Deadlock complex in Drosophila melanogaster and simulans In both species, one Rhino binds the N-terminal helix-hairpin-helix motif of one Deadlock protein through a novel interface formed by the beta-sheet in the Rhino chromoshadow domain. Disrupting the interface leads to infertility and transposon hyperactivation in flies. Our structural and functional experiments indicate that electrostatic repulsion at the interaction interface causes cross-species incompatibility between the sibling species. By determining the molecular architecture of this piRNA-producing machinery, we discover a novel HP1-partner interacting mode that is crucial to piRNA biogenesis and transposon silencing. We thus explain the cross-species incompatibility of two sibling species at the molecular level.
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Affiliation(s)
- Bowen Yu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu An Lin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhaohui Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zz Zhao Zhang
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Ying Huang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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12
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Clinical importance of the EMSY gene expression and polymorphisms in ovarian cancer. Oncotarget 2018; 9:17735-17755. [PMID: 29707144 PMCID: PMC5915152 DOI: 10.18632/oncotarget.24878] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 02/28/2018] [Indexed: 11/25/2022] Open
Abstract
EMSY, a BRCA2–associated protein, is amplified and overexpressed in various sporadic cancers. This is the first study assessing the clinical impact of its expression and polymorphisms on ovarian cancer (OvCa) outcome in the context of the chemotherapy regimen used. In 134 frozen OvCa samples, we assessed EMSY mRNA expression with Reverse Transcription-quantitative PCR, and also investigated the EMSY gene sequence using SSCP and/or PCR-sequencing. Clinical relevance of changes in EMSY mRNA expression and DNA sequence was evaluated in two subgroups treated with either taxane/platinum (TP, n=102) or platinum/cyclophosphamide (PC, n=32). High EMSY expression negatively affected overall survival (OS), disease-free survival (DFS) and sensitivity to treatment (PS) in the TP-treated subgroup (p-values: 0.001, 0.002 and 0.010, respectively). Accordingly, our OvCa cell line studies showed that the EMSY gene knockdown sensitized A2780 and IGROV1 cells to paclitaxel. Interestingly, EMSY mRNA expression in surviving cells was similar as in the control cells. Additionally, we identified 24 sequence alterations in the EMSY gene, including the previously undescribed: c.720G>C, p.(Lys240Asn); c.1860G>A, p.(Lys620Lys); c.246-76A>G; c.421+68A>C. In the PC-treated subgroup, a heterozygous genotype comprising five SNPs (rs4300410, rs3814711, rs4245443, rs2508740, rs2513523) negatively correlated with OS (p-value=0.009). The same SNPs exhibited adverse borderline associations with PS in the TP-treated subgroup. This is the first study providing evidence that high EMSY mRNA expression is a negative prognostic and predictive factor in OvCa patients treated with TP, and that the clinical outcome may hinge on certain SNPs in the EMSY gene as well.
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13
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Liu Y, Qin S, Lei M, Tempel W, Zhang Y, Loppnau P, Li Y, Min J. Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1. J Biol Chem 2017; 292:5655-5664. [PMID: 28223359 DOI: 10.1074/jbc.m116.768374] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/16/2017] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PXVXL motif but also with a region of histone H3 that bears the similar PXXVXL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PXXVXL motif of histone H3. The HP1 C-terminal extension enhances the affinity, as does the increasing length of the H3 peptide. The crystal structure of the human HP1γ CSD (CSDγ) in complex with an H3 peptide suggests that recognition of H3 by CSDγ to some extent resembles CSD-PXVXL interaction. Nevertheless, the prolyl residue of the PXXVXL motif appears to play a role distinct from that of Pro in the known HP1β CSD-PXVXL complexes. We consequently generalize the historical CSD-PXVXL interaction model and expand the search scope for additional CSD binding partners.
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Affiliation(s)
- Yanli Liu
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Su Qin
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Ming Lei
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Wolfram Tempel
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Yuzhe Zhang
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Yanjun Li
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and
| | - Jinrong Min
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and .,the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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14
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Swenson JM, Colmenares SU, Strom AR, Costes SV, Karpen GH. The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic. eLife 2016; 5:e16096. [PMID: 27514026 PMCID: PMC4981497 DOI: 10.7554/elife.16096] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin is enriched for specific epigenetic factors including Heterochromatin Protein 1a (HP1a), and is essential for many organismal functions. To elucidate heterochromatin organization and regulation, we purified Drosophila melanogaster HP1a interactors, and performed a genome-wide RNAi screen to identify genes that impact HP1a levels or localization. The majority of the over four hundred putative HP1a interactors and regulators identified were previously unknown. We found that 13 of 16 tested candidates (83%) are required for gene silencing, providing a substantial increase in the number of identified components that impact heterochromatin properties. Surprisingly, image analysis revealed that although some HP1a interactors and regulators are broadly distributed within the heterochromatin domain, most localize to discrete subdomains that display dynamic localization patterns during the cell cycle. We conclude that heterochromatin composition and architecture is more spatially complex and dynamic than previously suggested, and propose that a network of subdomains regulates diverse heterochromatin functions.
