151
|
Ui A, Nagaura Y, Yasui A. Transcriptional Elongation Factor ENL Phosphorylated by ATM Recruits Polycomb and Switches Off Transcription for DSB Repair. Mol Cell 2015; 58:468-82. [DOI: 10.1016/j.molcel.2015.03.023] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 02/09/2015] [Accepted: 03/18/2015] [Indexed: 12/21/2022]
|
152
|
Aoshima K, Inoue E, Sawa H, Okada Y. Paternal H3K4 methylation is required for minor zygotic gene activation and early mouse embryonic development. EMBO Rep 2015; 16:803-12. [PMID: 25925669 DOI: 10.15252/embr.201439700] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 04/09/2015] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications, such as DNA methylation and histone modifications, are dynamically altered predominantly in paternal pronuclei soon after fertilization. To identify which histone modifications are required for early embryonic development, we utilized histone K-M mutants, which prevent endogenous histone methylation at the mutated site. We prepared four single K-M mutants for histone H3.3, K4M, K9M, K27M, and K36M, and demonstrate that overexpression of H3.3 K4M in embryos before fertilization results in developmental arrest, whereas overexpression after fertilization does not affect the development. Furthermore, loss of H3K4 methylation decreases the level of minor zygotic gene activation (ZGA) predominantly in the paternal pronucleus, and we obtained similar results from knockdown of the H3K4 methyltransferase Mll3/4. We therefore conclude that H3K4 methylation, likely established by Mll3/4 at the early pronuclear stage, is essential for the onset of minor ZGA in the paternal pronucleus, which is necessary for subsequent preimplantation development in mice.
Collapse
Affiliation(s)
- Keisuke Aoshima
- Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku Tokyo, Japan Division of Molecular Pathobiology, Center for Zoonosis Control, Hokkaido University, Kita-ku Sapporo, Japan Research Fellow of Japan Society for the Promotion of Science, Chiyoda-ku Tokyo, Japan
| | - Erina Inoue
- Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku Tokyo, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Center for Zoonosis Control, Hokkaido University, Kita-ku Sapporo, Japan
| | - Yuki Okada
- Laboratory of Pathology and Development, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku Tokyo, Japan PRESTO, Japan Science and Technology Agency (JST), Kawaguchi-Honcho Saitama, Japan
| |
Collapse
|
153
|
Reikvam H, Hoang TTV, Bruserud Ø. Emerging therapeutic targets in human acute myeloid leukemia (part 2) – bromodomain inhibition should be considered as a possible strategy for various patient subsets. Expert Rev Hematol 2015; 8:315-27. [DOI: 10.1586/17474086.2015.1036025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
154
|
Treviño LS, Wang Q, Walker CL. Phosphorylation of epigenetic "readers, writers and erasers": Implications for developmental reprogramming and the epigenetic basis for health and disease. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:8-13. [PMID: 25841987 DOI: 10.1016/j.pbiomolbio.2015.02.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/23/2015] [Indexed: 02/06/2023]
Abstract
Epigenetic reprogramming that occurs during critical periods of development can increase the susceptibility to many diseases in adulthood. Programming of the epigenome during development occurs via the activity of a variety of epigenetic modifiers, including "readers, writers and erasers" of histone methyl marks. Posttranslational modification of these programmers can alter their activity, resulting in global or gene-specific changes in histone methylation and gene transcription. This review summarizes what is currently known about phosphorylation of histone methyltransferases ("writers"), demethylases ("erasers") and effector proteins ("readers) that program the epigenome, and the impact of this posttranslational modification on their activity. Understanding how the activity of these epigenetic programmers is perturbed by environmental exposures via changes in phosphorylation is key to understanding mechanisms of developmental reprogramming and the epigenetic basis of health and disease.
Collapse
Affiliation(s)
- Lindsey S Treviño
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Quan Wang
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Cheryl L Walker
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA.
| |
Collapse
|
155
|
Abstract
Studies by cancer genome consortiums have identified frequent mutations in chromatin regulatory factors and histone proteins in human cancer, implicating them as major mediators in the pathogenesis of both hematological malignancies and solid tumors. Here, Morgan and Shilatifard review recent advances in our understanding of the role of chromatin in cancer, focusing on transcriptional regulatory complexes, enhancer-associated factors, histone point mutations, and alterations in heterochromatin-interacting factors. Changes in the pattern of gene expression play an important role in allowing cancer cells to acquire their hallmark characteristics, while genomic instability enables cells to acquire genetic alterations that promote oncogenesis. Chromatin plays central roles in both transcriptional regulation and the maintenance of genomic stability. Studies by cancer genome consortiums have identified frequent mutations in genes encoding chromatin regulatory factors and histone proteins in human cancer, implicating them as major mediators in the pathogenesis of both hematological malignancies and solid tumors. Here, we review recent advances in our understanding of the role of chromatin in cancer, focusing on transcriptional regulatory complexes, enhancer-associated factors, histone point mutations, and alterations in heterochromatin-interacting factors.
Collapse
Affiliation(s)
- Marc A Morgan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| |
Collapse
|
156
|
Rudolph A, Milne RL, Truong T, Knight JA, Seibold P, Flesch-Janys D, Behrens S, Eilber U, Bolla MK, Wang Q, Dennis J, Dunning AM, Shah M, Munday HR, Darabi H, Eriksson M, Brand JS, Olson J, Vachon CM, Hallberg E, Castelao JE, Carracedo A, Torres M, Li J, Humphreys K, Cordina-Duverger E, Menegaux F, Flyger H, Nordestgaard BG, Nielsen SF, Yesilyurt BT, Floris G, Leunen K, Engelhardt EG, Broeks A, Rutgers EJ, Glendon G, Mulligan AM, Cross S, Reed M, Gonzalez-Neira A, Perez JIA, Provenzano E, Apicella C, Southey MC, Spurdle A, Investigators KC, Group AOCS, Häberle L, Beckmann MW, Ekici AB, Dieffenbach AK, Arndt V, Stegmaier C, McLean C, Baglietto L, Chanock SJ, Lissowska J, Sherman ME, Brüning T, Hamann U, Ko YD, Orr N, Schoemaker M, Ashworth A, Kosma VM, Kataja V, Hartikainen JM, Mannermaa A, Swerdlow A, Giles GG, Brenner H, Fasching PA, Chenevix-Trench G, Hopper J, Benítez J, Cox A, Andrulis IL, Lambrechts D, Gago-Dominguez M, Couch F, Czene K, Bojesen SE, Easton DF, Schmidt MK, Guénel P, Hall P, Pharoah PDP, Garcia-Closas M, Chang-Claude J. Investigation of gene-environment interactions between 47 newly identified breast cancer susceptibility loci and environmental risk factors. Int J Cancer 2015; 136:E685-96. [PMID: 25227710 PMCID: PMC4289418 DOI: 10.1002/ijc.29188] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 12/21/2022]
Abstract
A large genotyping project within the Breast Cancer Association Consortium (BCAC) recently identified 41 associations between single nucleotide polymorphisms (SNPs) and overall breast cancer (BC) risk. We investigated whether the effects of these 41 SNPs, as well as six SNPs associated with estrogen receptor (ER) negative BC risk are modified by 13 environmental risk factors for BC. Data from 22 studies participating in BCAC were pooled, comprising up to 26,633 cases and 30,119 controls. Interactions between SNPs and environmental factors were evaluated using an empirical Bayes-type shrinkage estimator. Six SNPs showed interactions with associated p-values (pint ) <1.1 × 10(-3) . None of the observed interactions was significant after accounting for multiple testing. The Bayesian False Discovery Probability was used to rank the findings, which indicated three interactions as being noteworthy at 1% prior probability of interaction. SNP rs6828523 was associated with increased ER-negative BC risk in women ≥170 cm (OR = 1.22, p = 0.017), but inversely associated with ER-negative BC risk in women <160 cm (OR = 0.83, p = 0.039, pint = 1.9 × 10(-4) ). The inverse association between rs4808801 and overall BC risk was stronger for women who had had four or more pregnancies (OR = 0.85, p = 2.0 × 10(-4) ), and absent in women who had had just one (OR = 0.96, p = 0.19, pint = 6.1 × 10(-4) ). SNP rs11242675 was inversely associated with overall BC risk in never/former smokers (OR = 0.93, p = 2.8 × 10(-5) ), but no association was observed in current smokers (OR = 1.07, p = 0.14, pint = 3.4 × 10(-4) ). In conclusion, recently identified BC susceptibility loci are not strongly modified by established risk factors and the observed potential interactions require confirmation in independent studies.
