Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer

Rhabdoid Tumors: An Initial Clue to the Role of Chromatin Remodeling in Cancer

(2013) Ryan S. Lee et al.   BRAIN PATHOLOGY

Evaluation of Histone 3 Lysine 27 Trimethylation (H3K27me3) and Enhancer of Zest 2 (EZH2) in Pediatric Glial and Glioneuronal Tumors Shows Decreased H3K27me3 inH3F3AK27M Mutant Glioblastomas

(2013) Sriram Venneti et al.   BRAIN PATHOLOGY

Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer

(2013) Joachim Weischenfeldt et al.   CANCER CELL

SDH Mutations Establish a Hypermethylator Phenotype in Paraganglioma

(2013) Eric Letouzé et al.   CANCER CELL

Collections of Simultaneously Altered Genes as Biomarkers of Cancer Cell Drug Response

(2013) D. L. Masica et al.   CANCER RESEARCH

Interplay between the Cancer Genome and Epigenome

(2013) Hui Shen et al.   CELL

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression

(2013) K.-M. Chan et al.   GENES & DEVELOPMENT

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas

(2013)   NATURE GENETICS

Computational approaches to identify functional genetic variants in cancer genomes

(2013)   NATURE METHODS

The Spectrum of SWI/SNF Mutations, Ubiquitous in Human Cancers

(2013) A. Hunter Shain et al.   PLoS One

Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma

(2013) P. W. Lewis et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

An Inhibitor of Mutant IDH1 Delays Growth and Promotes Differentiation of Glioma Cells

(2013) D. Rohle et al.   SCIENCE

Histone H3.3 Mutations Drive Pediatric Glioblastoma through Upregulation of MYCN

(2013) Lynn Bjerke et al.   Cancer Discovery

Succinate Dehydrogenase Mutation Underlies Global Epigenomic Divergence in Gastrointestinal Stromal Tumor

(2013) J. Keith Killian et al.   Cancer Discovery

Methods for Identifying Higher-Order Chromatin Structure

(2012) Samin A. Sajan et al.   Annual Review of Genomics and Human Genetics

Mutant DNMT3A: a marker of poor prognosis in acute myeloid leukemia

(2012) A. F. T. Ribeiro et al.   BLOOD

SnapShot: Glioblastoma Multiforme

(2012) Svetlana Kotliarova et al.   CANCER CELL

Hotspot Mutations in H3F3A and IDH1 Define Distinct Epigenetic and Biological Subgroups of Glioblastoma

(2012) Dominik Sturm et al.   CANCER CELL

Cancer Genetics and Epigenetics: Two Sides of the Same Coin?

(2012) Jueng Soo You et al.   CANCER CELL

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

(2012) Andrew Adey et al.   GENOME RESEARCH

A DNA hypermethylation module for the stem/progenitor cell signature of cancer

(2012) H. Easwaran et al.   GENOME RESEARCH

Association of Age at Diagnosis and Genetic Mutations in Patients With Neuroblastoma

(2012) Nai-Kong V. Cheung   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

TET2 Mutations in Acute Myeloid Leukemia (AML): Results From a Comprehensive Genetic and Clinical Analysis of the AML Study Group

(2012) Verena I. Gaidzik et al.   JOURNAL OF CLINICAL ONCOLOGY

Multicenter, Randomized, Open-Label, Phase III Trial of Decitabine Versus Patient Choice, With Physician Advice, of Either Supportive Care or Low-Dose Cytarabine for the Treatment of Older Patients With Newly Diagnosed Acute Myeloid Leukemia

(2012) Hagop M. Kantarjian et al.   JOURNAL OF CLINICAL ONCOLOGY

Decitabine induces very early in vivo DNA methylation changes in blasts from patients with acute myeloid leukemia

(2012) Rainer Claus et al.   LEUKEMIA RESEARCH

Characterization of the EZH2-MMSET Histone Methyltransferase Regulatory Axis in Cancer

(2012) Irfan A. Asangani et al.   MOLECULAR CELL

IDH mutation impairs histone demethylation and results in a block to cell differentiation

(2012) Chao Lu et al.   NATURE

IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype

(2012) Sevin Turcan et al.   NATURE

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

(2012) Trevor J. Pugh et al.   NATURE

Dissecting the genomic complexity underlying medulloblastoma

(2012) David T. W. Jones et al.   NATURE

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

(2012) Jeremy Schwartzentruber et al.   NATURE

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

(2012) Andrew V. Biankin et al.   NATURE

EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations

(2012) Michael T. McCabe et al.   NATURE

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

(2012) Paul A. Northcott et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

The genetic landscape of mutations in Burkitt lymphoma

(2012) Cassandra Love et al.   NATURE GENETICS

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas

(2012) Gang Wu et al.   NATURE GENETICS

Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma

(2012) Mark Sausen et al.   NATURE GENETICS

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

(2012) Martin Peifer et al.   NATURE GENETICS

Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia

(2012) Tino Schenk et al.   NATURE MEDICINE

The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine

(2012) William A Pastor et al.   Nature Protocols

Mutations and deletions of ARID1A in breast tumors

(2012) S Cornen et al.   ONCOGENE

Genetic Events That Shape the Cancer Epigenome

(2012) R. J. H. Ryan et al.   SCIENCE

Detection of 2-Hydroxyglutarate in IDH-Mutated Glioma Patients by In Vivo Spectral-Editing and 2D Correlation Magnetic Resonance Spectroscopy

(2012) O. C. Andronesi et al.   Science Translational Medicine

Magnetic Resonance of 2-Hydroxyglutarate in IDH1-Mutated Low-Grade Gliomas

(2012) A. Elkhaled et al.   Science Translational Medicine

ARID1A Mutations in Cancer: Another Epigenetic Tumor Suppressor?