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Affiliation(s)
- Joel M Swenson
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Serafin U Colmenares
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Amy R Strom
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Sylvain V Costes
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Gary H Karpen
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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15
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Sleiman PMA, March M, Hakonarson H. The genetic basis of eosinophilic esophagitis. Best Pract Res Clin Gastroenterol 2015; 29:701-707. [PMID: 26552769 DOI: 10.1016/j.bpg.2015.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/02/2015] [Indexed: 01/31/2023]
Abstract
Eosinophilic esophagitis is characterized by destructive responses of the immune system to environmental allergens, including food, on the human esophagus. EoE is now reported as a major cause of upper gastrointestinal morbidity in children and adults and the incidence is reported to be on the increase. It is known that EoE has a high degree of heritability, with a majority of the phenotypic variation believed to be genetic in origin as shown by genetic epidemiology studies of twins and families. Prior to 2010, there were no known genetic risk factors for the disease. Three GWAS have since been published identifying 5 loci which influence risk for EoE in both children and adults. The information gained from GWAS has been of value in elucidating the pathways involved, such as IL4/STAT6, and more unexpected pathways such as epithelial apical transport and wound healing. We will review the results of the EoE GWAS and the known associated genes, concluding with a discussion of some future directions for genetic studies in EoE.
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Affiliation(s)
- Patrick M A Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, PA, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael March
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, PA, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, PA, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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16
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Romeo K, Louault Y, Cantaloube S, Loiodice I, Almouzni G, Quivy JP. The SENP7 SUMO-Protease Presents a Module of Two HP1 Interaction Motifs that Locks HP1 Protein at Pericentric Heterochromatin. Cell Rep 2015; 10:771-782. [PMID: 25660026 DOI: 10.1016/j.celrep.2015.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/08/2014] [Accepted: 12/24/2014] [Indexed: 12/17/2022] Open
Abstract
HP1 enrichment at pericentric heterochromatin is essential for proper chromosome segregation. While H3K9me3 is thought to be a major contributor to HP1 enrichment at pericentric domains, in mouse cells, the SUMO-protease SENP7 is required in addition to H3K9me3. How this is achieved remains elusive. Here, we find that loss of SENP7 leads to an increased time spent in mitosis. Furthermore, we reveal that a short module comprising two consecutive HP1 interaction motifs on SENP7 is the determinant for HP1 enrichment and acts by restricting HP1 mobility at pericentric domains. We propose a mechanism for maintenance of HP1 enrichment in which this module functions on top of H3K9me3 to lock contiguous HP1 molecules already docked on H3K9me3-modified nucleosomes. H3K9me3 would thus promote HP1 enrichment only if a locking system is in place. This mechanism may apply to other nuclear domains to contribute to the control of genome plasticity and integrity.
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Affiliation(s)
- Kelly Romeo
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Yann Louault
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Isabelle Loiodice
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France.
| | - Jean-Pierre Quivy
- Institut Curie, Centre de Recherche, Paris 75248, France; Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France; Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France; Sorbonne University, PSL, Paris 75005, France.
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17
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Wu W, Nishikawa H, Fukuda T, Vittal V, Asano M, Miyoshi Y, Klevit RE, Ohta T. Interaction of BARD1 and HP1 Is Required for BRCA1 Retention at Sites of DNA Damage. Cancer Res 2015; 75:1311-21. [PMID: 25634209 DOI: 10.1158/0008-5472.can-14-2796] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/31/2014] [Indexed: 12/12/2022]
Abstract
Stable retention of BRCA1/BARD1 complexes at sites of DNA damage is required for the proper response to DNA double-strand breaks (DSB). Here, we demonstrate that the BRCT domain of BARD1 is crucial for its retention through interaction with HP1. In response to DNA damage, BARD1 interacts with Lys9-dimethylated histone H3 (H3K9me2) in an ATM-dependent but RNF168-independent manner. This interaction is mediated primarily by HP1γ. A conserved HP1-binding motif in the BARD1 BRCT domain directly interacted with the chromoshadow domain of HP1 in vitro. Mutations in this motif (or simultaneous depletion of all three HP1 isoforms) disrupted retention of BARD1, BRCA1, and CtIP at DSB sites and allowed ectopic accumulation of RIF1, an effector of nonhomologous end-joining, at damaged loci in S-phase. UNC0638, a small-molecule inhibitor of histone lysine methyltransferase (HKMT), abolished retention and cooperated with the PARP inhibitor olaparib to block cancer cell growth. Taken together, our findings show how BARD1 promotes retention of the BRCA1/BARD1 complex at damaged DNA sites and suggest the use of HKMT inhibitors to leverage the application of PARP inhibitors to treat breast cancer.
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Affiliation(s)
- Wenwen Wu
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan. Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Hiroyuki Nishikawa
- Institute of Advanced Medical Science, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Takayo Fukuda
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan
| | - Vinayak Vittal
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Masahide Asano
- Divisions of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Yasuo Miyoshi
- Division of Breast and Endocrine Surgery, Department of Surgery, Hyogo College of Medicine, Hyogo, Japan
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Tomohiko Ohta
- Department of Translational Oncology, St. Marianna University Graduate School of Medicine, Kawasaki, Japan. Division of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University Graduate School of Medicine, Kawasaki, Japan.