Collapse
Affiliation(s)
- Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Thérèse Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- Unité Mixte de Recherche Scientifique (UMRS) 1018, University Paris-Sud, Villejuif, France
| | - Julia A. Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ursula Eilber
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hannah R. Munday
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Judith S. Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Janet Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Celine M. Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - J. Esteban Castelao
- Oncology and Genetics Unit, Biomedical Research Institute of Vigo (IBIV), Complejo Hospitalario Universitario de Vigo, Servicio Galego de Saude (SERGAS), Vigo, Spain
| | - Angel Carracedo
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Servicio Galego de Saude (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- National Genotyping Center - Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), University of Santiago de Compostela, Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, KSA
| | - Maria Torres
- National Genotyping Center - Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), University of Santiago de Compostela, Spain
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Cordina-Duverger
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- Unité Mixte de Recherche Scientifique (UMRS) 1018, University Paris-Sud, Villejuif, France
| | - Florence Menegaux
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- Unité Mixte de Recherche Scientifique (UMRS) 1018, University Paris-Sud, Villejuif, France
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Børge G. Nordestgaard
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sune F. Nielsen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Giuseppe Floris
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Leuven, Belgium
| | - Karin Leunen
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Leuven, Belgium
| | - Ellen G. Engelhardt
- Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Annegien Broeks
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Emiel J. Rutgers
- Department of Surgery, Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Gord Glendon
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Marie Mulligan
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Simon Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, UK
| | - Malcolm Reed
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Anna Gonzalez-Neira
- Human Genotyping Unit-CEGEN, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Elena Provenzano
- Cancer Research UK Cambridge Institute, Cambridge, UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | | | - Amanda Spurdle
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - AOCS Group
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Lothar Häberle
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Aida Karina Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland
| | - Mark E. Sherman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, USA
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Minouk Schoemaker
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Oncology and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Jaana M. Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
- Division of Breast Cancer Research, Institute of Cancer Research, Sutton, Surrey, UK
| | - GENICA-Network
- The GENICA Network: Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tübingen, Germany; Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany, Institute of Pathology, University of Bonn, Germany, Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany, and Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany; Institute of Occupational Medicine and Maritime Medicine, University Medical Center Hamburg-Eppendorf, Germany
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, CA, USA
| | | | - John Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, Australia
| | - Javier Benítez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Irene L. Andrulis
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Servicio Galego de Saude (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Doug F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, Villejuif, France
- Unité Mixte de Recherche Scientifique (UMRS) 1018, University Paris-Sud, Villejuif, France
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Montserrat Garcia-Closas
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
157
|
Ekumi KM, Paculova H, Lenasi T, Pospichalova V, Bösken CA, Rybarikova J, Bryja V, Geyer M, Blazek D, Barboric M. Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex. Nucleic Acids Res 2015; 43:2575-89. [PMID: 25712099 PMCID: PMC4357706 DOI: 10.1093/nar/gkv101] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 01/05/2015] [Accepted: 01/30/2015] [Indexed: 12/11/2022] Open
Abstract
The Cdk12/CycK complex promotes expression of a subset of RNA polymerase II genes, including those of the DNA damage response. CDK12 is among only nine genes with recurrent somatic mutations in high-grade serous ovarian carcinoma. However, the influence of these mutations on the Cdk12/CycK complex and their link to cancerogenesis remain ill-defined. Here, we show that most mutations prevent formation of the Cdk12/CycK complex, rendering the kinase inactive. By examining the mutations within the Cdk12/CycK structure, we find that they likely provoke structural rearrangements detrimental to Cdk12 activation. Our mRNA expression analysis of the patient samples containing the CDK12 mutations reveals coordinated downregulation of genes critical to the homologous recombination DNA repair pathway. Moreover, we establish that the Cdk12/CycK complex occupies these genes and promotes phosphorylation of RNA polymerase II at Ser2. Accordingly, we demonstrate that the mutant Cdk12 proteins fail to stimulate the faithful DNA double strand break repair via homologous recombination. Together, we provide the molecular basis of how mutated CDK12 ceases to function in ovarian carcinoma. We propose that CDK12 is a tumor suppressor of which the loss-of-function mutations may elicit defects in multiple DNA repair pathways, leading to genomic instability underlying the genesis of the cancer.
Collapse
Affiliation(s)
- Kingsley M Ekumi
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Hana Paculova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Tina Lenasi
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Vendula Pospichalova
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
| | - Christian A Bösken
- Center of Advanced European Studies and Research, Group Physical Biochemistry, 53175 Bonn, Germany
| | - Jana Rybarikova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Vitezslav Bryja
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Matthias Geyer
- Center of Advanced European Studies and Research, Group Physical Biochemistry, 53175 Bonn, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Matjaz Barboric
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| |
Collapse
|
158
|
Jonkers I, Lis JT. Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2015; 16:167-77. [PMID: 25693130 PMCID: PMC4782187 DOI: 10.1038/nrm3953] [Citation(s) in RCA: 572] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances in sequencing techniques that measure nascent transcripts and that reveal the positioning of RNA polymerase II (Pol II) have shown that the pausing of Pol II in promoter-proximal regions and its release to initiate a phase of productive elongation are key steps in transcription regulation. Moreover, after the release of Pol II from the promoter-proximal region, elongation rates are highly dynamic throughout the transcription of a gene, and vary on a gene-by-gene basis. Interestingly, Pol II elongation rates affect co-transcriptional processes such as splicing, termination and genome stability. Increasing numbers of factors and regulatory mechanisms have been associated with the steps of transcription elongation by Pol II, revealing that elongation is a highly complex process. Elongation is thus now recognized as a key phase in the regulation of transcription by Pol II.
Collapse
Affiliation(s)
- Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, 416 Biotechnology Building, 14853, Ithaca, New York, USA
| |
Collapse
|
159
|
Weng X, Yu L, Liang P, Li L, Dai X, Zhou B, Wu X, Xu H, Fang M, Chen Q, Xu Y. A crosstalk between chromatin remodeling and histone H3K4 methyltransferase complexes in endothelial cells regulates angiotensin II-induced cardiac hypertrophy. J Mol Cell Cardiol 2015; 82:48-58. [PMID: 25712920 DOI: 10.1016/j.yjmcc.2015.02.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 02/10/2015] [Indexed: 02/08/2023]
Abstract
Angiotensin II (Ang II) induces cardiac hypertrophy and fibrosis in part by stimulating endothelin (ET-1) transcription. The involvement of the epigenetic machinery in this process is largely undefined. In the present study, we examined the epigenetic maneuvering underlying cardiac hypertrophy and fibrosis following ET-1 transactivation by Ang II. In response to Ang II stimulation, core components of the mammalian chromatin remodeling complex (Brahma-related gene 1, or Brg1, and Brahma or Brm) and histone H3K4 methylation complex (Ash2, absent, small, or homeotic discs 2, or Ash2 and WD domain repeat 5, or Wdr5) were recruited to the ET-1 promoter region in endothelial cells. Over-expression of Brg1/Brm or Ash2/Wdr5 enhanced while depletion of Brg1/Brm or Ash2/Wdr5 attenuated Ang II-induced ET-1 transactivation. Endothelial-specific knockdown of Brg1/Brm or Ash2/Wdr5 ameliorated cardiac hypertrophy both in vitro and in vivo. More important, Brg1/Brm interacted with Ash2/Wdr5 on the ET-1 promoter to catalyze H3K4 methylation. The crosstalk between Brg11/Brm and Ash2/Wdr5 was mediated by myocardin-related transcription factor A (MRTF-A). In conclusion, our data have unveiled an epigenetic complex that links ET-1 transactivation in endothelial cells to Ang II-induced cardiac hypertrophy and fibrosis.
Collapse
Affiliation(s)
- Xinyu Weng
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Liming Yu
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Peng Liang
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Luyang Li
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xin Dai
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Bisheng Zhou
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xiaoyan Wu
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Huihui Xu
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Mingming Fang
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China; Department of Nursing, Jiangsu Jiankang Vocational University, Nanjing, China.
| | - Qi Chen
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yong Xu
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.
| |
Collapse
|
160
|
Dobenecker MW, Kim JK, Marcello J, Fang TC, Prinjha R, Bosselut R, Tarakhovsky A. Coupling of T cell receptor specificity to natural killer T cell development by bivalent histone H3 methylation. ACTA ACUST UNITED AC 2015; 212:297-306. [PMID: 25687282 PMCID: PMC4354372 DOI: 10.1084/jem.20141499] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The fidelity of T cell immunity depends greatly on coupling T cell receptor signaling with specific T cell effector functions. Here, we describe a chromatin-based mechanism that enables integration of TCR specificity into definite T cell lineage commitment. Using natural killer T cells (iNKT cell) as a model of a T cell subset that differentiates in response to specific TCR signaling, we identified a key role of histone H3 lysine 27 trimethylation (H3K27me3) in coupling iNKT cell TCR specificity with the generation of iNKT cells. We found that the Zbtb16/PLZF gene promoter that drives iNKT cell differentiation possesses a bivalent chromatin state characterized by the simultaneous presence of negative and positive H3K27me3 and H3K4me3 modifications. Depletion of H3K27me3 at the Zbtb16/PLZF promoter leads to uncoupling of iNKT cell development from TCR specificity and is associated with accumulation of iNKT-like CD4(+) cells that express a non-iNKT cell specific T cell repertoire. In turn, stabilization of H3K27me3 leads to a drastic reduction of the iNKT cell population. Our data suggest that H3K27me3 levels at the bivalent Zbtb16/PLZF gene define a threshold enabling precise coupling of TCR specificity to lineage commitment.
Collapse
Affiliation(s)
- Marc-Werner Dobenecker
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065
| | - Jong Kyong Kim
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jonas Marcello
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065
| | - Terry C Fang
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065
| | - Rab Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Stevenage SG1 2NY, England, UK
| | - Remy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY 10065
| |
Collapse
|
161
|
di Masi A, Leboffe L, De Marinis E, Pagano F, Cicconi L, Rochette-Egly C, Lo-Coco F, Ascenzi P, Nervi C. Retinoic acid receptors: from molecular mechanisms to cancer therapy. Mol Aspects Med 2015; 41:1-115. [PMID: 25543955 DOI: 10.1016/j.mam.2014.12.003] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/15/2014] [Indexed: 02/07/2023]
Abstract
Retinoic acid (RA), the major bioactive metabolite of retinol or vitamin A, induces a spectrum of pleiotropic effects in cell growth and differentiation that are relevant for embryonic development and adult physiology. The RA activity is mediated primarily by members of the retinoic acid receptor (RAR) subfamily, namely RARα, RARβ and RARγ, which belong to the nuclear receptor (NR) superfamily of transcription factors. RARs form heterodimers with members of the retinoid X receptor (RXR) subfamily and act as ligand-regulated transcription factors through binding specific RA response elements (RAREs) located in target genes promoters. RARs also have non-genomic effects and activate kinase signaling pathways, which fine-tune the transcription of the RA target genes. The disruption of RA signaling pathways is thought to underlie the etiology of a number of hematological and non-hematological malignancies, including leukemias, skin cancer, head/neck cancer, lung cancer, breast cancer, ovarian cancer, prostate cancer, renal cell carcinoma, pancreatic cancer, liver cancer, glioblastoma and neuroblastoma. Of note, RA and its derivatives (retinoids) are employed as potential chemotherapeutic or chemopreventive agents because of their differentiation, anti-proliferative, pro-apoptotic, and anti-oxidant effects. In humans, retinoids reverse premalignant epithelial lesions, induce the differentiation of myeloid normal and leukemic cells, and prevent lung, liver, and breast cancer. Here, we provide an overview of the biochemical and molecular mechanisms that regulate the RA and retinoid signaling pathways. Moreover, mechanisms through which deregulation of RA signaling pathways ultimately impact on cancer are examined. Finally, the therapeutic effects of retinoids are reported.
