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Castiglioni S, Di Fede E, Bernardelli C, Lettieri A, Parodi C, Grazioli P, Colombo EA, Ancona S, Milani D, Ottaviano E, Borghi E, Massa V, Ghelma F, Vignoli A, Lesma E, Gervasini C. KMT2A: Umbrella Gene for Multiple Diseases. Genes (Basel) 2022; 13:genes13030514. [PMID: 35328068 PMCID: PMC8949091 DOI: 10.3390/genes13030514] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 02/05/2023] Open
Abstract
KMT2A (Lysine methyltransferase 2A) is a member of the epigenetic machinery, encoding a lysine methyltransferase responsible for the transcriptional activation through lysine 4 of histone 3 (H3K4) methylation. KMT2A has a crucial role in gene expression, thus it is associated to pathological conditions when found mutated. KMT2A germinal mutations are associated to Wiedemann–Steiner syndrome and also in patients with initial clinical diagnosis of several other chromatinopathies (i.e., Coffin–Siris syndromes, Kabuki syndrome, Cornelia De Lange syndrome, Rubinstein–Taybi syndrome), sharing an overlapping phenotype. On the other hand, KMT2A somatic mutations have been reported in several tumors, mainly blood malignancies. Due to its evolutionary conservation, the role of KMT2A in embryonic development, hematopoiesis and neurodevelopment has been explored in different animal models, and in recent decades, epigenetic treatments for disorders linked to KMT2A dysfunction have been extensively investigated. To note, pharmaceutical compounds acting on tumors characterized by KMT2A mutations have been formulated, and even nutritional interventions for chromatinopathies have become the object of study due to the role of microbiota in epigenetic regulation.
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Affiliation(s)
- Silvia Castiglioni
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Elisabetta Di Fede
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Clara Bernardelli
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Antonella Lettieri
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, 20142 Milan, Italy
| | - Chiara Parodi
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Paolo Grazioli
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Elisa Adele Colombo
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Silvia Ancona
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università Degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Emerenziana Ottaviano
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Elisa Borghi
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Valentina Massa
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, 20142 Milan, Italy
| | - Filippo Ghelma
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Aglaia Vignoli
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
- Child NeuroPsychiatry Unit, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy
| | - Elena Lesma
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
| | - Cristina Gervasini
- Department of Health Sciences, Università Degli Studi di Milano, 20142 Milan, Italy; (S.C.); (E.D.F.); (C.B.); (A.L.); (C.P.); (P.G.); (E.A.C.); (S.A.); (E.O.); (E.B.); (V.M.); (F.G.); (A.V.); (E.L.)
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, 20142 Milan, Italy
- Correspondence: ; Tel.: +39-0250-3230-28
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Structure, Activity and Function of the Protein Arginine Methyltransferase 6. Life (Basel) 2021; 11:life11090951. [PMID: 34575100 PMCID: PMC8470942 DOI: 10.3390/life11090951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/25/2022] Open
Abstract
Members of the protein arginine methyltransferase (PRMT) family methylate the arginine residue(s) of several proteins and regulate a broad spectrum of cellular functions. Protein arginine methyltransferase 6 (PRMT6) is a type I PRMT that asymmetrically dimethylates the arginine residues of numerous substrate proteins. PRMT6 introduces asymmetric dimethylation modification in the histone 3 at arginine 2 (H3R2me2a) and facilitates epigenetic regulation of global gene expression. In addition to histones, PRMT6 methylates a wide range of cellular proteins and regulates their functions. Here, we discuss (i) the biochemical aspects of enzyme kinetics, (ii) the structural features of PRMT6 and (iii) the diverse functional outcomes of PRMT6 mediated arginine methylation. Finally, we highlight how dysregulation of PRMT6 is implicated in various types of cancers and response to viral infections.
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DNMT3A mutants provide proliferating advantage with augmentation of self-renewal activity in the pathogenesis of AML in KMT2A-PTD-positive leukemic cells. Oncogenesis 2020; 9:7. [PMID: 32015320 PMCID: PMC6997180 DOI: 10.1038/s41389-020-0191-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/11/2019] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) with partial tandem duplication of histone-lysine N-methyltransferase 2A (KMT2A-PTD) is a subtype of AML and is associated with adverse survival, yet the molecular pathogenesis of KMT2A-PTD is not fully understood. DNA methyltransferase 3A (DNMT3A) is mutated in various myeloid neoplasms including AML, especially at the Arg882. Recently, it has been found that DNMT3A mutations frequently coexisted with KMT2A-PTD and are associated with inferior outcomes. We aimed to understand the biological role of DNMT3A mutation in KMT2A-PTD-positive cells. Herein, we found that overexpression of DNMT3A mutants (MT) in KMT2A-PTD-positive EOL-1 cells augmented cell proliferation and clonogenicity. Serial colony replating assays indicated that DNMT3A-MT increased the self-renewal ability of Kmt2a-PTD-expressing mouse bone marrow cells with immature morphology. At 10 months post bone marrow transplantation, mice with the combined Kmt2a-PTD and DNMT3A-MT showed hepatosplenomegaly and leukocytosis with a shorter latency compared to control and DNMT3A-wild-type. Gene expression microarray analyses of bone marrow samples from human AML with KMT2A-PTD/DNMT3A-MT showed a stem cell signature and myeloid hematopoietic lineage with dysregulation of HOXB gene expression. In addition, human bone marrow AML cells carrying KMT2A-PTD/DNMT3A-MT showed abnormal growth and augmented self-renewal activity in primary cell culture. The present study provides information underlying the pathogenic role of DNMT3A-MT with KMT2A-PTD in proliferating advantage with augmentation of self-renewal activity in human leukemia, which may help to better understand the disease and to design better therapy for AML patients with these mutations.
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Theeler BJ, Dalal Y, Monje M, Shilatifard A, Suvà ML, Aboud O, Camphausen K, Cordova C, Finch E, Heiss JD, Packer RJ, Romo CG, Aldape K, Penas-Prado M, Armstrong T, Gilbert MR. NCI-CONNECT: Comprehensive Oncology Network Evaluating Rare CNS Tumors-Histone Mutated Midline Glioma Workshop Proceedings. Neurooncol Adv 2020; 2:vdaa007. [PMID: 32642676 DOI: 10.1093/noajnl/vdaa007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Histone mutations occur in approximately 4% of different cancer types. In 2012, mutations were found in the gene encoding histone variant H3.3 (H3F3A gene) in pediatric diffuse intrinsic pontine gliomas and pediatric hemispheric gliomas. Tumors with mutations in the H3F3A gene are generally characterized as histone mutated gliomas (HMGs) or diffuse midline gliomas. HMGs are a rare subtype of glial tumor that is malignant and fast growing, carrying a poor prognosis. In 2017, the Beau Biden Cancer Moonshot Program appropriated $1.7 billion toward cancer care in 10 select areas. The National Cancer Institute (NCI) was granted support to focus specifically on rare central nervous system (CNS) tumors through NCI-CONNECT. Its mission is to address the challenges and unmet needs in CNS cancer research and treatment by connecting patients, providers, researchers, and advocacy organizations to work in partnership. On September 27, 2018, NCI-CONNECT convened a workshop on histone mutated midline glioma, one of the 12 CNS cancers included in its initial portfolio. Three leaders in the field provided an overview of advances in histone mutated midline glioma research. These experts shared observations and experiences related to common scientific and clinical challenges in studying these tumors. Although the clinical focus of this workshop was on adult patients, one important objective was to start a collaborative dialogue between pediatric and adult clinicians and researchers. Meeting participants identified needs for diagnostic and treatment standards, disease biology and biological targets for this cancer, disease-specific trial designs, and developed a list of action items and future direction.
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Affiliation(s)
- Brett J Theeler
- Department of Neurology and John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michelle Monje
- Stanford University Hospital, Departments of Neurology, Neurosurgery, Pathology, and Pediatrics, Palo Alto, California, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, Illinois, USA
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Orwa Aboud
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin Camphausen
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Christine Cordova
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Elizabeth Finch
- Brain Tumor Institute, Children's National Health System, Washington, District of Columbia, USA
| | - John D Heiss
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Roger J Packer
- Brain Tumor Institute, Children's National Health System, Washington, District of Columbia, USA
- Center for Neuroscience and Behavioral Health, Children's National Health System, Washington, District of Columbia, USA
| | - Carlos G Romo
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Marta Penas-Prado
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Terri Armstrong
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Hayashi Y, Zhang Y, Yokota A, Yan X, Liu J, Choi K, Li B, Sashida G, Peng Y, Xu Z, Huang R, Zhang L, Freudiger GM, Wang J, Dong Y, Zhou Y, Wang J, Wu L, Bu J, Chen A, Zhao X, Sun X, Chetal K, Olsson A, Watanabe M, Romick-Rosendale LE, Harada H, Shih LY, Tse W, Bridges JP, Caligiuri MA, Huang T, Zheng Y, Witte DP, Wang QF, Qu CK, Salomonis N, Grimes HL, Nimer SD, Xiao Z, Huang G. Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes. Cancer Discov 2018; 8:1438-1457. [PMID: 30139811 DOI: 10.1158/2159-8290.cd-17-1203] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 06/26/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022]
Abstract
Myelodysplastic syndromes (MDS) are heterogeneous hematopoietic disorders that are incurable with conventional therapy. Their incidence is increasing with global population aging. Although many genetic, epigenetic, splicing, and metabolic aberrations have been identified in patients with MDS, their clinical features are quite similar. Here, we show that hypoxia-independent activation of hypoxia-inducible factor 1α (HIF1A) signaling is both necessary and sufficient to induce dysplastic and cytopenic MDS phenotypes. The HIF1A transcriptional signature is generally activated in MDS patient bone marrow stem/progenitors. Major MDS-associated mutations (Dnmt3a, Tet2, Asxl1, Runx1, and Mll1) activate the HIF1A signature. Although inducible activation of HIF1A signaling in hematopoietic cells is sufficient to induce MDS phenotypes, both genetic and chemical inhibition of HIF1A signaling rescues MDS phenotypes in a mouse model of MDS. These findings reveal HIF1A as a central pathobiologic mediator of MDS and as an effective therapeutic target for a broad spectrum of patients with MDS.Significance: We showed that dysregulation of HIF1A signaling could generate the clinically relevant diversity of MDS phenotypes by functioning as a signaling funnel for MDS driver mutations. This could resolve the disconnection between genotypes and phenotypes and provide a new clue as to how a variety of driver mutations cause common MDS phenotypes. Cancer Discov; 8(11); 1438-57. ©2018 AACR. See related commentary by Chen and Steidl, p. 1355 This article is highlighted in the In This Issue feature, p. 1333.