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18
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Cianferoni A, Spergel JM, Muir A. Recent advances in the pathological understanding of eosinophilic esophagitis. Expert Rev Gastroenterol Hepatol 2015; 9:1501-10. [PMID: 26470602 PMCID: PMC4943572 DOI: 10.1586/17474124.2015.1094372] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Eosinophilic esophagitis (EoE) is a chronic allergen-mediated inflammatory disease of the esophagus. This inflammation leads to feeding difficulties, failure to thrive and vomiting in young children, and causes food impaction and esophageal stricture in adolescents and adults. In the 20 years since EoE was first described, we have gained a great deal of knowledge regarding the genetic predisposition of disease, the inflammatory milieu associated with EoE and the long-term complications of chronic inflammation. Herein, we summarize the important breakthroughs in the field including both in vitro and in vivo analysis. We discuss insights that we have gained from large-scale unbiased genetic analysis, a multitude of genetically and chemically altered mouse models of EoE and most importantly, the results of clinical trials of various pharmacologic agents. Understanding these successes and failures may be the key to developing more effective therapeutic strategies.
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Affiliation(s)
- Antonella Cianferoni
- Division of Allergy and Immunology, University of Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania.,Corresponding Authors: Antonella Cianferoni, MD, Assistant Professor of Pediatrics, The Children's Hospital of Philadelphia, Division of Allergy and Immunology, 3550 Market Street, Philadelphia, PA 19104, , Amanda Muir, MD, Assistant Professor of Pediatrics, The Children's Hospital of Philadelphia, Division of Gastroenterology, 34 and Civic Center Boulevard, Philadelphia, PA 19104,
| | - Jonathan M. Spergel
- Division of Allergy and Immunology, University of Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Amanda Muir
- Division of Gastroenterology and Nutrition, The Children's Hospital of Philadelphia, University of Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania.,Corresponding Authors: Antonella Cianferoni, MD, Assistant Professor of Pediatrics, The Children's Hospital of Philadelphia, Division of Allergy and Immunology, 3550 Market Street, Philadelphia, PA 19104, , Amanda Muir, MD, Assistant Professor of Pediatrics, The Children's Hospital of Philadelphia, Division of Gastroenterology, 34 and Civic Center Boulevard, Philadelphia, PA 19104,
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19
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Wang T, Li Y, Wang W, Tuerhanjiang A, Wu Z, Yang R, Yuan M, Ma D, Wang W, Wang S. Twist2, the key Twist isoform related to prognosis, promotes invasion of cervical cancer by inducing epithelial-mesenchymal transition and blocking senescence. Hum Pathol 2014; 45:1839-46. [PMID: 24974259 DOI: 10.1016/j.humpath.2014.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/04/2014] [Accepted: 05/07/2014] [Indexed: 01/28/2023]
Abstract
In response to tumor development, cells initially undergo invasion and metastasis followed by epithelial-mesenchymal transition (EMT, a process by which cells acquire motility) and overriding senescence (an endogenous defense mechanism against tumor progression). Oncogenic activation of Twist1 and Twist2 is essential for EMT and senescence; however, little is known about the specific contributions of Twist1 versus Twist2 to prognosis, metastasis, and the mechanism underlying cervical carcinoma. Here, we investigated the similarities and differences between Twist1 and Twist2 in assessing prognosis and promoting invasion and metastasis of cervical carcinoma as well as their roles in the underlying molecular mechanisms. By monitoring the survival of 144 clinical cervical cancer patients, we demonstrated that Twist2 shows more effective predictive performance compared with Twist1 and is more closely correlated with International Federation of Gynecology and Obstetrics stage and lymph node metastasis. Compared with Twist1, Twist2 more strongly promotes invasivity and motility by inducing EMT and overriding senescence. Differences between Twist1 and Twist2 in regulating senescence and the cell cycle might be due to their individual roles in regulating the cyclin D1/cyclin dependent kinase 4 (Cdk4) pathway. Overall, our data indicate that Twist2 is the key Twist isoform coupling aberrant signals from EMT to senescence and is an important candidate biomarker for cervical cancer prognosis.
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Affiliation(s)
- Tian Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Yan Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Wenwen Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Abidan Tuerhanjiang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Zhangying Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Runfeng Yang
- Department of Gynecologic Oncology, Tumor Hospital of Hubei Provincial, Wuhan, Hubei, 430079, PR China
| | - Ming Yuan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China.
| | - Wei Wang
- Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, PR China.
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, PR China.
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20
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Hou J, Wang Z, Yang L, Guo X, Yang G. The function of EMSY in cancer development. Tumour Biol 2014; 35:5061-6. [PMID: 24609898 DOI: 10.1007/s13277-013-1584-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 12/19/2013] [Indexed: 10/25/2022] Open
Abstract
EMSY was first reported to bind BRCA2 and to inactivate the function of BRCA2, leading to the development of sporadic breast and ovarian cancers. The function of EMSY may also be involved in DNA damage repair, genomic instability, and chromatin remolding. Recent studies have shown that amplification of EMSY was also associated with other cancers such as prostate and pancreatic cancers and linked to tumor phenotypes and clinical outcomes. By reviewing literatures published since 2003, here, we have summarized the recent advances of EMSY in cancer development.