Collapse
Affiliation(s)
- Alessandra di Masi
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Loris Leboffe
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Elisabetta De Marinis
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100
| | - Francesca Pagano
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100
| | - Laura Cicconi
- Department of Biomedicine and Prevention, University of Roma "Tor Vergata", Via Montpellier 1, Roma I-00133, Italy; Laboratory of Neuro-Oncohematology, Santa Lucia Foundation, Via Ardeatina, 306, Roma I-00142, Italy
| | - Cécile Rochette-Egly
- Department of Functional Genomics and Cancer, IGBMC, CNRS UMR 7104 - Inserm U 964, University of Strasbourg, 1 rue Laurent Fries, BP10142, Illkirch Cedex F-67404, France.
| | - Francesco Lo-Coco
- Department of Biomedicine and Prevention, University of Roma "Tor Vergata", Via Montpellier 1, Roma I-00133, Italy; Laboratory of Neuro-Oncohematology, Santa Lucia Foundation, Via Ardeatina, 306, Roma I-00142, Italy.
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, Roma I-00146, Italy.
| | - Clara Nervi
- Department of Medical and Surgical Sciences and Biotechnologies, University of Roma "La Sapienza", Corso della Repubblica 79, Latina I-04100.
| |
Collapse
|
162
|
Fong N, Kim H, Zhou Y, Ji X, Qiu J, Saldi T, Diener K, Jones K, Fu XD, Bentley DL. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev 2015; 28:2663-76. [PMID: 25452276 PMCID: PMC4248296 DOI: 10.1101/gad.252106.114] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Fong et al. examined cotranscriptional pre-mRNA splicing using RNA polymerase II mutants that change average elongation rates genome-wide. Slow and fast elongation affected constitutive and alternative splicing and often both increased or both decreased inclusion of a particular exon or retained intron. These results suggest that an optimal rate of transcriptional elongation is required for normal cotranscriptional pre-mRNA splicing. Alternative splicing modulates expression of most human genes. The kinetic model of cotranscriptional splicing suggests that slow elongation expands and that fast elongation compresses the “window of opportunity” for recognition of upstream splice sites, thereby increasing or decreasing inclusion of alternative exons. We tested the model using RNA polymerase II mutants that change average elongation rates genome-wide. Slow and fast elongation affected constitutive and alternative splicing, frequently altering exon inclusion and intron retention in ways not predicted by the model. Cassette exons included by slow and excluded by fast elongation (type I) have weaker splice sites, shorter flanking introns, and distinct sequence motifs relative to “slow-excluded” and “fast-included” exons (type II). Many rate-sensitive exons are misspliced in tumors. Unexpectedly, slow and fast elongation often both increased or both decreased inclusion of a particular exon or retained intron. These results suggest that an optimal rate of transcriptional elongation is required for normal cotranscriptional pre-mRNA splicing.
Collapse
Affiliation(s)
- Nova Fong
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Hyunmin Kim
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Yu Zhou
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California at San Diego, San Diego, California 92093, USA
| | - Xiong Ji
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California at San Diego, San Diego, California 92093, USA
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California at San Diego, San Diego, California 92093, USA
| | - Tassa Saldi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Katrina Diener
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Ken Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California at San Diego, San Diego, California 92093, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA;
| |
Collapse
|
163
|
Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM. Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts. Mol Cell Biol 2015; 35:468-78. [PMID: 25384976 PMCID: PMC4272423 DOI: 10.1128/mcb.01157-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 10/07/2014] [Accepted: 11/01/2014] [Indexed: 01/05/2023] Open
Abstract
Transcriptional cyclin-dependent kinases (CDKs) regulate RNA polymerase II initiation and elongation as well as cotranscriptional mRNA processing. In this report, we describe an important role for CDK12 in the epidermal growth factor (EGF)-induced c-FOS proto-oncogene expression in mammalian cells. This kinase was found in the exon junction complexes (EJC) together with SR proteins and was thus recruited to RNA polymerase II. In cells depleted of CDK12 or eukaryotic translation initiation factor 4A3 (eIF4A3) from the EJC, EGF induced fewer c-FOS transcripts. In these cells, phosphorylation of serines at position 2 in the C-terminal domain (CTD) of RNA polymerase II, as well as levels of cleavage-stimulating factor 64 (Cstf64) and 73-kDa subunit of cleavage and polyadenylation specificity factor (CPSF73), was reduced at the c-FOS gene. These effects impaired 3' end processing of c-FOS transcripts. Mutant CDK12 proteins lacking their Arg-Ser-rich (RS) domain or just the RS domain alone acted as dominant negative proteins. Thus, CDK12 plays an important role in cotranscriptional processing of c-FOS transcripts.
Collapse
Affiliation(s)
- Tristan T Eifler
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Wei Shao
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Koen Bartholomeeusen
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Koh Fujinaga
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Stefanie Jäger
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California, USA California Institute for Quantitative Biosciences, QB3, San Francisco, California, USA
| | - Jeff R Johnson
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California, USA California Institute for Quantitative Biosciences, QB3, San Francisco, California, USA
| | - Zeping Luo
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California, USA California Institute for Quantitative Biosciences, QB3, San Francisco, California, USA
| | - B Matija Peterlin
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| |
Collapse
|
164
|
Liu C, Yu Y, Liu F, Wei X, Wrobel JA, Gunawardena HP, Zhou L, Jin J, Chen X. A chromatin activity-based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing. Nat Commun 2014; 5:5733. [PMID: 25502336 PMCID: PMC4360912 DOI: 10.1038/ncomms6733] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 11/02/2014] [Indexed: 12/17/2022] Open
Abstract
Immune cells develop endotoxin tolerance (ET) after prolonged stimulation. ET increases the level of a repression mark H3K9me2 in the transcriptional-silent chromatin specifically associated with pro-inflammatory genes. However, it is not clear what proteins are functionally involved in this process. Here we show that a novel chromatin activity based chemoproteomic (ChaC) approach can dissect the functional chromatin protein complexes that regulate ET-associated inflammation. Using UNC0638 that binds the enzymatically active H3K9-specific methyltransferase G9a/GLP, ChaC reveals that G9a is constitutively active at a G9a-dependent mega-dalton repressome in primary endotoxin-tolerant macrophages. G9a/GLP broadly impacts the ET-specific reprogramming of the histone code landscape, chromatin remodeling, and the activities of select transcription factors. We discover that the G9a-dependent epigenetic environment promotes the transcriptional repression activity of c-Myc for gene-specific co-regulation of chronic inflammation. ChaC may be also applicable to dissect other functional protein complexes in the context of phenotypic chromatin architectures.
Collapse
Affiliation(s)
- Cui Liu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Yanbao Yu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Xin Wei
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - John A Wrobel
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Harsha P Gunawardena
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Li Zhou
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jian Jin
- Department of Structural and Chemical Biology, Department of Oncological Sciences, and Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Xian Chen
- 1] Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA [2] Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA [3] Department of Chemistry, Fudan University, Shanghai 200433, China
| |
Collapse
|
165
|
Riggi N, Knoechel B, Gillespie SM, Rheinbay E, Boulay G, Suvà ML, Rossetti NE, Boonseng WE, Oksuz O, Cook EB, Formey A, Patel A, Gymrek M, Thapar V, Deshpande V, Ting DT, Hornicek FJ, Nielsen GP, Stamenkovic I, Aryee MJ, Bernstein BE, Rivera MN. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell 2014; 26:668-681. [PMID: 25453903 PMCID: PMC4492343 DOI: 10.1016/j.ccell.2014.10.004] [Citation(s) in RCA: 286] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/14/2014] [Accepted: 10/06/2014] [Indexed: 01/10/2023]
Abstract
The aberrant transcription factor EWS-FLI1 drives Ewing sarcoma, but its molecular function is not completely understood. We find that EWS-FLI1 reprograms gene regulatory circuits in Ewing sarcoma by directly inducing or repressing enhancers. At GGAA repeat elements, which lack evolutionary conservation and regulatory potential in other cell types, EWS-FLI1 multimers induce chromatin opening and create de novo enhancers that physically interact with target promoters. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors. These divergent chromatin-remodeling patterns repress tumor suppressors and mesenchymal lineage regulators while activating oncogenes and potential therapeutic targets, such as the kinase VRK1. Our findings demonstrate how EWS-FLI1 establishes an oncogenic regulatory program governing both tumor survival and differentiation.