(2012) Jennifer N. Wu et al.   Cancer Discovery

Linking DNA Methyltransferases to Epigenetic Marks and Nucleosome Structure Genome-wide in Human Tumor Cells

(2012) Bilian Jin et al.   Cell Reports

Small Molecule Inhibitors of Histone Acetyltransferases as Epigenetic Tools and Drug Candidates

(2011) Silviya D. Furdas et al.   ARCHIV DER PHARMAZIE

Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

(2011) Wei Xu et al.   CANCER CELL

In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

(2011) Florian A. Karreth et al.   CELL

BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc

(2011) Jake E. Delmore et al.   CELL

ATP-dependent chromatin remodeling: genetics, genomics and mechanisms

(2011) Diana C Hargreaves et al.   CELL RESEARCH

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

(2011) Juan Sandoval et al.   Epigenetics

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

Large-scale methylation domains mark a functional subset of neuronally expressed genes

(2011) D. I. Schroeder et al.   GENOME RESEARCH

The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9

(2011) Arunkumar Dhayalan et al.   HUMAN MOLECULAR GENETICS

H3K36 Methylation Antagonizes PRC2-mediated H3K27 Methylation

(2011) Wen Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Low-Dose Decitabine Versus Best Supportive Care in Elderly Patients With Intermediate- or High-Risk Myelodysplastic Syndrome (MDS) Ineligible for Intensive Chemotherapy: Final Results of the Randomized Phase III Study of the European Organisation for Research and Treatment of Cancer Leukemia Group and the German MDS Study Group

(2011) Michael Lübbert et al.   JOURNAL OF CLINICAL ONCOLOGY

Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks

(2011) Frank W. Schmitges et al.   MOLECULAR CELL

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

(2011) Ignacio Varela et al.   NATURE

Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia

(2011) Mark A. Dawson et al.   NATURE

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

(2011) Xiao-Jing Yan et al.   NATURE GENETICS

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

(2011) Mazhar Adli et al.   Nature Protocols

ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome

(2011) Shigeki Iwase et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin

(2011) Sebastian Eustermann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Targeting MYC dependence in cancer by inhibiting BET bromodomains

(2011) J. A. Mertz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Altered Telomeres in Tumors with ATRX and DAXX Mutations

(2011) C. M. Heaphy et al.   SCIENCE

DAXX/ATRX, MEN1, and mTOR Pathway Genes Are Frequently Altered in Pancreatic Neuroendocrine Tumors

(2011) Y. Jiao et al.   SCIENCE

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Role of TET2 Mutations in Myeloproliferative Neoplasms

(2011) Elodie Pronier et al.   Current Hematologic Malignancy Reports

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

(2010) Houtan Noushmehr et al.   CANCER CELL

Leukemic IDH1 and IDH2 Mutations Result in a Hypermethylation Phenotype, Disrupt TET2 Function, and Impair Hematopoietic Differentiation

(2010) Maria E. Figueroa et al.   CANCER CELL

A phase I study of oral panobinostat alone and in combination with docetaxel in patients with castration-resistant prostate cancer

(2010) Dana Rathkopf et al.   CANCER CHEMOTHERAPY AND PHARMACOLOGY

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

New functions for an old variant: no substitute for histone H3.3

(2010) Simon J Elsaesser et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

ATRX interacts with H3.3 in maintaining telomere structural integrity in pluripotent embryonic stem cells

(2010) L. H. Wong et al.   GENOME RESEARCH

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

(2010) Shinsuke Ito et al.   NATURE

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes

(2010) Gorica Nikoloski et al.   NATURE GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

DNMT3AMutations in Acute Myeloid Leukemia

(2010) Timothy J. Ley et al.   NEW ENGLAND JOURNAL OF MEDICINE

Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas

(2010) C. J. Sneeringer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genetic Landscape of the Childhood Cancer Medulloblastoma

(2010) D. W. Parsons et al.   SCIENCE

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies

(2009) O. Abdel-Wahab et al.   BLOOD

Preliminary evidence of disease response to the pan deacetylase inhibitor panobinostat (LBH589) in refractory Hodgkin Lymphoma

(2009) Michael Dickinson et al.   BRITISH JOURNAL OF HAEMATOLOGY

Histone acetyl transferases as emerging drug targets

(2009) Frank J. Dekker et al.   DRUG DISCOVERY TODAY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

H3K79 Methylation Profiles Define Murine and Human MLL-AF4 Leukemias

(2008) Andrei V. Krivtsov et al.   CANCER CELL

DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45

(2008) Kunal Rai et al.   CELL

Histone Deacetylase Inhibitor Panobinostat Induces Clinical Responses with Associated Alterations in Gene Expression Profiles in Cutaneous T-Cell Lymphoma

(2008) L. Ellis et al.   CLINICAL CANCER RESEARCH

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

The structural basis of protein acetylation by the p300/CBP transcriptional coactivator

(2008) Xin Liu et al.   NATURE

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

Genomic Loss of microRNA-101 Leads to Overexpression of Histone Methyltransferase EZH2 in Cancer

(2008) S. Varambally et al.   SCIENCE