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Affiliation(s)
- Jing Hou
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
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21
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Correlation of Twist upregulation and senescence bypass during the progression and metastasis of cervical cancer. Front Med 2014; 8:106-12. [PMID: 24402692 DOI: 10.1007/s11684-014-0307-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/27/2013] [Indexed: 01/16/2023]
Abstract
Cervical carcinoma is associated with high propensity for local invasion and lymph node metastasis. However, the molecular alterations that drive progression and metastasis of cervical cancer remain unclear. Cellular senescence has been proposed as the mechanism that protects an organism against cancer progression and metastasis. In addition, Twist, a basic helix-loop-helix transcription factor, has been suggested as an oncogene because it is overexpressed in many types of human cancer. This gene also exhibits a positive function in regulating invasion and metastasis. In this study, Twist was strongly and positively expressed in normal tissue, squamous cell carcinoma (SCC) IA-IIA, and SCC IIB-IIIB (4.3%, 44%, and 88.9%, respectively). The strong positive expressions of the senescence marker CBX3 were 39.1%, 32%, and 15.6%, respectively. The strong positive expressions of Twist in the SCC groups with or without lymph node metastasis were 80.8% and 50%. For CBX3, such expressions were 7.7% and 29.5%, respectively. Results also showed that the expression of Twist was inversely correlated with that of CBX3. Moreover, the knockdown of Twist with target siRNA in SiHa triggered the induction of the chromatin marker of the cellular senescence CBX3 and senescence-associated β-galactosidase activity. Our results suggested that the expression of Twist increased during the progression and metastasis of cervical cancer. Furthermore, Twist-induced senescence bypass is important in this process.
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22
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Rezaei-Ghaleh N, Klama F, Munari F, Zweckstetter M. Vorhersage der Rotationskorrelationszeit in dynamischen Mehrdomänenproteinen und supramolekularen Komplexen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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23
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Rezaei-Ghaleh N, Klama F, Munari F, Zweckstetter M. Predicting the Rotational Tumbling of Dynamic Multidomain Proteins and Supramolecular Complexes. Angew Chem Int Ed Engl 2013; 52:11410-4. [DOI: 10.1002/anie.201305094] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Indexed: 01/10/2023]
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24
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Mendez DL, Mandt RE, Elgin SCR. Heterochromatin Protein 1a (HP1a) partner specificity is determined by critical amino acids in the chromo shadow domain and C-terminal extension. J Biol Chem 2013; 288:22315-23. [PMID: 23793104 DOI: 10.1074/jbc.m113.468413] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Drosophila melanogaster Heterochromatin Protein 1a (HP1a) is an essential protein critical for heterochromatin assembly and regulation. Its chromo shadow domain (CSD) homodimerizes, a requirement for binding protein partners that contain a PXVXL motif. How does HP1a select among its many different PXVXL-containing partners? HP1a binds tightly to Heterochromatin Protein 2 (HP2), but weakly to PIWI. We investigated differences in homodimerization and the impact of the C-terminal extension (CTE) by contrasting HP1a to its paralogue, HP1b. HP1a and HP1b differ in the dimerization interface, with HP1a having an Arg at position 188 rather than Glu. We find that while this substitution reduces the dimerization constant, it does not impact the binding surface as demonstrated by unchanged partner binding affinities. However, the CTE (only 4 residues in HP1a as compared with 87 residues in HP1b) is critical; the charged residues in HP1a are necessary for tight peptide binding. Examining a panel of amino acid substitutions in the HP1a CSD, we find that Leu-165 in HP1a interacts with HP2 but not PIWI, supporting the conclusion that different sites in the binding surface provide discrimination for partner selection. Partner sequence is also critical for affinity, as the remaining difference in binding between HP2 and PIWI polypeptides is eliminated by swapping the PXVXL motifs between the two. Taken together, these studies indicate that the binding surface of the HP1a CSD plus its short CTE provide the needed discrimination among HP1a's partners, and that the CTE is important for differentiating the interactions of the Drosophila HP1 paralogs.
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Affiliation(s)
- Deanna L Mendez
- Department of Biology, Washington University, Saint Louis, Missouri 63130, USA
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25
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Munari F, Rezaei-Ghaleh N, Xiang S, Fischle W, Zweckstetter M. Structural plasticity in human heterochromatin protein 1β. PLoS One 2013; 8:e60887. [PMID: 23585859 PMCID: PMC3621757 DOI: 10.1371/journal.pone.0060887] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/04/2013] [Indexed: 01/12/2023] Open
Abstract
As essential components of the molecular machine assembling heterochromatin in eukaryotes, HP1 (Heterochromatin Protein 1) proteins are key regulators of genome function. While several high-resolution structures of the two globular regions of HP1, chromo and chromoshadow domains, in their free form or in complex with recognition-motif peptides are available, less is known about the conformational behavior of the full-length protein. Here, we used NMR spectroscopy in combination with small angle X-ray scattering and dynamic light scattering to characterize the dynamic and structural properties of full-length human HP1β (hHP1β) in solution. We show that the hinge region is highly flexible and enables a largely unrestricted spatial search by the two globular domains for their binding partners. In addition, the binding pockets within the chromo and chromoshadow domains experience internal dynamics that can be useful for the versatile recognition of different binding partners. In particular, we provide evidence for the presence of a distinct structural propensity in free hHP1β that prepares a binding-competent interface for the formation of the intermolecular β-sheet with methylated histone H3. The structural plasticity of hHP1β supports its ability to bind and connect a wide variety of binding partners in epigenetic processes.