Collapse
Affiliation(s)
- Nicolò Riggi
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Birgit Knoechel
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shawn M Gillespie
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Esther Rheinbay
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gaylor Boulay
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikki E Rossetti
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wannaporn E Boonseng
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ozgur Oksuz
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Edward B Cook
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Aurélie Formey
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Anoop Patel
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Neurosurgery Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Melissa Gymrek
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Vishal Thapar
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Francis J Hornicek
- Center for Sarcoma and Connective Tissue Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - G Petur Nielsen
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ivan Stamenkovic
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Martin J Aryee
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Miguel N Rivera
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|
166
|
Shi X, Zhang Z, Zhan X, Cao M, Satoh T, Akira S, Shpargel K, Magnuson T, Li Q, Wang R, Wang C, Ge K, Wu J. An epigenetic switch induced by Shh signalling regulates gene activation during development and medulloblastoma growth. Nat Commun 2014; 5:5425. [PMID: 25370275 DOI: 10.1038/ncomms6425] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 09/30/2014] [Indexed: 12/15/2022] Open
Abstract
The Sonic hedgehog (Shh) signalling pathway plays important roles during development and in cancer. Here we report a Shh-induced epigenetic switch that cooperates with Gli to control transcription outcomes. Before induction, poised Shh target genes are marked by a bivalent chromatin domain containing a repressive histone H3K27me3 mark and an active H3K4me3 mark. Shh activation induces a local switch of epigenetic cofactors from the H3K27 methyltransferase polycomb repressive complex 2 (PRC2) to an H3K27me3 demethylase Jmjd3/Kdm6b-centred coactivator complex. We also find that non-enzymatic activities of Jmjd3 are important and that Jmjd3 recruits the Set1/MLL H3K4 methyltransferase complexes in a Shh-dependent manner to resolve the bivalent domain. In vivo, changes of the bivalent domain accompanied Shh-activated cerebellar progenitor proliferation. Overall, our results reveal a regulatory mechanism that underlies the activation of Shh target genes and provides insight into the causes of various diseases and cancers exhibiting altered Shh signalling.
Collapse
Affiliation(s)
- Xuanming Shi
- Department of Physiology and Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Zilai Zhang
- Department of Physiology and Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Xiaoming Zhan
- Department of Physiology and Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Mou Cao
- Department of Physiology and Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Takashi Satoh
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center and Department of Host Defense, RIMD, Osaka University, Osaka, Japan
| | - Shizuo Akira
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center and Department of Host Defense, RIMD, Osaka University, Osaka, Japan
| | - Karl Shpargel
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Terry Magnuson
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Qingtian Li
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, Texas 77030, USA
| | - Rongfu Wang
- Center for Inflammation and Epigenetics, The Methodist Hospital Research Institute, Houston, Texas 77030, USA
| | | | - Kai Ge
- NIDDK, NIH, Bethesda, Maryland 20892, USA
| | - Jiang Wu
- Department of Physiology and Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| |
Collapse
|
167
|
Li Y, Wen H, Xi Y, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Dent SY, Li W, Li H, Shi X. AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylation. Cell 2014; 159:558-71. [PMID: 25417107 PMCID: PMC4344132 DOI: 10.1016/j.cell.2014.09.049] [Citation(s) in RCA: 274] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/18/2014] [Accepted: 09/18/2014] [Indexed: 01/07/2023]
Abstract
The recognition of modified histones by "reader" proteins constitutes a key mechanism regulating gene expression in the chromatin context. Compared with the great variety of readers for histone methylation, few protein modules that recognize histone acetylation are known. Here, we show that the AF9 YEATS domain binds strongly to histone H3K9 acetylation and, to a lesser extent, H3K27 and H3K18 acetylation. Crystal structural studies revealed that AF9 YEATS adopts an eight-stranded immunoglobin fold and utilizes a serine-lined aromatic "sandwiching" cage for acetyllysine readout, representing a novel recognition mechanism that is distinct from that of known acetyllysine readers. ChIP-seq experiments revealed a strong colocalization of AF9 and H3K9 acetylation genome-wide, which is important for the chromatin recruitment of the H3K79 methyltransferase DOT1L. Together, our studies identified the evolutionarily conserved YEATS domain as a novel acetyllysine-binding module and established a direct link between histone acetylation and DOT1L-mediated H3K79 methylation in transcription control.
Collapse
Affiliation(s)
- Yuanyuan Li
- Collaborative Innovation Center for Biotherapy, MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine,Department of Basic Medical Sciences, School of Medicine,Tsinghua-Peking Center for Life Sciences Tsinghua University, Beijing 100084, China
| | - Hong Wen
- Department of Molecular Carcinogenesis,Center for Cancer Epigenetics The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuanxin Xi
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kaori Tanaka
- Center for Cancer Epigenetics The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Haibo Wang
- Collaborative Innovation Center for Biotherapy, MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine,Department of Basic Medical Sciences, School of Medicine
| | | | - Yongfeng Ren
- Collaborative Innovation Center for Biotherapy, MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine,Department of Basic Medical Sciences, School of Medicine
| | | | - Sharon Y.R. Dent
- Department of Molecular Carcinogenesis,Center for Cancer Epigenetics The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA,Genes and Development and Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haitao Li
- Collaborative Innovation Center for Biotherapy, MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine,Department of Basic Medical Sciences, School of Medicine,Correspondence and requests for materials should be addressed to or
| | - Xiaobing Shi
- Department of Molecular Carcinogenesis,Center for Cancer Epigenetics The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA,Genes and Development and Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA,Correspondence and requests for materials should be addressed to or
| |
Collapse
|
168
|
Park KS, Bayles I, Szlachta-McGinn A, Paul J, Boiko J, Santos P, Liu J, Wang Z, Borghesi L, Milcarek C. Transcription elongation factor ELL2 drives Ig secretory-specific mRNA production and the unfolded protein response. THE JOURNAL OF IMMUNOLOGY 2014; 193:4663-74. [PMID: 25238757 DOI: 10.4049/jimmunol.1401608] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Differentiation of B cells into Ab-secreting cells induces changes in gene transcription, IgH RNA processing, the unfolded protein response (UPR), and cell architecture. The transcription elongation factor eleven nineteen lysine-rich leukemia gene (ELL2) stimulates the processing of the secreted form of the IgH mRNA from the H chain gene. Mice (mus musculus) with the ELL2 gene floxed in either exon 1 or exon 3 were constructed and crossed to CD19-driven cre/CD19(+). The B cell-specific ELL2 conditional knockouts (cKOs; ell2(loxp/loxp) CD19(cre/+)) exhibit curtailed humoral responses both in 4-hydroxy-3-nitrophenyl acetyl-Ficoll and in 4-hydroxy-3-nitrophenyl acetyl-keyhole limpet hemocyanin immunized animals; recall responses were also diminished. The number of immature and recirculating B cells in the bone marrow is increased in the cKOs, whereas plasma cells in spleen are reduced relative to control animals. There are fewer IgG1 Ab-producing cells in the bone marrow of cKOs. LPS ex vivo-stimulated B220(lo)CD138(+) cells from ELL2-deficient mouse spleens are 4-fold less abundant than from control splenic B cells; have a paucity of secreted IgH; and have distended, abnormal-appearing endoplasmic reticulum. IRE1α is efficiently phosphorylated, but the amounts of Ig κ, ATF6, BiP, Cyclin B2, OcaB (BOB1, Pou2af1), and XBP1 mRNAs, unspliced and spliced, are severely reduced in ELL2-deficient cells. ELL2 enhances the expression of BCMA (also known as Tnfrsf17), which is important for long-term survival. Transcription yields from the cyclin B2 and the canonical UPR promoter elements are upregulated by ELL2 cDNA. Thus, ELL2 is important for many aspects of Ab secretion, XBP1 expression, and the UPR.
Collapse
Affiliation(s)
- Kyung Soo Park
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - Ian Bayles
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | | | - Joshua Paul
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - Julie Boiko
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - Patricia Santos
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - June Liu
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - Zhou Wang
- Department of Urology, University of Pittsburgh Cancer Institute, Shadyside Medical Center, Pittsburgh, PA 15232
| | - Lisa Borghesi
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - Christine Milcarek
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| |
Collapse
|
169
|
Geissler K. Translational hematology. Wien Med Wochenschr 2014; 164:487-96. [PMID: 25205187 DOI: 10.1007/s10354-014-0306-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/18/2014] [Indexed: 11/24/2022]
Abstract
Translational research is scientific research that helps to make findings from basic science useful for practical applications in the clinic. The successful use of a drug that interferes with the specific molecular pathophysiology of cancer remains the ultimate vision in cancer medicine. Translational research is a multistep process including the discovery of a cytogenetic/molecular aberration as well as the demonstration of its pathophysiological relevance and its druggability by in vitro experiments and in vivo animal models. Information obtained from preclinical research paves the way for clinical trials in which a drug of interest is developed until its clinical application. Modern pathophysiology-oriented anticancer drugs that have been developed by translational research are available for clinical applications since the beginning of this millennium. By using these drugs higher efficacy and lower toxicity could be achieved as compared with previous treatments. In this article, we will present some of the most prominent examples of this translational approach.
Collapse
Affiliation(s)
- Klaus Geissler
- 5th Department of Internal Medicine-Oncology/Hematology, Vienna and Ludwig Boltzmann Institute for Clinical Oncology, Krankenhaus Hietzing, Wolkersbergenstraße 1, 1130, Vienna, Austria,
| |
Collapse
|
170
|
Aumann S, Abdel-Wahab O. Somatic alterations and dysregulation of epigenetic modifiers in cancers. Biochem Biophys Res Commun 2014; 455:24-34. [PMID: 25111821 DOI: 10.1016/j.bbrc.2014.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/19/2014] [Accepted: 08/01/2014] [Indexed: 12/18/2022]
Abstract
Genomic discovery efforts in patients with cancer have been critical in identifying a recurrent theme of mutations in epigenetic modifiers. A number of novel and exciting basic biological findings have come from this work including the discovery of an enzymatic pathway for DNA cytosine demethylation, a link between cancer metabolism and epigenetics, and the critical importance of post-translational modifications at specific histone residues in malignant transformation. Identification of cancer cell dependency on a number of these mutations has quickly resulted in the development of therapies targeting several of these genetic alterations. This includes, the development of mutant-selective IDH1 and IDH2 inhibitors, DOT1L inhibitors for MLL rearranged leukemias, EZH2 inhibitors for several cancer types, and the development of bromodomain inhibitors for many cancer types--all of which are in early phase clinical trials. In many cases, however, specific genetic targets linked to malignant transformation following mutations in individual epigenetic modifiers are not yet known. In this review we present functional evidence of how alterations in frequently mutated epigenetic modifiers promote malignant transformation and how these alterations are being targeted for cancer therapeutics.