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Affiliation(s)
- Yoshihiro Hayashi
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Yue Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Asumi Yokota
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Xiaomei Yan
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jinqin Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Kwangmin Choi
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Bing Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Goro Sashida
- International Research Center for Medical Sciences, Kumamoto University, Chuo-ku, Kumamoto, Japan
| | - Yanyan Peng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Zefeng Xu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Rui Huang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lulu Zhang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - George M Freudiger
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jingya Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yunzhu Dong
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Yile Zhou
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jieyu Wang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lingyun Wu
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Hematology, Sixth Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Jiachen Bu
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Aili Chen
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinghui Zhao
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Xiujuan Sun
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Andre Olsson
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Miki Watanabe
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lindsey E Romick-Rosendale
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hironori Harada
- Laboratory of Oncology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Lee-Yung Shih
- Department of Hematology and Oncology, Chang Gung Memorial Hospital-Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - William Tse
- James Graham Brown Cancer Center, University of Louisville Hospital, Louisville, Kentucky
| | - James P Bridges
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Yi Zheng
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David P Witte
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Qian-Fei Wang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Kui Qu
- Division of Hematology/Oncology, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, Georgia
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - H Leighton Grimes
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Gang Huang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio. .,State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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Yang H, Basquin D, Pauli D, Oliver B. Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults. BMC Genomics 2017; 18:384. [PMID: 28521739 PMCID: PMC5436443 DOI: 10.1186/s12864-017-3755-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/03/2017] [Indexed: 11/22/2022] Open
Abstract
Background Transcriptional elongation is a generic function, but is also regulated to allow rapid transcription responses. Following relatively long initiation and promoter clearance, RNA polymerase II can pause and then rapidly elongate following recruitment of positive elongation factors. Multiple elongation complexes exist, but the role of specific components in adult Drosophila is underexplored. Results We conducted RNA-seq experiments to analyze the effect of RNAi knockdown of Suppressor of Triplolethal and lilliputian. We similarly analyzed the effect of expressing a dominant negative Cyclin-dependent kinase 9 allele. We observed that almost half of the genes expressed in adults showed reduced expression, supporting a broad role for the three tested genes in steady-state transcript abundance. Expression profiles following lilliputian and Suppressor of Triplolethal RNAi were nearly identical raising the possibility that they are obligatory co-factors. Genes showing reduced expression due to these RNAi treatments were short and enriched for genes encoding metabolic or enzymatic functions. The dominant-negative Cyclin-dependent kinase 9 profiles showed both overlapping and specific differential expression, suggesting involvement in multiple complexes. We also observed hundreds of genes with sex-biased differential expression following treatment. Conclusion Transcriptional profiles suggest that Lilliputian and Suppressor of Triplolethal are obligatory cofactors in the adult and that they can also function with Cyclin-dependent kinase 9 at a subset of loci. Our results suggest that transcriptional elongation control is especially important for rapidly expressed genes to support digestion and metabolism, many of which have sex-biased function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3755-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haiwang Yang
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA.
| | - Denis Basquin
- Department of Genetics & Evolution, Sciences III, University of Geneva, Boulevard d'Yvoy 4, CH 1205, Geneva, Switzerland
| | - Daniel Pauli
- Department of Genetics & Evolution, Sciences III, University of Geneva, Boulevard d'Yvoy 4, CH 1205, Geneva, Switzerland
| | - Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA
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Hyun K, Jeon J, Park K, Kim J. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017; 49:e324. [PMID: 28450737 PMCID: PMC6130214 DOI: 10.1038/emm.2017.11] [Citation(s) in RCA: 706] [Impact Index Per Article: 100.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 02/08/2023] Open
Abstract
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
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Affiliation(s)
- Kwangbeom Hyun
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongcheol Jeon
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kihyun Park
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jaehoon Kim
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Spangle JM, Roberts TM, Zhao JJ. The emerging role of PI3K/AKT-mediated epigenetic regulation in cancer. Biochim Biophys Acta Rev Cancer 2017; 1868:123-131. [PMID: 28315368 DOI: 10.1016/j.bbcan.2017.03.002] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 12/27/2022]
Abstract
The PI3-kinase/AKT pathway integrates signals from external cellular stimuli to regulate essential cellular functions, and is frequently aberrantly activated in human cancers. Recent research demonstrates that tight regulation of the epigenome is critical in preserving and restricting transcriptional activation, which can impact cellular growth and proliferation. In this review we examine mechanisms by which the PI3K/AKT pathway regulates the epigenome to promote oncogenesis, and highlight how connections between PI3K/AKT and the epigenome may impact the future therapeutic treatment of cancers featuring a hyperactivated PI3K/AKT pathway.
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Affiliation(s)
- Jennifer M Spangle
- Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 44 Binney St, Boston, MA 02115, USA.
| | - Thomas M Roberts
- Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 44 Binney St, Boston, MA 02115, USA
| | - Jean J Zhao
- Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 44 Binney St, Boston, MA 02115, USA.
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9
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Aihara H, Nakagawa T, Mizusaki H, Yoneda M, Kato M, Doiguchi M, Imamura Y, Higashi M, Ikura T, Hayashi T, Kodama Y, Oki M, Nakayama T, Cheung E, Aburatani H, Takayama KI, Koseki H, Inoue S, Takeshima Y, Ito T. Histone H2A T120 Phosphorylation Promotes Oncogenic Transformation via Upregulation of Cyclin D1. Mol Cell 2016; 64:176-188. [DOI: 10.1016/j.molcel.2016.09.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/30/2016] [Accepted: 09/08/2016] [Indexed: 01/04/2023]
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10
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Antonacci S, Forand D, Wolf M, Tyus C, Barney J, Kellogg L, Simon MA, Kerr G, Wells KL, Younes S, Mortimer NT, Olesnicky EC, Killian DJ. Conserved RNA-binding proteins required for dendrite morphogenesis in Caenorhabditis elegans sensory neurons. G3 (BETHESDA, MD.) 2015; 5:639-53. [PMID: 25673135 PMCID: PMC4390579 DOI: 10.1534/g3.115.017327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/09/2015] [Indexed: 01/22/2023]
Abstract
The regulation of dendritic branching is critical for sensory reception, cell-cell communication within the nervous system, learning, memory, and behavior. Defects in dendrite morphology are associated with several neurologic disorders; thus, an understanding of the molecular mechanisms that govern dendrite morphogenesis is important. Recent investigations of dendrite morphogenesis have highlighted the importance of gene regulation at the posttranscriptional level. Because RNA-binding proteins mediate many posttranscriptional mechanisms, we decided to investigate the extent to which conserved RNA-binding proteins contribute to dendrite morphogenesis across phyla. Here we identify a core set of RNA-binding proteins that are important for dendrite morphogenesis in the PVD multidendritic sensory neuron in Caenorhabditis elegans. Homologs of each of these genes were previously identified as important in the Drosophila melanogaster dendritic arborization sensory neurons. Our results suggest that RNA processing, mRNA localization, mRNA stability, and translational control are all important mechanisms that contribute to dendrite morphogenesis, and we present a conserved set of RNA-binding proteins that regulate these processes in diverse animal species. Furthermore, homologs of these genes are expressed in the human brain, suggesting that these RNA-binding proteins are candidate regulators of dendrite development in humans.
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Affiliation(s)
- Simona Antonacci
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Daniel Forand
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Margaret Wolf
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Courtney Tyus
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Julia Barney
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Leah Kellogg
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Margo A Simon
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Genevieve Kerr
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Kristen L Wells
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
| | - Serena Younes
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Nathan T Mortimer
- Department of Biological Sciences, University of Denver, Denver, Colorado 80208
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado 80918
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado 80903
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11
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Pascual-Garcia P, Jeong J, Capelson M. Nucleoporin Nup98 associates with Trx/MLL and NSL histone-modifying complexes and regulates Hox gene expression. Cell Rep 2014; 9:433-42. [PMID: 25310983 DOI: 10.1016/j.celrep.2014.09.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/19/2014] [Accepted: 08/28/2014] [Indexed: 01/04/2023] Open
Abstract
The nuclear pore complex is a transport channel embedded in the nuclear envelope and made up of 30 different components termed nucleoporins (Nups). In addition to their classical role in transport, a subset of Nups has a conserved role in the regulation of transcription via direct binding to chromatin. The molecular details of this function remain obscure, and it is unknown how metazoan Nups are recruited to their chromatin locations or what transcription steps they regulate. Here, we demonstrate genome-wide and physical association between Nup98 and histone-modifying complexes MBD-R2/NSL [corrected] and Trx/MLL. Importantly, we identify a requirement for MBD-R2 in recruitment of Nup98 to many of its genomic target sites. Consistent with its interaction with the Trx/MLL complex, Nup98 is shown to be necessary for Hox gene expression in developing fly tissues. These findings introduce roles of Nup98 in epigenetic regulation that may underlie the basis of oncogenicity of Nup98 fusions in leukemia.