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Affiliation(s)
- Francesca Munari
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Shengqi Xiang
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Markus Zweckstetter
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
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Hinge and chromoshadow of HP1α participate in recognition of K9 methylated histone H3 in nucleosomes. J Mol Biol 2012; 425:54-70. [PMID: 23142645 DOI: 10.1016/j.jmb.2012.10.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/26/2012] [Accepted: 10/28/2012] [Indexed: 11/22/2022]
Abstract
The majority of the genome in eukaryotes is packaged into transcriptionally inactive chromatin. Heterochromatin protein 1 (HP1) is a major player in the establishment and maintenance of heterochromatin. HP1 specifically recognizes a methylated lysine residue at position 9 in histone H3 through its N-terminal chromo domain (CD). To elucidate the binding properties of HP1α to nucleosomes in vitro, we reconstituted nucleosomes containing histone H3 trimethylated at lysine 9. HP1α exhibited high-affinity binding to nucleosomes containing methylated histone H3 in a nucleosome core-number-dependent manner. The hinge region (HR) connecting the CD and C-terminal chromoshadow domain (CSD), and the CSD contributed to the selective binding of HP1α to histone H3 with trimethylated lysine 9 through weak DNA binding and by suppressing the DNA binding, respectively. We propose that not only the specific recognition of lysine 9 methylation of histone H3 by the CD but also the HR and the CSD cooperatively contribute to the selective binding of HP1α to histone H3 lysine 9 methylated nucleosomes.
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27
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Ruan J, Ouyang H, Amaya MF, Ravichandran M, Loppnau P, Min J, Zang J. Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a. PLoS One 2012; 7:e35376. [PMID: 22514736 PMCID: PMC3325965 DOI: 10.1371/journal.pone.0035376] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 03/15/2012] [Indexed: 01/03/2023] Open
Abstract
Background HP1 proteins are highly conserved heterochromatin proteins, which have been identified to be structural adapters assembling a variety of macromolecular complexes involved in regulation of gene expression, chromatin remodeling and heterochromatin formation. Much evidence shows that HP1 proteins interact with numerous proteins including methylated histones, histone methyltransferases and so on. Cbx3 is one of the paralogues of HP1 proteins, which has been reported to specifically recognize trimethylated histone H3K9 mark, and a consensus binding motif has been defined for the Cbx3 chromodomain. Methodology/Principal Findings Here, we found that the Cbx3 chromodomain can bind to H1K26me2 and G9aK185me3 with comparable binding affinities compared to H3K9me3. We also determined the crystal structures of the human Cbx3 chromodomain in complex with dimethylated histone H1K26 and trimethylated G9aK185 peptides, respectively. The complex structures unveil that the Cbx3 chromodomain specifically bind methylated histone H1K26 and G9aK185 through a conserved mechanism. Conclusions/Significance The Cbx3 chromodomain binds with comparable affinities to all of the methylated H3K9, H1K26 and G9aK185 peptides. It is suggested that Cbx3 may regulate gene expression via recognizing both histones and non-histone proteins.
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Affiliation(s)
- Jianbin Ruan
- Hefei National Laboratory for Physical Sciences, Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Hui Ouyang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Maria F. Amaya
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Mani Ravichandran
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (JM); (JZ)
| | - Jianye Zang
- Hefei National Laboratory for Physical Sciences, Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
- * E-mail: (JM); (JZ)
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28
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Lomberk G, Mathison AJ, Grzenda A, Seo S, DeMars CJ, Rizvi S, Bonilla-Velez J, Calvo E, Fernandez-Zapico ME, Iovanna J, Buttar NS, Urrutia R. Sequence-specific recruitment of heterochromatin protein 1 via interaction with Krüppel-like factor 11, a human transcription factor involved in tumor suppression and metabolic diseases. J Biol Chem 2012; 287:13026-39. [PMID: 22318730 PMCID: PMC3339955 DOI: 10.1074/jbc.m112.342634] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/06/2012] [Indexed: 12/17/2022] Open
Abstract
Heterochromatin protein 1 (HP1) proteins are "gatekeepers" of epigenetic gene silencing that is mediated by lysine 9 of histone H3 methylation (H3K9me). Current knowledge supports a paradigm whereby HP1 proteins achieve repression by binding to H3K9me marks and interacting to H3K9 histone methyltransferases (HMTs), such as SUV39H1, which methylate this residue on adjacent nucleosomes thereby compacting chromatin and silencing gene expression. However, the mechanism underlying the recruitment of this epigenetic regulator to target gene promoters remains poorly characterized. In the current study, we reveal for the first time a mechanism whereby HP1 is recruited to promoters by a well characterized Krüppel-like transcription factor (KLF), in a sequence-specific manner, to mediate complex biological phenomena. A PXVXL HP1-interacting domain identified at position 487-491 of KLF11 mediates the binding of HP1α and KLF11 in vitro and in cultured cells. KLF11 also recruits HP1α and its histone methyltransferase, SUV39H1, to promoters to limit KLF11-mediated gene activation. Indeed, a KLF11ΔHP1 mutant derepresses KLF11-regulated cancer genes, by inhibiting HP1-SUV39H1 recruitment, decreasing H3K9me3, while increasing activation-associated marks. Biologically, impairment of KLF11-mediated HP1-HMT recruitment abolishes tumor suppression, providing direct evidence that HP1-HMTs act in a sequence-specific manner to achieve this function rather than its well characterized binding to methylated chromatin without intermediary. Collectively, these studies reveal a novel role for HP1 as a cofactor in tumor suppression, expand our mechanistic understanding of a KLF associated to human disease, and outline cellular and biochemical mechanisms underlying this phenomenon, increasing the specificity of targeting HP1-HMT complexes to gene promoters.