Collapse
Affiliation(s)
- Shlomzion Aumann
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
171
|
Ji X, Lu H, Zhou Q, Luo K. LARP7 suppresses P-TEFb activity to inhibit breast cancer progression and metastasis. eLife 2014; 3:e02907. [PMID: 25053741 PMCID: PMC4126343 DOI: 10.7554/elife.02907] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Transcriptional elongation by RNA polymerase (Pol) II is essential for gene expression during cell growth and differentiation. The positive transcription elongation factor b (P-TEFb) stimulates transcriptional elongation by phosphorylating Pol II and antagonizing negative elongation factors. A reservoir of P-TEFb is sequestered in the inactive 7SK snRNP where 7SK snRNA and the La-related protein LARP7 are required for the integrity of this complex. Here, we show that P-TEFb activity is important for the epithelial–mesenchymal transition (EMT) and breast cancer progression. Decreased levels of LARP7 and 7SK snRNA redistribute P-TEFb to the transcriptionally active super elongation complex, resulting in P-TEFb activation and increased transcription of EMT transcription factors, including Slug, FOXC2, ZEB2, and Twist1, to promote breast cancer EMT, invasion, and metastasis. Our data provide the first demonstration that the transcription elongation machinery plays a key role in promoting breast cancer progression by directly controlling the expression of upstream EMT regulators. DOI:http://dx.doi.org/10.7554/eLife.02907.001 To express a gene to make a protein, the gene's DNA must first be transcribed to produce molecules of messenger RNA. The start of the transcription process features two milestones. First, an enzyme called RNA Polymerase II starts the process. Shortly afterwards, however, the process pauses and only starts again when other proteins are recruited. This second step, called transcriptional elongation, is essential for gene expression in cells that are growing and specializing into specific cell types. However, it is unclear how important this second step is for the progression of human cancers, such as breast cancer. In humans, two proteins join together to form a complex called ‘positive transcription elongation factor b’ (or P-TEFb for short). This elongation factor encourages the transcriptional elongation step by adding phosphate groups onto RNA Polymerase II and by outcompeting other proteins that act to stop the process. However, some of the P-TEFb proteins in the cell's nucleus are unable to do this because they are held within a complex, which also contains an RNA molecule and some other proteins including one called LARP7. This protein–RNA complex is thought to help to prevent a number of cancers, for example breast cancer or stomach cancer; however the effect of P-TEFb proteins on cancers in humans is not known. Less LARP7 protein is made in breast cancer cells compared to healthy cells. And when Ji et al. reduced the levels of the LARP7 protein (or the RNA molecule involved in the complex), the P-TEFb proteins were released from the complex and were free to encourage transcriptional elongation. This led to the increased expression of other proteins that switch other genes on or off, including genes that allow breast cancer cells to spread around the body. On the other hand, Ji et al. revealed that freeing the P-TEFb proteins from the complex in the nucleus did not appear to cause new tumors to develop or existing tumors to grow. Ji et al. suggest that the LARP7 protein normally helps to prevent the spread of breast cancers by keeping the P-TEFb proteins inactive as a part of the protein–RNA complex. One of the next challenges will be to see if drugs that can inhibit the P-TEFb proteins might be useful as new treatments for late stage breast cancer. DOI:http://dx.doi.org/10.7554/eLife.02907.002
Collapse
Affiliation(s)
- Xiaodan Ji
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Huasong Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Kunxin Luo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| |
Collapse
|
172
|
Abstract
Histone modifiers like acetyltransferases, methyltransferases, and demethylases are critical regulators of most DNA-based nuclear processes, de facto controlling cell cycle progression and cell fate. These enzymes perform very precise post-translational modifications on specific histone residues, which in turn are recognized by different effector modules/proteins. We now have a better understanding of how these enzymes exhibit such specificity. As they often reside in multisubunit complexes, they use associated factors to target their substrates within chromatin structure and select specific histone mark-bearing nucleosomes. In this review, we cover the current understanding of how histone modifiers select their histone targets. We also explain how different experimental approaches can lead to conflicting results about the histone specificity and function of these enzymes.
Collapse
Affiliation(s)
- Marie-Eve Lalonde
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
| |
Collapse
|
173
|
Ali A, Veeranki SN, Tyagi S. A SET-domain-independent role of WRAD complex in cell-cycle regulatory function of mixed lineage leukemia. Nucleic Acids Res 2014; 42:7611-24. [PMID: 24880690 PMCID: PMC4081079 DOI: 10.1093/nar/gku458] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular processes like cell-cycle regulation are not well studied. Here we show that the MLL has a regulatory role during multiple phases of the cell cycle. RNAi-mediated knockdown reveals that MLL regulates S-phase progression and, proper segregation and cytokinesis during M phase. Using deletions and mutations, we narrow the cell-cycle regulatory role to the C subunit of MLL. Our analysis reveals that the transactivation domain and not the SET domain is important for the S-phase function of MLL. Surprisingly, disruption of MLL–WRAD interaction is sufficient to disrupt proper mitotic progression. These mitotic functions of WRAD are independent of SET domain of MLL and, therefore, define a new role of WRAD in subset of MLL functions. Finally, we address the overlapping and unique roles of the different SET family members in the cell cycle.
Collapse
Affiliation(s)
- Aamir Ali
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| | - Sailaja Naga Veeranki
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| |
Collapse
|
174
|
Bowman EA, Kelly WG. RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases. Nucleus 2014; 5:224-36. [PMID: 24879308 DOI: 10.4161/nucl.29347] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The transition between initiation and productive elongation during RNA Polymerase II (Pol II) transcription is a well-appreciated point of regulation across many eukaryotes. Elongating Pol II is modified by phosphorylation of serine 2 (Ser2) on its carboxy terminal domain (CTD) by two kinases, Bur1/Ctk1 in yeast and Cdk9/Cdk12 in metazoans. Here, we discuss the roles and regulation of these kinases and their relationship to Pol II elongation control, and focus on recent data from work in C. elegans that point out gaps in our current understand of transcription elongation.
Collapse
Affiliation(s)
- Elizabeth A Bowman
- National Institute of Environmental Health Sciences; Research Triangle Park, NC USA
| | | |
Collapse
|
175
|
Garriga J, Graña X. CDK9 inhibition strategy defines distinct sets of target genes. BMC Res Notes 2014; 7:301. [PMID: 24886624 PMCID: PMC4045923 DOI: 10.1186/1756-0500-7-301] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/08/2014] [Indexed: 12/02/2022] Open
Abstract
Background CDK9 is the catalytic subunit of the Positive Transcription Elongation Factor b (P-TEFb), which phosphorylates the CTD of RNAPII and negative elongation factors enabling for productive elongation after initiation. CDK9 associates with T-type cyclins and cyclin K and its activity is tightly regulated in cells at different levels. CDK9 is also the catalytic subunit of TAK (Tat activating Kinase), essential for HIV1 replication. Because of CDK9′s potential as a therapeutic target in AIDS, cancer, inflammation, and cardiomyophathy it is important to understand the consequences of CDK9 inhibition. A previous gene expression profiling study performed with human glioblastoma T98G cells in which CDK9 activity was inhibited either with a dominant negative mutant form of CDK9 (dnCDK9) or the pharmacological inhibitor Flavopiridol unveiled striking differences in gene expression effects. In the present report we extended these studies by (1) using both immortalized normal human fibroblasts and primary human astrocytes, (2) eliminating potential experimental variability due to transduction methodology and (3) also modulating CDK9 activity with siRNA. Findings Striking differences in the effects on gene expression resulting from the strategy used to inhibit CDK9 activity (dnCDK9 or FVP) remain even when potential variability due to viral transduction is eliminated. siRNA mediated CDK9 knockdown in human fibroblasts and astrocytes efficiently reduced CDK9 expression and led to potent changes in gene expression that exhibit little correlation with the effects of dnCDK9 or FVP. Interestingly, HEXIM1 a validated CDK9 target gene, was found to be potently downregulated by dnCDK9, FVP and siCDK9, but the cluster of genes with expression profiles similar to HEXIM1 was small. Finally, cluster analysis of all treatments revealed higher correlation between treatments than cell type origin. Conclusion The nature of the strategy used to inhibit CDK9 profoundly affects the patterns of gene expression resulting from CDK9 inhibition. These results suggest multiple variables that affect outcome, including kinetics of inhibition, potency, off-target effects, and selectivity issues. This is particularly important when considering CDK9 as a potential target for therapeutic intervention.
Collapse
Affiliation(s)
| | - Xavier Graña
- Fels Institute for Cancer Research and Molecular Biology, AHP bldg,, room 308, 3307 North Broad St,, Philadelphia, PA 19140, USA.
| |
Collapse
|
176
|
Prange KHM, Singh AA, Martens JHA. The genome-wide molecular signature of transcription factors in leukemia. Exp Hematol 2014; 42:637-50. [PMID: 24814246 DOI: 10.1016/j.exphem.2014.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 01/08/2023]
Abstract
Transcription factors control expression of genes essential for the normal functioning of the hematopoietic system and regulate development of distinct blood cell types. During leukemogenesis, aberrant regulation of transcription factors such as RUNX1, CBFβ, MLL, C/EBPα, SPI1, GATA, and TAL1 is central to the disease. Here, we will discuss the mechanisms of transcription factor deregulation in leukemia and how in recent years next-generation sequencing approaches have helped to elucidate the molecular role of many of these aberrantly expressed transcription factors. We will focus on the complexes in which these factors reside, the role of posttranslational modification of these factors, their involvement in setting up higher order chromatin structures, and their influence on the local epigenetic environment. We suggest that only comprehensive knowledge on all these aspects will increase our understanding of aberrant gene expression in leukemia as well as open new entry points for therapeutic intervention.