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Affiliation(s)
- Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Penn Epigenetics Program, University of Pennsylvania, 9-101 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Jieun Jeong
- Department of Cell and Developmental Biology, Penn Epigenetics Program, University of Pennsylvania, 9-101 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Maya Capelson
- Department of Cell and Developmental Biology, Penn Epigenetics Program, University of Pennsylvania, 9-101 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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12
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Qi J, Huo L, Zhu YT, Zhu YJ. Absent, small or homeotic 2-like protein (ASH2L) enhances the transcription of the estrogen receptor α gene through GATA-binding protein 3 (GATA3). J Biol Chem 2014; 289:31373-81. [PMID: 25258321 DOI: 10.1074/jbc.m114.579839] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
ASH2L is a component of MLL complexes that confer H3K4 trimethylation. The ASH2L gene is located at 8q11-12, which is often amplified in breast cancers. We found that increased ASH2L expression, which can result from gene amplification, is often correlated with increased ERα expression in both breast cancer cell lines and primary breast cancers. Forced expression of ASH2L induced ERα expression in mammary epithelial cells, whereas depletion of ASH2L suppressed ERα expression in breast cancer cells. To understand the mechanism by which ASH2L regulates ERα expression, we identified GATA3 as the binding protein of ASH2L. ASH2L was shown to potentiate the transcriptional activity of GATA3. ASH2L was recruited to the enhancer of the ERα gene through GATA3 to promote ERα transcription. This study established that ASH2L enhances ERα expression as a coactivator of GATA3 in breast cancers.
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Affiliation(s)
- Jin Qi
- From the Maternal and Child Hospital of Shaanxi Province, Xian, Shaanxi, China
| | - Lei Huo
- the Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, and
| | - Yiwei Tony Zhu
- the Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Yi-Jun Zhu
- the Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
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13
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Choi SC, Lee S, Kim SR, Lee YS, Liu C, Cao X, An G. Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3. PLANT PHYSIOLOGY 2014; 164:1326-37. [PMID: 24420930 PMCID: PMC3938623 DOI: 10.1104/pp.113.228049] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Trithorax group proteins are chromatin-remodeling factors that activate target gene expression by antagonistically functioning against the Polycomb group. In Arabidopsis (Arabidopsis thaliana), Arabidopsis Trithorax protein1 (ATX1) regulates flowering time and floral organ identity. Here, we observed that suppression of Oryza sativa Trithorax1 (OsTrx1), an ortholog of ATX1, delayed flowering time in rice (Oryza sativa). Because the delay occurred only under long-day conditions, we evaluated the flowering signal pathways that specifically function under long-day conditions. Among them, the OsMADS50 and Heading date1 pathways were not affected by the mutation. However, the Grain number, plant height, and heading date7 (Ghd7) pathway was altered in ostrx1. Transcript levels of OsGI, phytochrome genes, and Early heading date3 (Ehd3), which function upstream of Ghd7, were unchanged in the mutant. Because Trx group proteins form a complex with other proteins to modify the chromatin structure of target genes, we investigated whether OsTrx1 interacts with a previously identified protein that functions upstream of Ghd7. We demonstrated that the plant homeodomain motif of OsTrx1 binds to native histone H3 from the calf thymus and that OsTrx1 binds to Ehd3 through the region between the plant homeodomain and SET domains. Finally, we showed that the SET domain at the C-terminal end of OsTrx1 has histone H3 methyltransferase activity when incubated with oligonucleosomes. Our results suggest that OsTrx1 plays an important role in regulating flowering time in rice by modulating chromatin structure.
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Valentine MC, Linabery AM, Chasnoff S, Hughes AEO, Mallaney C, Sanchez N, Giacalone J, Heerema NA, Hilden JM, Spector LG, Ross JA, Druley TE. Excess congenital non-synonymous variation in leukemia-associated genes in MLL- infant leukemia: a Children's Oncology Group report. Leukemia 2013; 28:1235-41. [PMID: 24301523 PMCID: PMC4045651 DOI: 10.1038/leu.2013.367] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/19/2013] [Accepted: 11/29/2013] [Indexed: 12/11/2022]
Abstract
Infant leukemia (IL) is a rare sporadic cancer with a grim prognosis. Although most cases are accompanied by MLL rearrangements and harbor very few somatic mutations, less is known about the genetics of the cases without MLL translocations. We performed the largest exome-sequencing study to date on matched non-cancer DNA from pairs of mothers and IL patients to characterize congenital variation that may contribute to early leukemogenesis. Using the COSMIC database to define acute leukemia-associated candidate genes, we find a significant enrichment of rare, potentially functional congenital variation in IL patients compared with randomly selected genes within the same patients and unaffected pediatric controls. IL acute myeloid leukemia (AML) patients had more overall variation than IL acute lymphocytic leukemia (ALL) patients, but less of that variation was inherited from mothers. Of our candidate genes, we found that MLL3 was a compound heterozygote in every infant who developed AML and 50% of infants who developed ALL. These data suggest a model by which known genetic mechanisms for leukemogenesis could be disrupted without an abundance of somatic mutation or chromosomal rearrangements. This model would be consistent with existing models for the establishment of leukemia clones in utero and the high rate of IL concordance in monozygotic twins.
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Affiliation(s)
- M C Valentine
- 1] Department of Genetics, Washington University School of Medicine, St Louis, MO, USA [2] Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - A M Linabery
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - S Chasnoff
- 1] Department of Genetics, Washington University School of Medicine, St Louis, MO, USA [2] Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - A E O Hughes
- 1] Department of Genetics, Washington University School of Medicine, St Louis, MO, USA [2] Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - C Mallaney
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - N Sanchez
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - J Giacalone
- 1] Department of Genetics, Washington University School of Medicine, St Louis, MO, USA [2] Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - N A Heerema
- Department of Pathology, Ohio State University, Columbus, OH, USA
| | - J M Hilden
- Department of Oncology/Hematology, Peyton Manning Children's Hospital at St Vincent, Indianapolis, IN, USA
| | - L G Spector
- 1] Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA [2] Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - J A Ross
- 1] Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA [2] Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - T E Druley
- 1] Department of Genetics, Washington University School of Medicine, St Louis, MO, USA [2] Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
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15
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DPY30 regulates pathways in cellular senescence through ID protein expression. EMBO J 2013; 32:2217-30. [PMID: 23872946 DOI: 10.1038/emboj.2013.159] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 06/20/2013] [Indexed: 11/08/2022] Open
Abstract
Cellular senescence is an intrinsic defense mechanism to various cellular stresses: while still metabolically active, senescent cells stop dividing and enter a proliferation arrest. Here, we identify DPY30, a member of all mammalian histone H3K4 histone methyltransferases (HMTases), as a key regulator of the proliferation potential of human primary cells. Following depletion of DPY30, cells show a severe proliferation defect and display a senescent phenotype, including a flattened and enlarged morphology, elevated level of reactive oxygen species (ROS), increased SA-β-galactosidase activity, and formation of senescence-associated heterochromatin foci (SAHFs). While DPY30 depletion leads to a reduced level of H3K4me3-marked active chromatin, we observed a concomitant activation of CDK inhibitors, including p16INK4a, independent of H3K4me3. ChIP experiments show that key regulators of cell-cycle progression, including ID proteins, are under direct control of DPY30. Because ID proteins are negative regulators of the transcription factors ETS1/2, depletion of DPY30 leads to the transcriptional activation of p16INK4a by ETS1/2 and thus to a senescent-like phenotype. Ectoptic re-introduction of ID protein expression can partially rescue the senescence-like phenotype induced by DPY30 depletion. Thus, our data indicate that DPY30 controls proliferation by regulating ID proteins expression, which in turn lead to senescence bypass.
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16
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Genomic hallmarks of genes involved in chromosomal translocations in hematological cancer. PLoS Comput Biol 2012; 8:e1002797. [PMID: 23236267 PMCID: PMC3516532 DOI: 10.1371/journal.pcbi.1002797] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/07/2012] [Indexed: 12/31/2022] Open
Abstract
Reciprocal chromosomal translocations (RCTs) leading to the formation of fusion genes are important drivers of hematological cancers. Although the general requirements for breakage and fusion are fairly well understood, quantitative support for a general mechanism of RCT formation is still lacking. The aim of this paper is to analyze available high-throughput datasets with computational and robust statistical methods, in order to identify genomic hallmarks of translocation partner genes (TPGs). Our results show that fusion genes are generally overexpressed due to increased promoter activity of 5′ TPGs and to more stable 3′-UTR regions of 3′ TPGs. Furthermore, expression profiling of 5′ TPGs and of interaction partners of 3′ TPGs indicates that these features can help to explain tissue specificity of hematological translocations. Analysis of protein domains retained in fusion proteins shows that the co-occurrence of specific domain combinations is non-random and that distinct functional classes of fusion proteins tend to be associated with different components of the gene fusion network. This indicates that the configuration of fusion proteins plays an important role in determining which 5′ and 3′ TPGs will combine in specific fusion genes. It is generally accepted that chromosomal proximity in the nucleus can explain the specific pairing of 5′ and 3′ TPGS and the recurrence of hematological translocations. Using recently available data for chromosomal contact probabilities (Hi-C) we show that TPGs are preferentially located in early replicated regions and occupy distinct clusters in the nucleus. However, our data suggest that, in general, nuclear position of TPGs in hematological cancers explains neither TPG pairing nor clinical frequency. Taken together, our results support a model in which genomic features related to regulation of expression and replication timing determine the set of candidate genes more likely to be translocated in hematological tissues, with functional constraints being responsible for specific gene combinations. A common genetic lesion leading to hematological cancer is the creation of fusion genes as a result of reciprocal translocations between chromosomes. Such translocations are non-random, in the sense that certain genes are more likely to be fused than others, and they appear to be tissue-specific. Current models tend to explain the non-random nature of chromosomal translocations suggesting that chromosome breaks are favored at certain sites and that the distance between genes in the nucleus determines the probability of their being fused together. In this work we have analyzed several genomic features in a large collection of genes involved in chromosomal translocations in hematological cancers, using robust computational methods. Our findings suggest that nuclear distance is a general pre-requisite but does not determine the specific combinations of genes fused together. We find that genomic features related to transcription and replication, together with constraints derived from the functional domains present in the proteins encoded by fusion genes, better explain which genes participate in specific chromosomal translocations and the tissue types in which they are found. The association of such genomic features with the position occupied by genes in the nucleus explains the apparent causal role attributed to spatial position.