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Affiliation(s)
- Gwen Lomberk
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
| | - Angela J. Mathison
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
| | - Adrienne Grzenda
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
| | - Seungmae Seo
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
| | - Cathrine J. DeMars
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
| | - Sumera Rizvi
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
| | - Juliana Bonilla-Velez
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
| | - Ezequiel Calvo
- the Molecular Endocrinology and Oncology Research Center, CHUL Research Center, Quebec 61V 462, Canada, and
| | | | - Juan Iovanna
- INSERM U.624, Parc Scientifique et Technologique de Luminy, Marseille F-13288, France
| | - Navtej S. Buttar
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
| | - Raul Urrutia
- From the Department of Biochemistry and Molecular Biology, Laboratory of Epigenetics and Chromatin Dynamics, GIH Division, and
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29
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Richart AN, Brunner CIW, Stott K, Murzina NV, Thomas JO. Characterization of chromoshadow domain-mediated binding of heterochromatin protein 1α (HP1α) to histone H3. J Biol Chem 2012; 287:18730-7. [PMID: 22493481 PMCID: PMC3365711 DOI: 10.1074/jbc.m111.337204] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The chromoshadow domain (CSD) of heterochromatin protein 1 (HP1) was recently shown to contribute to chromatin binding and transcriptional regulation through interaction with histone H3. Here, we demonstrate the structural basis of this interaction for the CSD of HP1α. This mode of H3 binding is dependent on dimerization of the CSD and recognition of a PxVxL-like motif, as for other CSD partners. NMR chemical shift mapping showed that the H3 residues that mediate the CSD interaction occur in and adjacent to the αN helix just within the nucleosome core. Access to the binding region would require some degree of unwrapping of the DNA near the nucleosomal DNA entry/exit site.
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30
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Structural biology of the chromodomain: form and function. Gene 2012; 496:69-78. [PMID: 22285924 DOI: 10.1016/j.gene.2012.01.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/23/2011] [Accepted: 01/05/2012] [Indexed: 11/20/2022]
Abstract
The chromodomain motif is found among certain chromosomal proteins of all eukaryotes. The chromodomain fold - three beta strands packed against a C-terminal alpha helix - mediates protein-protein and/or protein-nucleic acid interactions. In some cases, the affinity of chromodomain binding is regulated by lysine methylation, which appears to target chromodomain proteins and associated complexes to specific sites in chromatin. In this review, our current knowledge of chromodomain structure and function is summarized.
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31
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Abstract
The chromatin organization modifier domain (chromodomain) was first identified as a motif associated with chromatin silencing in Drosophila. There is growing evidence that chromodomains are evolutionary conserved across different eukaryotic species to control diverse aspects of epigenetic regulation. Although originally reported as histone H3 methyllysine readers, the chromodomain functions have now expanded to recognition of other histone and non-histone partners as well as interaction with nucleic acids. Chromodomain binding to a diverse group of targets is mediated by a conserved substructure called the chromobox homology region. This motif can be used to predict methyllysine binding and distinguish chromodomains from related Tudor "Royal" family members. In this review, we discuss and classify various chromodomains according to their context, structure and the mechanism of target recognition.
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Affiliation(s)
- Bartlomiej J Blus
- Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL, USA
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32
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Mendez DL, Kim D, Chruszcz M, Stephens GE, Minor W, Khorasanizadeh S, Elgin SCR. The HP1a disordered C terminus and chromo shadow domain cooperate to select target peptide partners. Chembiochem 2011; 12:1084-96. [PMID: 21472955 DOI: 10.1002/cbic.201000598] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Indexed: 11/09/2022]
Abstract
Drosophila melanogaster heterochromatin protein 1a (HP1a) is essential for compacted heterochromatin structure and the associated gene silencing. Its chromo shadow domain (CSD) is well known for binding to peptides that contain a PXVXL motif. Heterochromatin protein 2 (HP2) is a non-histone chromosomal protein that associates with HP1a in the pericentric heterochromatin, telomeres, and the fourth chromosome. Using NMR spectroscopy, fluorescence polarization, and site-directed mutagenesis, we identified an LCVKI motif in HP2 that binds to the HP1a CSD. The binding affinity of the HP2 fragment is approximately two orders of magnitude higher than that of peptides from PIWI (with a PRVKV motif), AF10 (with a PLVVL motif), or CG15356 (with LYPLL and LSIVA motifs). To delineate differential interactions of the HP1a CSD, we characterized its structure, backbone dynamics, and dimerization constant. We found that the dimerization constant is bracketed by the affinities of HP2 and PIWI, which dock to the same HP1a homodimer surface. This suggests that HP2, but not PIWI, interaction can drive the homodimerization of HP1a. Interestingly, the integrity of the disordered C-terminal extension (CTE) of HP1a is essential for discriminatory binding, whereas swapping the PXVXL motifs does not confer specificity. Serine phosphorylation at the peptide binding surface of the CSD is thought to regulate heterochromatin assembly. Glutamic acid substitution at these sites destabilizes HP1a dimers, but improves the interaction with both binding partners. Our studies underscore the importance of CSD dimerization and cooperation with the CTE in forming distinct complexes of HP1a.