Collapse
Affiliation(s)
- Koen H M Prange
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Abhishek A Singh
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
| |
Collapse
|
177
|
Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, Dostie J. Classifying leukemia types with chromatin conformation data. Genome Biol 2014; 15:R60. [PMID: 24995990 PMCID: PMC4038739 DOI: 10.1186/gb-2014-15-4-r60] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/30/2014] [Indexed: 11/10/2022] Open
Abstract
Background Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. Results Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. Conclusions Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.
Collapse
|
178
|
Dai Q, Luan G, Deng L, Lei T, Kang H, Song X, Zhang Y, Xiao ZX, Li Q. Primordial dwarfism gene maintains Lin28 expression to safeguard embryonic stem cells from premature differentiation. Cell Rep 2014; 7:735-46. [PMID: 24768001 DOI: 10.1016/j.celrep.2014.03.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 01/15/2014] [Accepted: 03/20/2014] [Indexed: 01/09/2023] Open
Abstract
Primordial dwarfism (PD) is characterized by global growth failure, both during embryogenesis and postnatally. Loss-of-function germline mutations in La ribonucleoprotein domain family, member 7 (LAPR7) have recently been linked to PD. Paradoxically, LARP7 deficiency was previously assumed to be associated with increased cell growth and proliferation via activation of positive transcription elongation factor b (P-TEFb). Here, we show that Larp7 deficiency likely does not significantly increase P-TEFb activity. We further discover that Larp7 knockdown does not affect pluripotency but instead primes embryonic stem cells (ESCs) for differentiation via downregulation of Lin28, a positive regulator of organismal growth. Mechanistically, we show that Larp7 interacts with a poly(A) polymerase Star-PAP to maintain Lin28 mRNA stability. We propose that proper regulation of Lin28 and PTEFb is essential for embryonic cells to achieve a sufficient number of cell divisions prior to differentiation and ultimately to maintain proper organismal size.
Collapse
Affiliation(s)
- Qian Dai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Guangxin Luan
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Li Deng
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Tingjun Lei
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Han Kang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Xu Song
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Yujun Zhang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China
| | - Qintong Li
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, and State Key Laboratory of Biotherapy, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
| |
Collapse
|
179
|
Huether R, Dong L, Chen X, Wu G, Parker M, Wei L, Ma J, Edmonson MN, Hedlund EK, Rusch MC, Shurtleff SA, Mulder HL, Boggs K, Vadordaria B, Cheng J, Yergeau D, Song G, Becksfort J, Lemmon G, Weber C, Cai Z, Dang J, Walsh M, Gedman AL, Faber Z, Easton J, Gruber T, Kriwacki RW, Partridge JF, Ding L, Wilson RK, Mardis ER, Mullighan CG, Gilbertson RJ, Baker SJ, Zambetti G, Ellison DW, Zhang J, Downing JR. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun 2014; 5:3630. [PMID: 24710217 DOI: 10.1038/ncomms4630] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 03/12/2014] [Indexed: 02/07/2023] Open
Abstract
Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known epigenetic regulatory proteins, in over 1,000 paediatric tumours to define the landscape of somatic mutations in epigenetic regulators in paediatric cancer. Our results demonstrate a marked variation in the frequency of gene mutations across 21 different paediatric cancer subtypes, with the highest frequency of mutations detected in high-grade gliomas, T-lineage acute lymphoblastic leukaemia and medulloblastoma, and a paucity of mutations in low-grade glioma and retinoblastoma. The most frequently mutated genes are H3F3A, PHF6, ATRX, KDM6A, SMARCA4, ASXL2, CREBBP, EZH2, MLL2, USP7, ASXL1, NSD2, SETD2, SMC1A and ZMYM3. We identify novel loss-of-function mutations in the ubiquitin-specific processing protease 7 (USP7) in paediatric leukaemia, which result in decreased deubiquitination activity. Collectively, our results help to define the landscape of mutations in epigenetic regulatory genes in paediatric cancer and yield a valuable new database for investigating the role of epigenetic dysregulations in cancer.
Collapse
Affiliation(s)
- Robert Huether
- 1] Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2]
| | - Li Dong
- 1] Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2]
| | - Xiang Chen
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gang Wu
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Matthew Parker
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Lei Wei
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jing Ma
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael N Edmonson
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Erin K Hedlund
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael C Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Sheila A Shurtleff
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Heather L Mulder
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Kristy Boggs
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Bhavin Vadordaria
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinjun Cheng
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Donald Yergeau
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Guangchun Song
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jared Becksfort
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gordon Lemmon
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Catherine Weber
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Zhongling Cai
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinjun Dang
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Michael Walsh
- Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Amanda L Gedman
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Zachary Faber
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - John Easton
- The Pediatric Cancer Genome Project Laboratory, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Tanja Gruber
- 1] Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA [2] Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Janet F Partridge
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Li Ding
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Richard K Wilson
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Elaine R Mardis
- 1] The Genome Institute, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St Louis, Missouri 63108, USA
| | - Charles G Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard J Gilbertson
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Gerard Zambetti
- Department of Biochemistry, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - James R Downing
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| |
Collapse
|
180
|
Role of noncoding RNAs in the regulation of P-TEFb availability and enzymatic activity. BIOMED RESEARCH INTERNATIONAL 2014; 2014:643805. [PMID: 24701579 PMCID: PMC3950470 DOI: 10.1155/2014/643805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/13/2014] [Indexed: 11/23/2022]
Abstract
P-TEFb is a transcriptional factor that specifically regulates the elongation step of RNA polymerase II-dependent transcription and its activity strictly required for Human Immunodeficiency Virus (HIV) infection and during cardiac differentiation. P-TEFb role has emerged as a crucial regulator of transcription elongation and its activity found finely tuned in vivo at transcriptional level as well as posttranscriptionally by dynamic association with different multisubunit molecular particles. Both physiological and pathological cellular signals rapidly converge on P-TEFb regulation by modifying expression and activity of the complex to allow cells to properly respond to different stimuli. In this review we will give a panoramic view on P-TEFb regulation by noncoding RNAs in both physiological and pathological conditions.
Collapse
|
181
|
Villicaña C, Cruz G, Zurita M. The basal transcription machinery as a target for cancer therapy. Cancer Cell Int 2014; 14:18. [PMID: 24576043 PMCID: PMC3942515 DOI: 10.1186/1475-2867-14-18] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/21/2014] [Indexed: 01/11/2023] Open
Abstract
General transcription is required for the growth and survival of all living cells. However, tumor cells require extraordinary levels of transcription, including the transcription of ribosomal RNA genes by RNA polymerase I (RNPI) and mRNA by RNA polymerase II (RNPII). In fact, cancer cells have mutations that directly enhance transcription and are frequently required for cancer transformation. For example, the recent discovery that MYC enhances the transcription of the majority genes in the genome correlates with the fact that several transcription interfering drugs preferentially kill cancer cells. In recent years, advances in the mechanistic studies of the basal transcription machinery and the discovery of drugs that interfere with multiple components of transcription are being used to combat cancer. For example, drugs such as triptolide that targets the general transcription factors TFIIH and JQ1 to inhibit BRD4 are administered to target the high proliferative rate of cancer cells. Given the importance of finding new strategies to preferentially sensitize tumor cells, this review primarily focuses on several transcription inhibitory drugs to demonstrate that the basal transcription machinery constitutes a potential target for the design of novel cancer drugs. We highlight the drugs’ mechanisms for interfering with tumor cell survival, their importance in cancer treatment and the challenges of clinical application.
Collapse
Affiliation(s)
| | | | - Mario Zurita
- Departament of Developmental Genetics, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico, Mexico.
| |
Collapse
|
182
|
Yang YW, Flynn RA, Chen Y, Qu K, Wan B, Wang KC, Lei M, Chang HY. Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. eLife 2014; 3:e02046. [PMID: 24521543 PMCID: PMC3921674 DOI: 10.7554/elife.02046] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The WDR5 subunit of the MLL complex enforces active chromatin and can bind RNA; the relationship between these two activities is unclear. Here we identify a RNA binding pocket on WDR5, and discover a WDR5 mutant (F266A) that selectively abrogates RNA binding without affecting MLL complex assembly or catalytic activity. Complementation in ESCs shows that WDR5 F266A mutant is unable to accumulate on chromatin, and is defective in gene activation, maintenance of histone H3 lysine 4 trimethylation, and ESC self renewal. We identify a family of ESC messenger and lncRNAs that interact with wild type WDR5 but not F266A mutant, including several lncRNAs known to be important for ESC gene expression. These results suggest that specific RNAs are integral inputs into the WDR5-MLL complex for maintenance of the active chromatin state and embryonic stem cell fates. DOI: http://dx.doi.org/10.7554/eLife.02046.001.
Collapse
Affiliation(s)
- Yul W Yang
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
| | | | | | | | | | | | | | | |
Collapse
|
183
|
Regulation of NO synthesis, local inflammation, and innate immunity to pathogens by BET family proteins. Mol Cell Biol 2013; 34:415-27. [PMID: 24248598 DOI: 10.1128/mcb.01353-13] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Transcriptional activation of the Nos2 gene, encoding inducible nitric oxide synthase (iNOS), during infection or inflammation requires coordinate assembly of an initiation complex by the transcription factors NF-κB and type I interferon-activated ISGF3. Here we show that infection of macrophages with the intracellular bacterial pathogen Listeria monocytogenes caused binding of the BET proteins Brd2, Brd3, and, most prominently, Brd4 to the Nos2 promoter and that a profound reduction of Nos2 expression occurred in the presence of the BET inhibitor JQ1. RNA polymerase activity at the Nos2 gene was regulated through Brd-mediated C-terminal domain (CTD) phosphorylation at serine 5. Underscoring the critical importance of Brd for the regulation of immune responses, application of JQ1 reduced NO production in mice infected with L. monocytogenes, as well as innate resistance to L. monocytogenes and influenza virus. In a murine model of inflammatory disease, JQ1 treatment increased the colitogenic activity of dextran sodium sulfate (DSS). The data presented in our study suggest that BET protein inhibition in a clinical setting poses the risk of altering the innate immune response to infectious or inflammatory challenge.