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17
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Disordered epigenetic regulation in MLL-related leukemia. Int J Hematol 2012; 96:428-37. [DOI: 10.1007/s12185-012-1180-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 09/07/2012] [Accepted: 09/12/2012] [Indexed: 12/16/2022]
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18
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Lee JH, Skalnik DG. Rbm15-Mkl1 interacts with the Setd1b histone H3-Lys4 methyltransferase via a SPOC domain that is required for cytokine-independent proliferation. PLoS One 2012; 7:e42965. [PMID: 22927943 PMCID: PMC3424240 DOI: 10.1371/journal.pone.0042965] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
The Rbm15-Mkl1 fusion protein is associated with acute megakaryoblastic leukemia (AMKL), although little is known regarding the molecular mechanism(s) whereby this fusion protein contributes to leukemogenesis. Here, we show that both Rbm15 and the leukemogenic Rbm15-Mkl1 fusion protein interact with the Setd1b histone H3-Lys4 methyltransferase (also known as KMT2G). This interaction is direct and requires the Rbm15 SPOC domain and the Setd1b LSD motif. Over-expression of Rbm15-Mkl1 in the 6133 megakaryoblastic leukemia cell line, previously established by expression of the Rbm15-Mkl1 fusion protein in mice (Mercher et al., [2009] J. Clin. Invest. 119, 852-864), leads to decreased levels of endogenous Rbm15 and increased levels of endogenous Mkl1. These cells exhibit enhanced proliferation and cytokine-independent cell growth, which requires an intact Rbm15 SPOC domain that mediates interaction between the Rbm15-Mkl1 fusion protein and the Setd1b methyltransferase. These results reveal altered Setd1b complex function and consequent altered epigenetic regulation as a possible molecular mechanism that mediates the leukemogenic activity of the Rbm15-Mkl1 fusion protein in AMKL.
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Affiliation(s)
- Jeong-Heon Lee
- Wells Center for Pediatric Research, Departments of Pediatrics and Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail: (DGS); (JHL)
| | - David G. Skalnik
- Wells Center for Pediatric Research, Departments of Pediatrics and Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Biology, Indiana University-Purdue University Indianapolis School of Science, Indianapolis, Indiana, United States of America
- * E-mail: (DGS); (JHL)
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Stress hematopoiesis reveals abnormal control of self-renewal, lineage bias, and myeloid differentiation in Mll partial tandem duplication (Mll-PTD) hematopoietic stem/progenitor cells. Blood 2012; 120:1118-29. [PMID: 22740449 DOI: 10.1182/blood-2012-02-412379] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
One mechanism for disrupting the MLL gene in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) is through partial tandem duplication (MLL-PTD); however, the mechanism by which MLL-PTD contributes to MDS and AML development and maintenance is currently unknown. Herein, we investigated hematopoietic stem/progenitor cell (HSPC) phenotypes of Mll-PTD knock-in mice. Although HSPCs (Lin(-)Sca1(+)Kit(+) (LSK)/SLAM(+) and LSK) in Mll(PTD/WT) mice are reduced in absolute number in steady state because of increased apoptosis, they have a proliferative advantage in colony replating assays, CFU-spleen assays, and competitive transplantation assays over wild-type HSPCs. The Mll(PTD/WT)-derived phenotypic short-term (ST)-HSCs/multipotent progenitors and granulocyte/macrophage progenitors have self-renewal capability, rescuing hematopoiesis by giving rise to long-term repopulating cells in recipient mice with an unexpected myeloid differentiation blockade and lymphoid-lineage bias. However, Mll(PTD/WT) HSPCs never develop leukemia in primary or recipient mice, suggesting that additional genetic and/or epigenetic defects are necessary for full leukemogenic transformation. Thus, the Mll-PTD aberrantly alters HSPCs, enhances self-renewal, causes lineage bias, and blocks myeloid differentiation. These findings provide a framework by which we can ascertain the underlying pathogenic role of MLL-PTD in the clonal evolution of human leukemia, which should facilitate improved therapies and patient outcomes.
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20
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Zhang P, Lee H, Brunzelle JS, Couture JF. The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases. Nucleic Acids Res 2012; 40:4237-46. [PMID: 22266653 PMCID: PMC3351189 DOI: 10.1093/nar/gkr1235] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In mammals, the SET1 family of lysine methyltransferases (KMTs), which includes MLL1-5, SET1A and SET1B, catalyzes the methylation of lysine-4 (Lys-4) on histone H3. Recent reports have demonstrated that a three-subunit complex composed of WD-repeat protein-5 (WDR5), retinoblastoma-binding protein-5 (RbBP5) and absent, small, homeotic disks-2-like (ASH2L) stimulates the methyltransferase activity of MLL1. On the basis of studies showing that this stimulation is in part controlled by an interaction between WDR5 and a small region located in close proximity of the MLL1 catalytic domain [referred to as the WDR5-interacting motif (Win)], it has been suggested that WDR5 might play an analogous role in scaffolding the other SET1 complexes. We herein provide biochemical and structural evidence showing that WDR5 binds the Win motifs of MLL2-4, SET1A and SET1B. Comparative analysis of WDR5-Win complexes reveals that binding of the Win motifs is achieved by the plasticity of WDR5 peptidyl-arginine-binding cleft allowing the C-terminal ends of the Win motifs to be maintained in structurally divergent conformations. Consistently, enzymatic assays reveal that WDR5 plays an important role in the optimal stimulation of MLL2-4, SET1A and SET1B methyltransferase activity by the RbBP5-ASH2L heterodimer. Overall, our findings illustrate the function of WDR5 in scaffolding the SET1 family of KMTs and further emphasize on the important role of WDR5 in regulating global histone H3 Lys-4 methylation.
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Affiliation(s)
- Pamela Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada K1H 8M5 and Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, IL 60611, USA
| | - Hwabin Lee
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada K1H 8M5 and Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, IL 60611, USA
| | - Joseph S. Brunzelle
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada K1H 8M5 and Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, IL 60611, USA
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada K1H 8M5 and Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, IL 60611, USA,*To whom correspondence should be addressed. Tel: +613 562 5800 8854; Fax: +613 562 5655;
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21
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Shilatifard A. The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu Rev Biochem 2012; 81:65-95. [PMID: 22663077 PMCID: PMC4010150 DOI: 10.1146/annurev-biochem-051710-134100] [Citation(s) in RCA: 790] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Saccharomyces cerevisiae Set1/COMPASS was the first histone H3 lysine 4 (H3K4) methylase identified over 10 years ago. Since then, it has been demonstrated that Set1/COMPASS and its enzymatic product, H3K4 methylation, is highly conserved across the evolutionary tree. Although there is only one COMPASS in yeast, Drosophila possesses three and humans bear six COMPASS family members, each capable of methylating H3K4 with nonredundant functions. In yeast, the histone H2B monoubiquitinase Rad6/Bre1 is required for proper H3K4 and H3K79 trimethylations. The machineries involved in this process are also highly conserved from yeast to human. In this review, the process of histone H2B monoubiquitination-dependent and -independent histone H3K4 methylation as a mark of active transcription, enhancer signatures, and developmentally poised genes is discussed. The misregulation of histone H2B monoubiquitination and H3K4 methylation result in the pathogenesis of human diseases, including cancer. Recent findings in this regard are also examined.
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Affiliation(s)
- Ali Shilatifard
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.
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Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet 2011; 7:e1002401. [PMID: 22174696 PMCID: PMC3234212 DOI: 10.1371/journal.pgen.1002401] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/13/2011] [Indexed: 01/22/2023] Open
Abstract
Precise control of the innate immune response is required for resistance to microbial infections and maintenance of normal tissue homeostasis. Because this response involves coordinate regulation of hundreds of genes, it provides a powerful biological system to elucidate the molecular strategies that underlie signal- and time-dependent transitions of gene expression. Comprehensive genome-wide analysis of the epigenetic and transcription status of the TLR4-induced transcriptional program in macrophages suggests that Toll-like receptor 4 (TLR4)-dependent activation of nearly all immediate/early- (I/E) and late-response genes results from a sequential process in which signal-independent factors initially establish basal levels of gene expression that are then amplified by signal-dependent transcription factors. Promoters of I/E genes are distinguished from those of late genes by encoding a distinct set of signal-dependent transcription factor elements, including TATA boxes, which lead to preferential binding of TBP and basal enrichment for RNA polymerase II immediately downstream of transcriptional start sites. Global nuclear run-on (GRO) sequencing and total RNA sequencing further indicates that TLR4 signaling markedly increases the overall rates of both transcriptional initiation and the efficiency of transcriptional elongation of nearly all I/E genes, while RNA splicing is largely unaffected. Collectively, these findings reveal broadly utilized mechanisms underlying temporally distinct patterns of TLR4-dependent gene activation required for homeostasis and effective immune responses. The innate immune response is a complex biological program that is configured to allow host cells to rapidly respond to infection and tissue injury. An essential feature of this response is the sequential activation of large numbers of genes that play roles in amplification of the initial inflammatory response, exert anti-microbial activities, and initiate acquired immunity. Here, we use a combination of genome-wide approaches to characterize the basal and activated states of promoters that drive the expression of genes that are turned on at immediate/early or late times in macrophages following their stimulation with a mimetic of bacterial infection. These studies identify genetically encoded features that establish basal levels of expression and distinct temporal profiles of signal-dependent gene activation required for effective immune responses. The general features of immediate/early and late genes defined by these studies are likely to be instructive for understanding how other high-magnitude, temporally orchestrated programs of gene expression are established.