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Affiliation(s)
- Deanna L Mendez
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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33
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Brideau NJ, Barbash DA. Functional conservation of the Drosophila hybrid incompatibility gene Lhr. BMC Evol Biol 2011; 11:57. [PMID: 21366928 PMCID: PMC3060119 DOI: 10.1186/1471-2148-11-57] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 03/02/2011] [Indexed: 01/01/2023] Open
Abstract
Background Hybrid incompatibilities such as sterility and lethality are commonly modeled as being caused by interactions between two genes, each of which has diverged separately in one of the hybridizing lineages. The gene Lethal hybrid rescue (Lhr) encodes a rapidly evolving heterochromatin protein that causes lethality of hybrid males in crosses between Drosophila melanogaster females and D. simulans males. Previous genetic analyses showed that hybrid lethality is caused by D. simulans Lhr but not by D. melanogaster Lhr, confirming a critical prediction of asymmetry in the evolution of a hybrid incompatibility gene. Results Here we have examined the functional properties of Lhr orthologs from multiple Drosophila species, including interactions with other heterochromatin proteins, localization to heterochromatin, and ability to complement hybrid rescue in D. melanogaster/D. simulans hybrids. We find that these properties are conserved among most Lhr orthologs, including Lhr from D. melanogaster, D. simulans and the outgroup species D. yakuba. Conclusions We conclude that evolution of the hybrid lethality properties of Lhr between D. melanogaster and D. simulans did not involve extensive loss or gain of functions associated with protein interactions or localization to heterochromatin.
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Affiliation(s)
- Nicholas J Brideau
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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34
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Kang J, Chaudhary J, Dong H, Kim S, Brautigam CA, Yu H. Mitotic centromeric targeting of HP1 and its binding to Sgo1 are dispensable for sister-chromatid cohesion in human cells. Mol Biol Cell 2011; 22:1181-90. [PMID: 21346195 PMCID: PMC3078076 DOI: 10.1091/mbc.e11-01-0009] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Human Shugoshin 1 (Sgo1) protects centromeric sister-chromatid cohesion during mitosis. Heterochromatin protein 1 (HP1) has been proposed to recruit Sgo1 to mitotic centromeres. We show that the molecular interaction targeting HP1 to mitotic centromeres is incompatible with HP1 further recruiting Sgo1. Our results clarify the role of centromeric HP1 in chromosome segregation. Human Shugoshin 1 (Sgo1) protects centromeric sister-chromatid cohesion during prophase and prevents premature sister-chromatid separation. Heterochromatin protein 1 (HP1) has been proposed to protect centromeric sister-chromatid cohesion by directly targeting Sgo1 to centromeres in mitosis. Here we show that HP1α is targeted to mitotic centromeres by INCENP, a subunit of the chromosome passenger complex (CPC). Biochemical and structural studies show that both HP1–INCENP and HP1–Sgo1 interactions require the binding of the HP1 chromo shadow domain to PXVXL/I motifs in INCENP or Sgo1, suggesting that the INCENP-bound, centromeric HP1α is incapable of recruiting Sgo1. Consistently, a Sgo1 mutant deficient in HP1 binding is functional in centromeric cohesion protection and localizes normally to centromeres in mitosis. By contrast, INCENP or Sgo1 mutants deficient in HP1 binding fail to localize to centromeres in interphase. Therefore, our results suggest that HP1 binding by INCENP or Sgo1 is dispensable for centromeric cohesion protection during mitosis of human cells, but might regulate yet uncharacterized interphase functions of CPC or Sgo1 at the centromeres.
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Affiliation(s)
- Jungseog Kang
- Department of Pharmacology, Howard Hughes Medical Institute, USA
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35
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Xu X, Lee YJ, Holm JB, Terry MD, Oswald RE, Horne WA. The Ca2+ channel beta4c subunit interacts with heterochromatin protein 1 via a PXVXL binding motif. J Biol Chem 2011; 286:9677-87. [PMID: 21220418 DOI: 10.1074/jbc.m110.187864] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The β subunits of voltage-gated Ca(2+) channels are best known for their roles in regulating surface expression and gating of voltage-gated Ca(2+) channel α(1) subunits. Recent evidence, however, indicates that these proteins have a variety of Ca(2+) channel-independent functions. For example, on the molecular level, they regulate gene expression, and on the whole animal level, they regulate early cell movements in zebrafish development. In the present study, an alternatively spliced, truncated β4 subunit (β4c) is identified in the human brain and shown to be highly expressed in nuclei of vestibular neurons. Pull-down assays, nuclear magnetic resonance, and isothermal titration calorimetry demonstrate that the protein interacts with the chromo shadow domain (CSD) of heterochromatin protein 1γ. Site-directed mutagenesis reveals that the primary CSD interaction occurs through a β4c C-terminal PXVXL consensus motif, adding the β4c subunit to a growing PXVXL protein family with epigenetic responsibilities. These proteins have multiple nuclear functions, including transcription regulation (TIF1α) and nucleosome assembly (CAF1). An NMR-based two-site docking model of β4c in complex with dimerized CSD is presented. Possible roles for the interaction are discussed.