Collapse
|
184
|
MLL1 and menin: not partners in crime? Blood 2013; 122:1995. [PMID: 24052538 DOI: 10.1182/blood-2013-08-519827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this issue of Blood, Li et al report an unexpected but clinically relevant finding. They demonstrate that the mixed lineage leukemia (MLL1) gene acts independently from menin (Men1) in the hematopoietic system.
Collapse
|
185
|
Zhang C, Hong Z, Ma W, Ma D, Qian Y, Xie W, Tie F, Fang M. Drosophila UTX coordinates with p53 to regulate ku80 expression in response to DNA damage. PLoS One 2013; 8:e78652. [PMID: 24265704 PMCID: PMC3827076 DOI: 10.1371/journal.pone.0078652] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/13/2013] [Indexed: 01/08/2023] Open
Abstract
UTX is known as a general factor that activates gene transcription during development. Here, we demonstrate an additional essential role of UTX in the DNA damage response, in which it upregulates the expression of ku80 in Drosophila, both in cultured cells and in third instar larvae. We further showed that UTX mediates the expression of ku80 by the demethylation of H3K27me3 at the ku80 promoter upon exposure to ionizing radiation (IR) in a p53-dependent manner. UTX interacts physically with p53, and both UTX and p53 are recruited to the ku80 promoter following IR exposure in an interdependent manner. In contrast, the loss of utx has little impact on the expression of ku70, mre11, hid and reaper, suggesting the specific regulation of ku80 expression by UTX. Thus, our findings further elucidate the molecular function of UTX.
Collapse
Affiliation(s)
- Chengwan Zhang
- Institute of Life Sciences, Southeast University, State Ministry of Education Key Laboratory of Developmental Genes and Human Diseases, Nanjing, China
| | | | | | | | | | | | | | | |
Collapse
|
186
|
ELL, a novel TFIIH partner, is involved in transcription restart after DNA repair. Proc Natl Acad Sci U S A 2013; 110:17927-32. [PMID: 24127601 DOI: 10.1073/pnas.1305009110] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA lesions that block transcription may cause cell death even when repaired, if transcription does not restart to reestablish cellular metabolism. However, transcription resumption after individual DNA-lesion repair remains poorly described in mechanistic terms and its players are largely unknown. The general transcription factor II H (TFIIH) is a major actor of both nucleotide excision repair subpathways of which transcription-coupled repair highlights the interplay between DNA repair and transcription. Using an unbiased proteomic approach, we have identified the protein eleven-nineteen lysine-rich leukemia (ELL) as a TFIIH partner. Here we show that ELL is recruited to UV-damaged chromatin in a Cdk7- dependent manner (a component of the cyclin-dependent activating kinase subcomplex of TFIIH). We demonstrate that depletion of ELL strongly hinders RNA polymerase II (RNA Pol II) transcription resumption after lesion removal and DNA gap filling. Lack of ELL was also observed to increase RNA Pol II retention to the chromatin during this process. Identifying ELL as an essential player for RNA Pol II restart during cellular DNA damage response opens the way to obtaining a mechanistic description of transcription resumption after DNA repair.
Collapse
|
187
|
Jefferson WN, Chevalier DM, Phelps JY, Cantor AM, Padilla-Banks E, Newbold RR, Archer TK, Kinyamu HK, Williams CJ. Persistently altered epigenetic marks in the mouse uterus after neonatal estrogen exposure. Mol Endocrinol 2013; 27:1666-77. [PMID: 24002655 DOI: 10.1210/me.2013-1211] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Neonatal exposure to diethylstilbestrol (DES) causes permanent alterations in female reproductive tract gene expression, infertility, and uterine cancer in mice. To determine whether epigenetic mechanisms could explain these phenotypes, we first tested whether DES altered uterine expression of chromatin-modifying proteins. DES treatment significantly reduced expression of methylcytosine dioxygenase TET oncogene family, member 1 (TET1) on postnatal day 5; this decrease was correlated with a subtle decrease in DNA 5-hydroxymethylcytosine in adults. There were also significant reductions in histone methyltransferase enhancer of zeste homolog 2 (EZH2), histone lysine acetyltransferase 2A (KAT2A), and histone deacetylases HDAC1, HDAC2, and HDAC3. Uterine chromatin immunoprecipitation was used to analyze the locus-specific association of modified histones with 2 genes, lactoferrin (Ltf) and sine oculis homeobox 1 (Six1), which are permanently upregulated in adults after neonatal DES treatment. Three histone modifications associated with active transcription, histone H3 lysine 9 acetylation (H3K9ac), H3 lysine 4 trimethylation (H3K4me3), and H4 lysine 5 acetylation (H4K5ac) were enriched at specific Ltf promoter regions after DES treatment, but this enrichment was not maintained in adults. H3K9ac, H4K5ac, and H3K4me3 were enriched at Six1 exon 1 immediately after neonatal DES treatment. As adults, DES-treated mice had greater differences in H4K5ac and H3K4me3 occupancy at Six1 exon 1 and new differences in these histone marks at an upstream region. These findings indicate that neonatal DES exposure temporarily alters expression of multiple chromatin-modifying proteins and persistently alters epigenetic marks in the adult uterus at the Six1 locus, suggesting a mechanism for developmental exposures leading to altered reproductive function and increased cancer risk.
Collapse
Affiliation(s)
- Wendy N Jefferson
- National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, PO Box 12233, MD E4-05, Research Triangle Park, North Carolina 27709.
| | | | | | | | | | | | | | | | | |
Collapse
|
188
|
Distinct pathways regulated by menin and by MLL1 in hematopoietic stem cells and developing B cells. Blood 2013; 122:2039-46. [PMID: 23908472 DOI: 10.1182/blood-2013-03-486647] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mixed Lineage Leukemia (MLL1) translocations encode fusion proteins retaining the N terminus of MLL1, which interacts with the tumor suppressor, menin. This interaction is essential for leukemogenesis and thus is a promising drug target. However, wild-type MLL1 plays a critical role in sustaining hematopoietic stem cells (HSCs); therefore, disruption of an essential MLL1 cofactor would be expected to obliterate normal hematopoiesis. Here we show that rather than working together as a complex, menin and MLL1 regulate distinct pathways during normal hematopoiesis, particularly in HSCs and B cells. We demonstrate the lack of genetic interaction between menin and MLL1 in steady-state or regenerative hematopoiesis and in B-cell differentiation despite the fact that MLL1 is critical for these processes. In B cells, menin- or MLL1-regulated genes can be classified into 3 categories: (1) a relatively small group of coregulated genes including previously described targets Hoxa9 and Meis1 but also Mecom and Eya1, and much larger groups of (2) exclusively menin-regulated and (3) exclusively MLL1-regulated genes. Our results highlight the large degree of independence of these 2 proteins and demonstrate that menin is not a requisite cofactor for MLL1 during normal hematopoiesis. Furthermore, our data support the development of menin-MLL1-disrupting drugs as safe and selective leukemia targeting agents.
Collapse
|
189
|
Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
| |
Collapse
|
190
|
Chan KM, Han J, Fang D, Gan H, Zhang Z. A lesson learned from the H3.3K27M mutation found in pediatric glioma: a new approach to the study of the function of histone modifications in vivo? Cell Cycle 2013; 12:2546-52. [PMID: 23907119 DOI: 10.4161/cc.25625] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive primary brain tumor in human. Recent studies on high-grade pediatric GBM have identified two recurrent mutations (K27M and G34R/V) in genes encoding histone H3 (H3F3A for H3.3 and HIST1H3B for H3.1). The two histone H3 mutations are mutually exclusive and give rise to tumors in different brain compartments. Recently, we and others have shown that the histone H3 K27M mutation specifically altered the di- and tri-methylation of endogenous histone H3 at Lys27. Genome-wide studies using ChIP-seq on H3.3K27M patient samples indicate a global reduction of H3K27me3 on chromatin. Remarkably, we also found a dramatic enrichment of H3K27me3 and EZH2 (the catalytic subunit H3K27 methyltransferase) at hundreds of gene loci in H3.3K27M patient cells. Here, we discuss potential mechanisms whereby H3K27me3 is enriched at chromatin loci in cells expressing the H3.3K27M mutation and report effects of Lys-to-Met mutations of other well-studied lysine residues of histone H3.1/H3.3 and H4 on the corresponding endogenous lysine methylation. We suggest that mutation(s) on histones may be found in a variety of human diseases, and the expression of mutant histones may help to address the function of histone lysine methylation and possibly other modifications in mammalian cells.
Collapse
Affiliation(s)
- Kui Ming Chan
- Department of Biochemistry and Molecular Biology, Epigenomic Developmental Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | |
Collapse
|
191
|
Marquardt JU, Thorgeirsson SS. Linking MLL and the HGF-MET signaling pathway in liver cancer. J Clin Invest 2013; 123:2780-3. [PMID: 23934122 DOI: 10.1172/jci70235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mixed-lineage leukemia (MLL; also known as myeloid/lymphoid), the human homolog of trithorax in Drosophila, is a transcriptional coactivator that plays an essential role during early development and hematopoiesis. Furthermore, MLL is critically involved in the epigenetic regulation of cell cycle, senescence, DNA damage, and stem cell self-renewal. Chromosomal aberrations of MLL in acute leukemias are well documented, but the role of this gene in solid malignancies remains unclear. In this issue of the JCI, Takeda et al. describe a novel epigenetic link between MLL and the HGF-MET signaling pathway conferring invasive and metastatic properties to hepatocellular carcinoma cells.