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Affiliation(s)
- Laure Escoubet-Lozach
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Christopher Benner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Minna U. Kaikkonen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- A. I. Virtanen Institute, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jean Lozach
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Sven Heinz
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Nathan J. Spann
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Andrea Crotti
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Josh Stender
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Serena Ghisletti
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Donna Reichart
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Christine S. Cheng
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Rosa Luna
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Colleen Ludka
- Biomedical Genomics Microarray Laboratory (BIOGEM), University of California San Diego, La Jolla, California, United States of America
| | - Roman Sasik
- Biomedical Genomics Microarray Laboratory (BIOGEM), University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ivan Garcia-Bassets
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
| | - Alexander Hoffmann
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Gary Hardiman
- Biomedical Genomics Microarray Laboratory (BIOGEM), University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Michael G. Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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23
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Latham JA, Chosed RJ, Wang S, Dent SYR. Chromatin signaling to kinetochores: transregulation of Dam1 methylation by histone H2B ubiquitination. Cell 2011; 146:709-19. [PMID: 21884933 DOI: 10.1016/j.cell.2011.07.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Revised: 06/15/2011] [Accepted: 07/19/2011] [Indexed: 11/25/2022]
Abstract
Histone H3K4 trimethylation by the Set1/MLL family of proteins provides a hallmark for transcriptional activity from yeast to humans. In S. cerevisiae, H3K4 methylation is mediated by the Set1-containing COMPASS complex and is regulated in trans by prior ubiquitination of histone H2BK123. All of the events that regulate H2BK123ub and H3K4me are thought to occur at gene promoters. Here we report that this pathway is indispensable for methylation of the only other known substrate of Set1, K233 in Dam1, at kinetochores. Deletion of RAD6, BRE1, or Paf1 complex members abolishes Dam1 methylation, as does mutation of H2BK123. Our results demonstrate that Set1-mediated methylation is regulated by a general pathway regardless of substrate that is composed of transcriptional regulatory factors functioning independently of transcription. Moreover, our data identify a node of regulatory crosstalk in trans between a histone modification and modification on a nonhistone protein, demonstrating that changing chromatin states can signal functional changes in other essential cellular proteins and machineries.
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Affiliation(s)
- John A Latham
- Program in Genes and Development, University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
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24
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The ability of MLL to bind RUNX1 and methylate H3K4 at PU.1 regulatory regions is impaired by MDS/AML-associated RUNX1/AML1 mutations. Blood 2011; 118:6544-52. [PMID: 22012064 DOI: 10.1182/blood-2010-11-317909] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The mixed-lineage leukemia (MLL) H3K4 methyltransferase protein, and the heterodimeric RUNX1/CBFβ transcription factor complex, are critical for definitive and adult hematopoiesis, and both are frequently targeted in human acute leukemia. We identified a physical and functional interaction between RUNX1 (AML1) and MLL and show that both are required to maintain the histone lysine 4 trimethyl mark (H3K4me3) at 2 critical regulatory regions of the AML1 target gene PU.1. Similar to CBFβ, we show that MLL binds to AML1 abrogating its proteasome-dependent degradation. Furthermore, a subset of previously uncharacterized frame-shift and missense mutations at the N terminus of AML1, found in MDS and AML patients, impairs its interaction with MLL, resulting in loss of the H3K4me3 mark within PU.1 regulatory regions, and decreased PU.1 expression. The interaction between MLL and AML1 provides a mechanism for the sequence-specific binding of MLL to DNA, and identifies RUNX1 target genes as potential effectors of MLL function.
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25
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Poole RJ, Bashllari E, Cochella L, Flowers EB, Hobert O. A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in Caenorhabditis elegans. PLoS Genet 2011; 7:e1002109. [PMID: 21698137 PMCID: PMC3116913 DOI: 10.1371/journal.pgen.1002109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 04/14/2011] [Indexed: 11/19/2022] Open
Abstract
One of the central goals of developmental neurobiology is to describe and understand the multi-tiered molecular events that control the progression of a fertilized egg to a terminally differentiated neuron. In the nematode Caenorhabditis elegans, the progression from egg to terminally differentiated neuron has been visually traced by lineage analysis. For example, the two gustatory neurons ASEL and ASER, a bilaterally symmetric neuron pair that is functionally lateralized, are generated from a fertilized egg through an invariant sequence of 11 cellular cleavages that occur stereotypically along specific cleavage planes. Molecular events that occur along this developmental pathway are only superficially understood. We take here an unbiased, genome-wide approach to identify genes that may act at any stage to ensure the correct differentiation of ASEL. Screening a genome-wide RNAi library that knocks-down 18,179 genes (94% of the genome), we identified 245 genes that affect the development of the ASEL neuron, such that the neuron is either not generated, its fate is converted to that of another cell, or cells from other lineage branches now adopt ASEL fate. We analyze in detail two factors that we identify from this screen: (1) the proneural gene hlh-14, which we find to be bilaterally expressed in the ASEL/R lineages despite their asymmetric lineage origins and which we find is required to generate neurons from several lineage branches including the ASE neurons, and (2) the COMPASS histone methyltransferase complex, which we find to be a critical embryonic inducer of ASEL/R asymmetry, acting upstream of the previously identified miRNA lsy-6. Our study represents the first comprehensive, genome-wide analysis of a single neuronal cell fate decision. The results of this analysis provide a starting point for future studies that will eventually lead to a more complete understanding of how individual neuronal cell types are generated from a single-cell embryo.
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Affiliation(s)
- Richard J. Poole
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York, United States of America
- * E-mail: (RJP); (OH)
| | - Enkelejda Bashllari
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York, United States of America
| | - Luisa Cochella
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York, United States of America
| | - Eileen B. Flowers
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York, United States of America
| | - Oliver Hobert
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York, United States of America
- * E-mail: (RJP); (OH)
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26
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Avdic V, Zhang P, Lanouette S, Groulx A, Tremblay V, Brunzelle J, Couture JF. Structural and biochemical insights into MLL1 core complex assembly. Structure 2011; 19:101-8. [PMID: 21220120 DOI: 10.1016/j.str.2010.09.022] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 08/31/2010] [Accepted: 09/30/2010] [Indexed: 12/31/2022]
Abstract
Histone H3 Lys-4 methylation is predominantly catalyzed by a family of methyltransferases whose enzymatic activity depends on their interaction with a three-subunit complex composed of WDR5, RbBP5, and Ash2L. Here, we report that a segment of 50 residues of RbBP5 bridges the Ash2L C-terminal domain to WDR5. The crystal structure of WDR5 in ternary complex with RbBP5 and MLL1 reveals that both proteins binds peptide-binding clefts located on opposite sides of WDR5's β-propeller domain. RbBP5 engages in several hydrogen bonds and van der Waals contacts within a V-shaped cleft formed by the junction of two blades on WDR5. Mutational analyses of both the WDR5 V-shaped cleft and RbBP5 residues reveal that the interactions between RbBP5 and WDR5 are important for the stimulation of MLL1 methyltransferase activity. Overall, this study provides the structural basis underlying the formation of the WDR5-RbBP5 subcomplex and further highlight the crucial role of WDR5 in scaffolding the MLL1 core complex.
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Affiliation(s)
- Vanja Avdic
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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27
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Illi B, Colussi C, Rosati J, Spallotta F, Nanni S, Farsetti A, Capogrossi MC, Gaetano C. NO points to epigenetics in vascular development. Cardiovasc Res 2011; 90:447-56. [PMID: 21345806 DOI: 10.1093/cvr/cvr056] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Our understanding of epigenetic mechanisms important for embryonic vascular development and cardiovascular differentiation is still in its infancy. Although molecular analyses, including massive genome sequencing and/or in vitro/in vivo targeting of specific gene sets, has led to the identification of multiple factors involved in stemness maintenance or in the early processes of embryonic layers specification, very little is known about the epigenetic commitment to cardiovascular lineages. The object of this review will be to outline the state of the art in this field and trace the perspective therapeutic consequences of studies aimed at elucidating fundamental epigenetic networks. Special attention will be paid to the emerging role of nitric oxide in this field.
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Affiliation(s)
- Barbara Illi
- Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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28
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García-Alai MM, Allen MD, Joerger AC, Bycroft M. The structure of the FYR domain of transforming growth factor beta regulator 1. Protein Sci 2010; 19:1432-8. [PMID: 20506279 PMCID: PMC2970912 DOI: 10.1002/pro.404] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Many chromatin-associated proteins contain two sequence motifs rich in phenylalanine/tyrosine residues of unknown function. These so-called FYRN and FYRC motifs are also found in transforming growth factor beta regulator 1 (TBRG1)/nuclear interactor of ARF and MDM2 (NIAM), a growth inhibitory protein that also plays a role in maintaining chromosomal stability. We have solved the structure of a fragment of TBRG1, which encompasses both of these motifs. The FYRN and FYRC regions each form part of a single folded module (the FYR domain), which adopts a novel α + β fold. Proteins such as the histone H3K4 methyltransferases trithorax and mixed lineage leukemia (MLL), in which the FYRN and FYRC regions are separated by hundreds of amino acids, are expected to contain FYR domains with a large insertion between two of the strands of the β-sheet.
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Affiliation(s)
- María M García-Alai
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, United Kingdom
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29
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Menin and RNF20 recruitment is associated with dynamic histone modifications that regulate signal transducer and activator of transcription 1 (STAT1)-activated transcription of the interferon regulatory factor 1 gene (IRF1). Epigenetics Chromatin 2010; 3:16. [PMID: 20825659 PMCID: PMC2940767 DOI: 10.1186/1756-8935-3-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 09/08/2010] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Signal transducer and activator of transcription (STAT) activation of gene expression is both rapid and transient, and when properly executed it affects growth, differentiation, homeostasis and the immune response, but when dysregulated it contributes to human disease. Transcriptional activation is regulated by alterations to the chromatin template. However, the role of histone modification at gene loci that are activated for transcription in response to STAT signaling is poorly defined. RESULTS Using chromatin immunoprecipitation, we profiled several histone modifications during STAT1 activation of the interferon regulatory factor 1 gene (IRF1). Methylated lysine histone proteins H3K4me2, H3K4me3, H3K79me3, H3K36me3 and monoubiquitinated histone ubH2B are dynamic and correlate with interferon (IFN)γ induction of STAT1 activity. Chemical inhibition of H3K4 methylation downregulates IRF1 transcription and decreases RNA polymerase II (Pol II) occupancy at the IRF1 promoter. MEN1, a component of a complex proteins associated with Set1 (COMPASS)-like complex and the hBRE1 component, RNF20, are localized to IRF1 in the uninduced state and are further recruited when IRF1 is activated. RNAi-mediated depletion of RNF20 lowers both ubH2B and H3K4me3, but surprisingly, upregulates IFNγ induced IRF1 transcription. The dynamics of phosphorylation in the C-terminal domain (CTD) of Pol II are disrupted during gene activation as well. CONCLUSIONS H2B monoubiquitination promotes H3K4 methylation, but the E3 ubiquitin ligase, RNF20, is repressive of inducible transcription at the IRF1 gene locus, suggesting that ubH2B can, directly or indirectly, affect Pol II CTD phosphorylation cycling to exert control on ongoing transcription.