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Affiliation(s)
- Xingfu Xu
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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36
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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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37
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Billur M, Bartunik HD, Singh PB. The essential function of HP1 beta: a case of the tail wagging the dog? Trends Biochem Sci 2010; 35:115-23. [PMID: 19836960 DOI: 10.1016/j.tibs.2009.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/27/2009] [Accepted: 09/03/2009] [Indexed: 12/25/2022]
Abstract
A large body of work in various organisms has shown that the presence of HP1 structural proteins and methylated lysine 9 of histone H3 (H3K9me) represent the characteristic hallmarks of heterochromatin. We propose that a more critical assessment of the physiological importance of the H3K9me-HP1 interaction is warranted in light of recent studies on the mammalian HP1 beta protein. Based on this new research, we conclude that the essential function of HP1 beta (and perhaps that of its orthologues in other species) lies outside the canonical heterochromatic H3K9me-HP1 interaction. We suggest instead that binding of a small fraction of HP1 beta to the H3 histone fold performs a critical role in heterochromatin function and organismal survival.
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Affiliation(s)
- Mustafa Billur
- Division of Immunoepigenetics, Department of Immunology and Cell Biology, Forschungszentrum Borstel, D-23845 Borstel, Germany
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38
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Garapaty S, Xu CF, Trojer P, Mahajan MA, Neubert TA, Samuels HH. Identification and characterization of a novel nuclear protein complex involved in nuclear hormone receptor-mediated gene regulation. J Biol Chem 2009; 284:7542-52. [PMID: 19131338 DOI: 10.1074/jbc.m805872200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NRC/NCoA6 plays an important role in mediating the effects of ligand-bound nuclear hormone receptors as well as other transcription factors. NRC interacting factor 1 (NIF-1) was cloned as a novel factor that interacts in vivo with NRC. Although NIF-1 does not directly interact with nuclear hormone receptors, it enhances activation by nuclear hormone receptors presumably through its interaction with NRC. To further understand the cellular and biological function of NIF-1, we identified NIF-1-associated proteins by in-solution proteolysis followed by mass spectrometry. The identified components revealed factors involved in histone methylation and cell cycle control and include Ash2L, RbBP5, WDR5, HCF-1, DBC-1, and EMSY. Although the NIF-1 complex contains Ash2L, RbBP5, and WDR5, suggesting that the complex might methylate histone H3-Lys-4, we found that the complex contains a H3 methyltransferase activity that modifies a residue other than H3-Lys-4. The identified components form at least two distinctly sized NIF-1 complexes. DBC-1 and EMSY were identified as integral components of an NIF-1 complex of approximately 1.5 MDa and were found to play an important role in the regulation of nuclear receptor-mediated transcription. Stimulation of the Sox9 and HoxA1 genes by retinoic acid receptor-alpha was found to require both DBC-1 and EMSY in addition to NIF-1 for maximal transcriptional activation. Interestingly, NRC was not identified as a component of the NIF-1 complex, suggesting that NIF-1 and NRC do not exist as stable in vitro purified complexes, although the separate NIF-1 and NRC complexes appear to functionally interact in the cell.
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Affiliation(s)
- Shivani Garapaty
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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39
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Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Mol Cell Biol 2008; 28:6044-55. [PMID: 18678653 DOI: 10.1128/mcb.00823-08] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is involved in gene silencing and genomic stability in mammals, plants, and fungi. Genetics studies of Neurospora crassa have revealed that a DNA methyltransferase (DIM-2), a histone H3K9 methyltransferase (DIM-5), and heterochromatin protein 1 (HP1) are required for DNA methylation. We explored the interrelationships of these components of the methylation machinery. A yeast two-hybrid screen revealed that HP1 interacts with DIM-2. We confirmed the interaction in vivo and demonstrated that it involves a pair of PXVXL-related motifs in the N-terminal region of DIM-2 and the chromo shadow domain of HP1. Both regions are essential for proper DNA methylation. We also determined that DIM-2 and HP1 form a stable complex independently of the trimethylation of histone H3K9, although the association of DIM-2 with its substrate sequences depends on trimethyl-H3K9. The DIM-2/HP1 complex does not include DIM-5. We conclude that DNA methylation in Neurospora is largely or exclusively the result of a unidirectional pathway in which DIM-5 methylates histone H3K9 and then the DIM-2/HP1 complex recognizes the resulting trimethyl-H3K9 mark via the chromo domain of HP1.
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40
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Park PG, Lee H. Development of thymic lymphomas in mice disrupted of Brca2 allele in the thymus. Exp Mol Med 2008; 40:339-44. [PMID: 18587272 PMCID: PMC2679290 DOI: 10.3858/emm.2008.40.3.339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2008] [Indexed: 11/04/2022] Open
Abstract
Germ-line mutations in BRCA2 predispose to early-onset cancer. Homozygous mutant mouse, which has Brca2 truncated in exon 11 exhibit paradoxic occurrence of growth retardation and development of thymic lymphomas. However, due to its large embryonic lethality, cohort studies on the thymic lymphomas were not feasible. With the aid of Cre-loxP system, we demonstrate here that thymus-specific disruption of Brca2 allele without crossing it to p53-mutant background leads to the development of thymic lymphomas. Varying from 16 weeks to 66 weeks after birth, 25% of mice disrupted of Brca2 in the thymus died of thymic lymphomas, whereas previous report did not observe lymphomagenesis using similar Cre-loxP system. Future analysis of thymic lymphomas from these mice presented here will provide information on the cooperative mutations that are required for the BRCA2-associated pathogenesis of cancer.
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Affiliation(s)
- Pil-Gu Park
- Research Center for Functional Cellulomics, Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
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