Collapse
Affiliation(s)
- Jens U Marquardt
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | | |
Collapse
|
192
|
Flajollet S, Rachez C, Ploton M, Schulz C, Gallais R, Métivier R, Pawlak M, Leray A, Issulahi AA, Héliot L, Staels B, Salbert G, Lefebvre P. The elongation complex components BRD4 and MLLT3/AF9 are transcriptional coactivators of nuclear retinoid receptors. PLoS One 2013; 8:e64880. [PMID: 23762261 PMCID: PMC3677938 DOI: 10.1371/journal.pone.0064880] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/18/2013] [Indexed: 12/20/2022] Open
Abstract
Nuclear all-trans retinoic acid receptors (RARs) initiate early transcriptional events which engage pluripotent cells to differentiate into specific lineages. RAR-controlled transactivation depends mostly on agonist-induced structural transitions in RAR C-terminus (AF-2), thus bridging coactivators or corepressors to chromatin, hence controlling preinitiation complex assembly. However, the contribution of other domains of RAR to its overall transcriptional activity remains poorly defined. A proteomic characterization of nuclear proteins interacting with RAR regions distinct from the AF-2 revealed unsuspected functional properties of the RAR N-terminus. Indeed, mass spectrometry fingerprinting identified the Bromodomain-containing protein 4 (BRD4) and ALL1-fused gene from chromosome 9 (AF9/MLLT3), known to associate with and regulates the activity of Positive Transcription Elongation Factor b (P-TEFb), as novel RAR coactivators. In addition to promoter sequences, RAR binds to genomic, transcribed regions of retinoid-regulated genes, in association with RNA polymerase II and as a function of P-TEFb activity. Knockdown of either AF9 or BRD4 expression affected differentially the neural differentiation of stem cell-like P19 cells. Clusters of retinoid-regulated genes were selectively dependent on BRD4 and/or AF9 expression, which correlated with RAR association to transcribed regions. Thus RAR establishes physical and functional links with components of the elongation complex, enabling the rapid retinoid-induced induction of genes required for neuronal differentiation. Our data thereby extends the previously known RAR interactome from classical transcriptional modulators to components of the elongation machinery, and unravel a functional role of RAR in transcriptional elongation.
Collapse
Affiliation(s)
- Sébastien Flajollet
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Christophe Rachez
- Unité de Régulation Epigénétique, URA 2578 du CNRS, Département de Biologie du Développement, Institut Pasteur, Paris, France
| | - Maheul Ploton
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Céline Schulz
- Interdisciplinary Research Institute, Univ Lille 1, USR 3078 CNRS, Biophotonique Cellulaire Fonctionnelle, Villeneuve d’Ascq, France
| | - Rozenn Gallais
- Equipe SPARTE, UMR CNRS 6026-Université Rennes 1, Rennes, France
| | - Raphaël Métivier
- Equipe SPARTE, UMR CNRS 6026-Université Rennes 1, Rennes, France
| | - Michal Pawlak
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Aymeric Leray
- Interdisciplinary Research Institute, Univ Lille 1, USR 3078 CNRS, Biophotonique Cellulaire Fonctionnelle, Villeneuve d’Ascq, France
| | - Al Amine Issulahi
- Interdisciplinary Research Institute, Univ Lille 1, USR 3078 CNRS, Biophotonique Cellulaire Fonctionnelle, Villeneuve d’Ascq, France
| | - Laurent Héliot
- Interdisciplinary Research Institute, Univ Lille 1, USR 3078 CNRS, Biophotonique Cellulaire Fonctionnelle, Villeneuve d’Ascq, France
| | - Bart Staels
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Gilles Salbert
- Equipe SPARTE, UMR CNRS 6026-Université Rennes 1, Rennes, France
| | - Philippe Lefebvre
- European Genomic Institute for Diabetes (EGID), FR 3508, Lille, France
- INSERM UMR1011, Lille, France
- Univ Lille 2, Lille, France
- Institut Pasteur de Lille, Lille, France
- * E-mail:
| |
Collapse
|
193
|
Bywater MJ, Pearson RB, McArthur GA, Hannan RD. Dysregulation of the basal RNA polymerase transcription apparatus in cancer. Nat Rev Cancer 2013; 13:299-314. [PMID: 23612459 DOI: 10.1038/nrc3496] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mutations that directly affect transcription by RNA polymerases rank among the most central mediators of malignant transformation, but the frequency of new anticancer drugs that selectively target defective transcription apparatus entering the clinic has been limited. This is because targeting the large protein-protein and protein-DNA interfaces that control both generic and selective aspects of RNA polymerase transcription has proved extremely difficult. However, recent technological advances have led to a 'quantum leap' in our comprehension of the structure and function of the core RNA polymerase components, how they are dysregulated in a broad range of cancers and how they may be targeted for 'transcription therapy'.
Collapse
Affiliation(s)
- Megan J Bywater
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne 8006, Victoria, Australia
| | | | | | | |
Collapse
|
194
|
Maethner E, Garcia-Cuellar MP, Breitinger C, Takacova S, Divoky V, Hess JL, Slany RK. MLL-ENL inhibits polycomb repressive complex 1 to achieve efficient transformation of hematopoietic cells. Cell Rep 2013; 3:1553-66. [PMID: 23623499 DOI: 10.1016/j.celrep.2013.03.038] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 03/12/2013] [Accepted: 03/22/2013] [Indexed: 01/08/2023] Open
Abstract
Stimulation of transcriptional elongation is a key activity of leukemogenic MLL fusion proteins. Here, we provide evidence that MLL-ENL also inhibits Polycomb-mediated silencing as a prerequisite for efficient transformation. Biochemical studies identified ENL as a scaffold that contacted the elongation machinery as well as the Polycomb repressive complex 1 (PRC1) component CBX8. These interactions were mutually exclusive in vitro, corresponding to an antagonistic behavior of MLL-ENL and CBX8 in vivo. CBX8 inhibited elongation in a specific reporter assay, and this effect was neutralized by direct association with ENL. Correspondingly, CBX8-binding-defective MLL-ENL could not fully activate gene loci necessary for transformation. Finally, we demonstrate dimerization of MLL-ENL as a neomorphic activity that may augment Polycomb inhibition and transformation.
Collapse
Affiliation(s)
- Emanuel Maethner
- Department of Genetics, University Erlangen, 91058 Erlangen, Germany
| | | | | | | | | | | | | |
Collapse
|
195
|
Jennings BH. Pausing for thought: disrupting the early transcription elongation checkpoint leads to developmental defects and tumourigenesis. Bioessays 2013; 35:553-60. [PMID: 23575664 PMCID: PMC3698693 DOI: 10.1002/bies.201200179] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/04/2013] [Indexed: 12/30/2022]
Abstract
Factors affecting transcriptional elongation have been characterized extensively in in vitro, single cell (yeast) and cell culture systems; however, data from the context of multicellular organisms has been relatively scarce. While studies in homogeneous cell populations have been highly informative about the underlying molecular mechanisms and prevalence of polymerase pausing, they do not reveal the biological impact of perturbing this regulation in an animal. The core components regulating pausing are expressed in all animal cells and are recruited to the majority of genes, however, disrupting their function often results in discrete phenotypic effects. Mutations in genes encoding key regulators of transcriptional pausing have been recovered from several genetic screens for specific phenotypes or interactions with specific factors in mice, zebrafish and flies. Analysis of these mutations has revealed that control of transcriptional pausing is critical for a diverse range of biological pathways essential for animal development and survival.
Collapse
|
196
|
Sawarkar R, Paro R. Hsp90@chromatin.nucleus: an emerging hub of a networker. Trends Cell Biol 2013; 23:193-201. [DOI: 10.1016/j.tcb.2012.11.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/19/2012] [Accepted: 11/20/2012] [Indexed: 02/06/2023]
|
197
|
Abstract
Human synovial sarcoma is caused by a chromosome translocation, which fuses DNA encoding SSX to that encoding the SS18 protein. Kadoch and Crabtree now show that the resulting cellular transformation stems from disruption of the normal architecture and function of the human SWI/SNF (BAF) complex.
Collapse
Affiliation(s)
- Jesper Q Svejstrup
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, UK.
| |
Collapse
|
198
|
Abstract
The molecular mechanisms underlying oncogenesis in leukemias associated with rearrangement of the Mixed Lineage Leukemia (MLL) gene have received a considerable amount of attention over the last two decades. In this review we will focus on recent studies, published over the past year, that reveal new insights into the multi-protein complexes formed by MLL and MLL fusion proteins, the role of epigenetic deregulation in MLL fusion function, downstream transcriptional target genes, the importance of the leukemia cell of origin, the role played by microRNAs, cooperating mutations and the implications that recent research has for the therapy of MLL-rearranged leukemia.
Collapse
|
199
|
Abstract
The gene expression programs that establish and maintain specific cell states in humans are controlled by thousands of transcription factors, cofactors, and chromatin regulators. Misregulation of these gene expression programs can cause a broad range of diseases. Here, we review recent advances in our understanding of transcriptional regulation and discuss how these have provided new insights into transcriptional misregulation in disease.
Collapse
Affiliation(s)
- Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts
| |
Collapse
|
200
|
Drosophila SETs its sights on cancer: Trr/MLL3/4 COMPASS-like complexes in development and disease. Mol Cell Biol 2013; 33:1698-701. [PMID: 23459940 DOI: 10.1128/mcb.00203-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
|