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30
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Pasini D, Malatesta M, Jung HR, Walfridsson J, Willer A, Olsson L, Skotte J, Wutz A, Porse B, Jensen ON, Helin K. Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes. Nucleic Acids Res 2010; 38:4958-69. [PMID: 20385584 PMCID: PMC2926606 DOI: 10.1093/nar/gkq244] [Citation(s) in RCA: 268] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Polycomb group (PcG) proteins are transcriptional repressors, which regulate proliferation and cell fate decisions during development, and their deregulated expression is a frequent event in human tumours. The Polycomb repressive complex 2 (PRC2) catalyzes trimethylation (me3) of histone H3 lysine 27 (K27), and it is believed that this activity mediates transcriptional repression. Despite the recent progress in understanding PcG function, the molecular mechanisms by which the PcG proteins repress transcription, as well as the mechanisms that lead to the activation of PcG target genes are poorly understood. To gain insight into these mechanisms, we have determined the global changes in histone modifications in embryonic stem (ES) cells lacking the PcG protein Suz12 that is essential for PRC2 activity. We show that loss of PRC2 activity results in a global increase in H3K27 acetylation. The methylation to acetylation switch correlates with the transcriptional activation of PcG target genes, both during ES cell differentiation and in MLL-AF9-transduced hematopoietic stem cells. Moreover, we provide evidence that the acetylation of H3K27 is catalyzed by the acetyltransferases p300 and CBP. Based on these data, we propose that the PcG proteins in part repress transcription by preventing the binding of acetyltransferases to PcG target genes.
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Affiliation(s)
- Diego Pasini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
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31
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Lin C, Smith ER, Takahashi H, Lai KC, Martin-Brown S, Florens L, Washburn MP, Conaway JW, Conaway RC, Shilatifard A. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Mol Cell 2010; 37:429-37. [PMID: 20159561 DOI: 10.1016/j.molcel.2010.01.026] [Citation(s) in RCA: 453] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 12/29/2009] [Accepted: 01/25/2010] [Indexed: 02/08/2023]
Abstract
Chromosomal translocations involving the MLL gene are associated with infant acute lymphoblastic and mixed lineage leukemia. There are a large number of translocation partners of MLL that share very little sequence or seemingly functional similarities; however, their translocations into MLL result in the pathogenesis of leukemia. To define the molecular reason why these translocations result in the pathogenesis of leukemia, we purified several of the commonly occurring MLL chimeras. We have identified super elongation complex (SEC) associated with all chimeras purified. SEC includes ELL, P-TEFb, AFF4, and several other factors. AFF4 is required for SEC stability and proper transcription by poised RNA polymerase II in metazoans. Knockdown of AFF4 in leukemic cells shows reduction in MLL chimera target gene expression, suggesting that AFF4/SEC could be a key regulator in the pathogenesis of leukemia through many of the MLL partners.
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Affiliation(s)
- Chengqi Lin
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
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32
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Kim DH, Doyle MR, Sung S, Amasino RM. Vernalization: winter and the timing of flowering in plants. Annu Rev Cell Dev Biol 2010; 25:277-99. [PMID: 19575660 DOI: 10.1146/annurev.cellbio.042308.113411] [Citation(s) in RCA: 338] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plants have evolved many systems to sense their environment and to modify their growth and development accordingly. One example is vernalization, the process by which flowering is promoted as plants sense exposure to the cold temperatures of winter. A requirement for vernalization is an adaptive trait that helps prevent flowering before winter and permits flowering in the favorable conditions of spring. In Arabidopsis and cereals, vernalization results in the suppression of genes that repress flowering. We describe recent progress in understanding the molecular basis of this suppression. In Arabidopsis, vernalization involves the recruitment of chromatin-modifying complexes to a clade of flowering repressors that are silenced epigenetically via histone modifications. We also discuss the similarities and differences in vernalization between Arabidopsis and cereals.
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Affiliation(s)
- Dong-Hwan Kim
- Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
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33
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Abstract
Epigenetic modifications are heritable chromatin alterations that contribute to the temporal and spatial interpretation of the genome. The epigenetic information is conveyed through a multitude of chemical modifications, including DNA methylation, reversible modifications of histones, and ATP-dependent nucleosomal remodeling. Deregulation of the epigenetic machinery contributes to the development of several pathologies, including cancer. Chromatin modifications are multiple and interdependent and they are dynamically modulated in the course of various biological processes. Combinations of chromatin modifications give rise to a complex code that is superimposed on the genetic code embedded into the DNA sequence to regulate cell function. This review addresses the role of epigenetic modifications in cancer, focusing primarily on histone methylation marks and the enzymes catalyzing their removal.
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Affiliation(s)
- Sotirios C Kampranis
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts 02111, USA
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34
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Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. Mol Cell Biol 2009; 29:6074-85. [PMID: 19703992 DOI: 10.1128/mcb.00924-09] [Citation(s) in RCA: 273] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions. Set1/COMPASS was the founding member and is the only H3K4 methylase in Saccharomyces cerevisiae; however, in mammals, at least six H3K4 methylases, Set1A and Set1B and MLL1 to MLL4, are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wide analysis of H3K4 methylation patterns in wild-type Mll1(+/+) and Mll1(-)(/)(-) mouse embryonic fibroblasts (MEFs). We found that Mll1 is required for the H3K4 trimethylation of less than 5% of promoters carrying this modification. Many of these genes, which include developmental regulators such as Hox genes, show decreased levels of RNA polymerase II recruitment and expression concomitant with the loss of H3K4 methylation. Although Mll1 is only required for the methylation of a subset of Hox genes, menin, a component of the Mll1 and Mll2 complexes, is required for the overwhelming majority of H3K4 methylation at Hox loci. However, the loss of MLL3/MLL4 and/or the Set1 complexes has little to no effect on the H3K4 methylation of Hox loci or their expression levels in these MEFs. Together these data provide insight into the redundancy and specialization of COMPASS-like complexes in mammals and provide evidence for a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation.
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35
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Eissenberg JC, Shilatifard A. Histone H3 lysine 4 (H3K4) methylation in development and differentiation. Dev Biol 2009; 339:240-9. [PMID: 19703438 DOI: 10.1016/j.ydbio.2009.08.017] [Citation(s) in RCA: 232] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 08/13/2009] [Accepted: 08/17/2009] [Indexed: 12/29/2022]
Abstract
Covalent modification of histones on chromatin is a dynamic mechanism by which various nuclear processes are regulated. Methylation of histone H3 on lysine 4 (H3K4) implemented by the macromolecular complex COMPASS and its related complexes is associated with transcriptionally active regions of chromatin. Enzymes that catalyze H3K4 methylation were initially characterized genetically as regulators of Hox loci, long before their catalytic functions were recognized. Since their discovery, genetic and biochemical studies of H3K4 methylases and demethylases have provided important mechanistic insight into the role of H3K4 methylation in HOX gene regulation during development.
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Affiliation(s)
- Joel C Eissenberg
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1100 South Grand Boulevard, St. Louis, MO 63104, USA.
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36
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Jackson J, Shilatifard A. Global proteomic analysis of Saccharomyces cerevisiae identifies molecular pathways of histone modifications. Methods Mol Biol 2009; 548:175-86. [PMID: 19521825 DOI: 10.1007/978-1-59745-540-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The very long DNA of the eukaryotic cells must remain functional when packaged into the cell nucleus. Although we know very little about this process, it is clear at this time that chromatin and its post-translational modifications play a pivotal role. Yeast Saccharomyces cerevisiae provides a powerful genetic and biochemical model system for deciphering the molecular machinery involved in chromatin modification and transcriptional regulation. In this chapter, we describe a novel method, the Global Proteomic analysis in S. cerevisiae (GPS), for the global analysis of the molecular machinery required for proper histone modifications. Since many of the molecular machineries involved in chromatin biology are highly conserved from yeast to humans, GPS has proven to be an outstanding method for the identification of the molecular pathways involved in chromatin modifications.
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Affiliation(s)
- Jessica Jackson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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37
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Ansari KI, Hussain I, Das HK, Mandal SS. Overexpression of human histone methylase MLL1 upon exposure to a food contaminant mycotoxin, deoxynivalenol. FEBS J 2009; 276:3299-307. [PMID: 19438726 DOI: 10.1111/j.1742-4658.2009.07055.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Mixed lineage leukemias (MLLs) are histone-methylating enzymes with critical roles in gene expression, epigenetics and cancer. Although MLLs are important gene regulators little is known about their own regulation. Herein, to understand the effects of toxic stress on MLL gene regulation, we treated human cells with a common food contaminant mycotoxin, deoxynivalenol (DON). Our results demonstrate that MLLs and Hox genes are overexpressed upon exposure to DON. Studies using specific inhibitors demonstrated that Src kinase families are involved in upstream events in DON-mediated upregulation of MLL1. Sequence analysis demonstrated that the MLL1 promoter contains multiple Sp1-binding sites and importantly, the binding of Sp1 is enriched in the MLL1 promoter upon exposure to DON. Moreover, antisense-mediated knockdown of Sp1 diminished DON-induced MLL1 upregulation. These results demonstrated that MLL1 gene expression is sensitive to toxic stress and Sp1 plays crucial roles in the stress-induced upregulation of MLL1.
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Affiliation(s)
- Khairul I Ansari
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, TX 76019, USA
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Regulation of H3K4 trimethylation via Cps40 (Spp1) of COMPASS is monoubiquitination independent: implication for a Phe/Tyr switch by the catalytic domain of Set1. Mol Cell Biol 2009; 29:3478-86. [PMID: 19398585 DOI: 10.1128/mcb.00013-09] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The multiprotein complex Set1/COMPASS is the founding member of the histone H3 lysine 4 (H3K4) methyltransferases, whose human homologs include the MLL and hSet1 complexes. COMPASS can mono-, di-, and trimethylate H3K4, but transitioning to di- and trimethylation requires prior H2B monoubiquitination followed by recruitment of the Cps35 (Swd2) subunit of COMPASS. Another subunit, Cps40 (Spp1), interacts directly with Set1 and is only required for transitioning to trimethylation. To investigate how the Set1 and COMPASS subunits establish the methylation states of H3K4, we generated a homology model of the catalytic domain of Saccharomyces cerevisiae yeast Set1 and identified several key residues within the Set1 catalytic pocket that are capable of regulating COMPASS's activity. We show that Tyr1052, a putative Phe/Tyr switch of Set1, plays an essential role in the regulation of H3K4 trimethylation by COMPASS and that the mutation to phenylalanine (Y1052F) suppresses the loss of Cps40 in H3K4 trimethylation levels, suggesting that Tyr1052 functions together with Cps40. However, the loss of H2B monoubiquitination is not suppressed by this mutation, while Cps40 is stably assembled in COMPASS on chromatin, demonstrating that Tyr1052- and Cps40-mediated H3K4 trimethylation takes place following and independently of H2B monoubiquitination. Our studies provide a molecular basis for the way in which H3K4 trimethylation is regulated by Tyr1052 and the Cps40 subunit of COMPASS.
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Yadav S, Singhal J, Singhal SS, Awasthi S. hSET1: a novel approach for colon cancer therapy. Biochem Pharmacol 2009; 77:1635-41. [PMID: 19426701 DOI: 10.1016/j.bcp.2009.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 02/19/2009] [Accepted: 02/23/2009] [Indexed: 11/17/2022]
Abstract
Histone-methyl transferases (HMTs) are key enzymes that post-translationally modify histones, and serve key role in gene expression, epigenetic regulation, and as determinants of survival in malignant cells. Recent studies have shed light on the role of hSET1 which is a key element of highly conserved multi-protein HMT complex that catalyze methylation of histone H3 lysine 4 (H3K4) regulating expression of specific proteins important for the malignant phenotype. To understand the importance of differential expression of H3K4 HMTs in cancer, we specifically down-regulated hSET1 the only H3K4 specific histone-methyl transferase present in yeast as well as in human that is directly involved in gene expression. hSET1 has been shown to be differentially over-expressed in the malignant cells as compared to the normal cells at the RNA as well as protein level. In a wide array of normal and malignant cells it has been demonstrated that phosphorothioate antisense against hSET1 (DN5) caused selective and differential apoptosis in malignant cells only while the normal cells remains unaffected. Down-regulation of hSET1 leads to rapid and complete regression of SW480 colon xenograft in mice model. These findings demonstrate that hSET1 over-expression promotes cell proliferation and cancer cell survival, and may be a novel target for cancer therapy.
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Affiliation(s)
- Sushma Yadav
- Department of Molecular Biology and Immunology, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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40
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Mishra BP, Ansari KI, Mandal SS. Dynamic association of MLL1, H3K4 trimethylation with chromatin and Hox gene expression during the cell cycle. FEBS J 2009; 276:1629-40. [PMID: 19220463 DOI: 10.1111/j.1742-4658.2009.06895.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mixed lineage leukemias (MLLs) are histone H3 at lysine 4 (H3K4)-specific methylases that play a critical role in regulating gene expression in humans. As chromatin condensation, relaxation and differential gene expression are keys to correct cell cycle progression, we analyzed the dynamic association of MLL and H3K4 trimethylation at different stages of the cell cycle. Interestingly, MLL1, which is normally associated with transcriptionally active chromatins (G1 phase), dissociates from condensed mitotic chromatin and returns at the end of telophase when the nucleus starts to relax. In contrast, H3K4 trimethylation mark, which is also normally associated with euchromatins (in G1), remains associated, even with condensed chromatin, throughout the cell cycle. The global levels of MLL1 and H3K4 trimethylation are not affected during the cell cycle, and H3Ser28 phosphorylation is only observed during mitosis. Interestingly, MLL target homeobox-containing (Hox) genes (HoxA5, HoxA7 and HoxA10) are differentially expressed during the cell cycle, and the recruitment of MLL1 and H3K4 trimethylation levels are modulated in the promoter of these Hox genes as a function of their expression. In addition, down-regulation of MLL1 results in cell cycle arrest at the G2/M phase. The fluctuation of H3K4 trimethylation marks at specific promoters, but not at the global level, indicates that H3K4 trimethylation marks that are present in the G1 phase may not be the same as the marks in other phases of the cell cycle; rather, old marks are removed and new marks are introduced. In conclusion, our studies demonstrate that MLL1 and H3K4 methylation have distinct dynamics during the cell cycle and play critical roles in the differential expression of Hox genes associated with cell cycle regulation.
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Affiliation(s)
- Bibhu P Mishra
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington 76019, TX, USA
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SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet 2008; 4:e1000280. [PMID: 19043555 PMCID: PMC2582956 DOI: 10.1371/journal.pgen.1000280] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 10/27/2008] [Indexed: 01/03/2023] Open
Abstract
De novo DNA methylation and the maintenance of DNA methylation in asymmetrical sequence contexts is catalyzed by homologous proteins in plants (DRM2) and animals (DNMT3a/b). In plants, targeting of DRM2 depends on small interfering RNAs (siRNAs), although the molecular details are still unclear. Here, we show that two SRA-domain proteins (SUVH9 and SUVH2) are also essential for DRM2-mediated de novo and maintenance DNA methylation in Arabidopsis thaliana. At some loci, SUVH9 and SUVH2 act redundantly, while at other loci only SUVH2 is required, and this locus specificity correlates with the differing DNA-binding affinity of the SRA domains within SUVH9 and SUVH2. Specifically, SUVH9 preferentially binds methylated asymmetric sites, while SUVH2 preferentially binds methylated CG sites. The suvh9 and suvh2 mutations do not eliminate siRNAs, suggesting a role for SUVH9 and SUVH2 late in the RNA-directed DNA methylation pathway. With these new results, it is clear that SRA-domain proteins are involved in each of the three pathways leading to DNA methylation in Arabidopsis. Our genetic heritage plays an important role in determining who we are and the characteristics we possess. However, in the past decade it has become increasingly clear that in addition to the genes we inherit, a second level of information is critical for expression of these genes. This information takes the form of modifications to either the DNA (DNA methylation) or the proteins that package the DNA (histones). These modifications can determine whether a gene is expressed or silenced. In this paper, we identify two new genes that are part of a DNA methylation–targeting pathway in the model plant A. thaliana. Disruption of these two closely related genes prevents DNA methylation by one of the cellular DNA methyltransferases. However, these genes are not simply redundant. They are both capable of binding methylated DNA, but differ in their preference for specific sequences in the genome. This ability to bind to methylated DNA suggests that these proteins help target or retain the modification apparatus at particular regions of the genome. These results are important in that they identify two new players in this vital cellular process and bring us closer to understanding how epigenetic modifications can be targeted to specific genes.
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Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS. Mol Cell Biol 2008; 28:7337-44. [PMID: 18838538 DOI: 10.1128/mcb.00976-08] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In yeast, the macromolecular complex Set1/COMPASS is capable of methylating H3K4, a posttranslational modification associated with actively transcribed genes. There is only one Set1 in yeast; yet in mammalian cells there are multiple H3K4 methylases, including Set1A/B, forming human COMPASS complexes, and MLL1-4, forming human COMPASS-like complexes. We have shown that Wdr82, which associates with chromatin in a histone H2B ubiquitination-dependent manner, is a specific component of Set1 complexes but not that of MLL1-4 complexes. RNA interference-mediated knockdown of Wdr82 results in a reduction in the H3K4 trimethylation levels, although these cells still possess active MLL complexes. Comprehensive in vitro enzymatic studies with Set1 and MLL complexes demonstrated that the Set1 complex is a more robust H3K4 trimethylase in vitro than the MLL complexes. Given our in vivo and in vitro observations, it appears that the human Set1 complex plays a more widespread role in H3K4 trimethylation than do the MLL complexes in mammalian cells.
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Hirst M, Marra MA. Epigenetics and human disease. Int J Biochem Cell Biol 2008; 41:136-46. [PMID: 18852064 DOI: 10.1016/j.biocel.2008.09.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2008] [Revised: 09/13/2008] [Accepted: 09/16/2008] [Indexed: 01/29/2023]
Abstract
Changes to covalent modifications of DNA and histones can be induced via environmental stimuli such as nutrients, hormones and drugs. These changes can be both transient and heritable in nature and provide a framework in which to investigate how environment and lifestyle choices impact disease susceptibility and progression. Furthermore, these modifications are central to chromatin dynamics and, as such, play key roles in many biological processes involving chromatin, such as DNA replication and repair, transcription and development. In this review we provide an overview of recent advances in our understanding of the roles that DNA and histone modification play in the onset and progression of human disease.
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Affiliation(s)
- Martin Hirst
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada, V5Z 1L3
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Shilatifard A. Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation. Curr Opin Cell Biol 2008; 20:341-8. [PMID: 18508253 DOI: 10.1016/j.ceb.2008.03.019] [Citation(s) in RCA: 370] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2008] [Revised: 03/17/2008] [Accepted: 03/20/2008] [Indexed: 10/22/2022]
Abstract
Chromosomal surfaces are ornamented with a variety of post-translational modifications of histones, which are required for the regulation of many of the DNA-templated processes. Such histone modifications include acetylation, sumoylation, phosphorylation, ubiquitination, and methylation. Histone modifications can either function by disrupting chromosomal contacts or by regulating non-histone protein interactions with chromatin. In this review, recent findings will be discussed regarding the regulation of the implementation and physiological significance for one such histone modification, histone H3 lysine 4 (H3K4) methylation by the yeast COMPASS and mammalian COMPASS-like complexes.
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Affiliation(s)
- Ali Shilatifard
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.
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Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, Florens L, Bhaumik SR, Shilatifard A. Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell 2008; 131:1084-96. [PMID: 18083099 DOI: 10.1016/j.cell.2007.09.046] [Citation(s) in RCA: 318] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Revised: 08/13/2007] [Accepted: 09/28/2007] [Indexed: 11/28/2022]
Abstract
COMPASS, the yeast homolog of the mammalian MLL complex, is a histone H3 lysine 4 (H3K4) methylase consisting of Set1 (KMT2) and seven other polypeptides, including Cps35, the only essential subunit. Histone H2B monoubiquitination by Rad6/Bre1 is required for both H3K4 methylation by COMPASS, and H3K79 methylation by Dot1. However, the molecular mechanism for such histone crosstalk is poorly understood. Here, we demonstrate that histone H2B monoubiquitination controls the binding of Cps35 with COMPASS complex. Cps 35 is required for COMPASS' catalytic activity in vivo, and the addition of exogenous purified Cps35 to COMPASS purified from a Deltarad6 background results in the generation of a methylation competent COMPASS. Cps35 associates with the chromatin of COMPASS-regulated genes in a H2BK123 monoubiquitination-dependent but Set1-independent manner. Cps35 is also required for proper H3K79 trimethylation. These findings offer insight into the molecular role of Cps35 in translating the H2B monoubiquitination signal into H3 methylation.
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Affiliation(s)
- Jung-Shin Lee
- Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA
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46
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Ansari KI, Mishra BP, Mandal SS. Human CpG binding protein interacts with MLL1, MLL2 and hSet1 and regulates Hox gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2007; 1779:66-73. [PMID: 18082152 DOI: 10.1016/j.bbagrm.2007.11.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 10/05/2007] [Accepted: 11/09/2007] [Indexed: 10/22/2022]
Abstract
Human encodes several histone H3-Lysine 4 (H3K4) specific methyl-transferases (HMTs) such as MLL1 (mixed lineage leukemia 1), MLL2, MLL3, hSet1 etc, that play critical roles in gene expression. These HMTs are present as distinct multi-protein complexes with several proteins in common. Herein, we have affinity purified and characterized human CpG binding protein (CGBP) and its interacting proteins from human cells. We demonstrated that CGBP is co-purified with three H3K4 specific HMTs MLL1, MLL2, and hSet1. We also performed independent immuno-precipitation of MLL1, MLL2 and hSet1 complexes from human cell and demonstrated that each of these complexes contains CGBP. In addition, CGBP is co-localized with MLL1, MLL2 and hSet1 in vivo and binds to the promoter of MLL target gene HoxA7. Antisense mediated knock down of CGBP diminished the recruitment of MLL1 and down regulated levels of H3K4 trimethylation in HoxA7 promoter affecting its expression. These results demonstrated that CGBP interacts with MLL1, MLL2 as well as hSet1 HMTs and plays critical roles in regulations of MLL target genes.
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Affiliation(s)
- Khairul I Ansari
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA
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47
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Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007; 130:77-88. [PMID: 17632057 PMCID: PMC3200295 DOI: 10.1016/j.cell.2007.05.042] [Citation(s) in RCA: 1507] [Impact Index Per Article: 88.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 04/06/2007] [Accepted: 05/17/2007] [Indexed: 12/18/2022]
Abstract
We describe the results of a genome-wide analysis of human cells that suggests that most protein-coding genes, including most genes thought to be transcriptionally inactive, experience transcription initiation. We found that nucleosomes with H3K4me3 and H3K9,14Ac modifications, together with RNA polymerase II, occupy the promoters of most protein-coding genes in human embryonic stem cells. Only a subset of these genes produce detectable full-length transcripts and are occupied by nucleosomes with H3K36me3 modifications, a hallmark of elongation. The other genes experience transcription initiation but show no evidence of elongation, suggesting that they are predominantly regulated at postinitiation steps. Genes encoding most developmental regulators fall into this group. Our results also identify a class of genes that are excluded from experiencing transcription initiation, at which mechanisms that prevent initiation must predominate. These observations extend to differentiated cells, suggesting that transcription initiation at most genes is a general phenomenon in human cells.
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Affiliation(s)
- Matthew G. Guenther
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Stuart S. Levine
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Laurie A. Boyer
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence:
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48
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Matthews AGW, Kuo AJ, Ramón-Maiques S, Han S, Champagne KS, Ivanov D, Gallardo M, Carney D, Cheung P, Ciccone DN, Walter KL, Utz PJ, Shi Y, Kutateladze TG, Yang W, Gozani O, Oettinger MA. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 2007; 450:1106-10. [PMID: 18033247 DOI: 10.1038/nature06431] [Citation(s) in RCA: 368] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 11/02/2007] [Indexed: 01/05/2023]
Abstract
Nuclear processes such as transcription, DNA replication and recombination are dynamically regulated by chromatin structure. Eukaryotic transcription is known to be regulated by chromatin-associated proteins containing conserved protein domains that specifically recognize distinct covalent post-translational modifications on histones. However, it has been unclear whether similar mechanisms are involved in mammalian DNA recombination. Here we show that RAG2--an essential component of the RAG1/2 V(D)J recombinase, which mediates antigen-receptor gene assembly--contains a plant homeodomain (PHD) finger that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3). The high-resolution crystal structure of the mouse RAG2 PHD finger bound to H3K4me3 reveals the molecular basis of H3K4me3-recognition by RAG2. Mutations that abrogate RAG2's recognition of H3K4me3 severely impair V(D)J recombination in vivo. Reducing the level of H3K4me3 similarly leads to a decrease in V(D)J recombination in vivo. Notably, a conserved tryptophan residue (W453) that constitutes a key structural component of the K4me3-binding surface and is essential for RAG2's recognition of H3K4me3 is mutated in patients with immunodeficiency syndromes. Together, our results identify a new function for histone methylation in mammalian DNA recombination. Furthermore, our results provide the first evidence indicating that disrupting the read-out of histone modifications can cause an inherited human disease.
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Affiliation(s)
- Adam G W Matthews
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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Guccione E, Bassi C, Casadio F, Martinato F, Cesaroni M, Schuchlautz H, Lüscher B, Amati B. Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature 2007; 449:933-7. [PMID: 17898714 DOI: 10.1038/nature06166] [Citation(s) in RCA: 350] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 08/10/2007] [Indexed: 12/11/2022]
Abstract
Eukaryotic genomes are organized into active (euchromatic) and inactive (heterochromatic) chromatin domains. Post-translational modifications of histones (or 'marks') are key in defining these functional states, particularly in promoter regions. Mutual regulatory interactions between these marks--and the enzymes that catalyse them--contribute to the shaping of this epigenetic landscape, in a manner that remains to be fully elucidated. We previously observed that asymmetric di-methylation of histone H3 arginine 2 (H3R2me2a) counter-correlates with di- and tri- methylation of H3 lysine 4 (H3K4me2, H3K4me3) on human promoters. Here we show that the arginine methyltransferase PRMT6 catalyses H3R2 di-methylation in vitro and controls global levels of H3R2me2a in vivo. H3R2 methylation by PRMT6 was prevented by the presence of H3K4me3 on the H3 tail. Conversely, the H3R2me2a mark prevented methylation of H3K4 as well as binding to the H3 tail by an ASH2/WDR5/MLL-family methyltransferase complex. Chromatin immunoprecipitation showed that H3R2me2a was distributed within the body and at the 3' end of human genes, regardless of their transcriptional state, whereas it was selectively and locally depleted from active promoters, coincident with the presence of H3K4me3. Hence, the mutual antagonism between H3R2 and H3K4 methylation, together with the association of MLL-family complexes with the basal transcription machinery, may contribute to the localized patterns of H3K4 tri-methylation characteristic of transcriptionally poised or active promoters in mammalian genomes.
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Affiliation(s)
- Ernesto Guccione
- Department of Experimental Oncology, European Institute of Oncology (IEO), IFOM-IEO Campus, Milan 20139, Italy
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50
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McClendon AK, Osheroff N. DNA topoisomerase II, genotoxicity, and cancer. Mutat Res 2007; 623:83-97. [PMID: 17681352 PMCID: PMC2679583 DOI: 10.1016/j.mrfmmm.2007.06.009] [Citation(s) in RCA: 300] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 06/06/2007] [Accepted: 06/16/2007] [Indexed: 12/23/2022]
Abstract
Type II topoisomerases are ubiquitous enzymes that play essential roles in a number of fundamental DNA processes. They regulate DNA under- and overwinding, and resolve knots and tangles in the genetic material by passing an intact double helix through a transient double-stranded break that they generate in a separate segment of DNA. Because type II topoisomerases generate DNA strand breaks as a requisite intermediate in their catalytic cycle, they have the potential to fragment the genome every time they function. Thus, while these enzymes are essential to the survival of proliferating cells, they also have significant genotoxic effects. This latter aspect of type II topoisomerase has been exploited for the development of several classes of anticancer drugs that are widely employed for the clinical treatment of human malignancies. However, considerable evidence indicates that these enzymes also trigger specific leukemic chromosomal translocations. In light of the impact, both positive and negative, of type II topoisomerases on human cells, it is important to understand how these enzymes function and how their actions can destabilize the genome. This article discusses both aspects of human type II topoisomerases.
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Affiliation(s)
- A. Kathleen McClendon
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- Corresponding author. Tel: +1 615 3224338; fax: +1 615 3431166, E-mail address: (N. Osheroff)
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