Unravelling the genomic targets of small molecules using high-throughput sequencing

Targeting MLL1 H3K4 Methyltransferase Activity in Mixed-Lineage Leukemia

(2014) Fang Cao et al.   MOLECULAR CELL

Every amino acid matters: essential contributions of histone variants to mammalian development and disease

(2014) Ian Maze et al.   NATURE REVIEWS GENETICS

Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens

(2014) C. Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chemical Inhibition of NAT10 Corrects Defects of Laminopathic Cells

(2014) D. Larrieu et al.   SCIENCE

Nucleosome Acidic Patch Promotes RNF168- and RING1B/BMI1-Dependent H2AX and H2A Ubiquitination and DNA Damage Signaling

(2014) Justin W. Leung et al.   PLoS Genetics

An Orally Bioavailable Chemical Probe of the Lysine Methyltransferases EZH2 and EZH1

(2013) Kyle D. Konze et al.   ACS Chemical Biology

From histones to RNA: role of methylation in cancer

(2013) B. Xhemalce   Briefings in Functional Genomics

Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma

(2013) Bjoern Chapuy et al.   CANCER CELL

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Identification of Early Replicating Fragile Sites that Contribute to Genome Instability

(2013) Jacqueline H. Barlow et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability

(2013) Boris P. Belotserkovskii et al.   CHEMICAL REVIEWS

A Small Molecule Inhibitor of the BLM Helicase Modulates Chromosome Stability in Human Cells

(2013) Giang Huong Nguyen et al.   CHEMISTRY & BIOLOGY

Doxorubicin Enhances Nucleosome Turnover around Promoters

(2013) Fan Yang et al.   CURRENT BIOLOGY

Mammalian DNA repair: HATs and HDACs make their mark through histone acetylation

(2013) Fade Gong et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Topoisomerases facilitate transcription of long genes linked to autism

(2013) Ian F. King et al.   NATURE

Replication stress links structural and numerical cancer chromosomal instability

(2013) Rebecca A. Burrell et al.   NATURE

Chromatin proteins and modifications as drug targets

(2013) Kristian Helin et al.   NATURE

BAF complexes facilitate decatenation of DNA by topoisomerase IIα

(2013) Emily C. Dykhuizen et al.   NATURE

Genome-wide localization of small molecules

(2013) Lars Anders et al.   NATURE BIOTECHNOLOGY

Self-renewal as a therapeutic target in human colorectal cancer

(2013) Antonija Kreso et al.   NATURE MEDICINE

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing

(2013) Nicola Crosetto et al.   NATURE METHODS

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

(2013) Christoph Plass et al.   NATURE REVIEWS GENETICS

Functional DNA demethylation is accompanied by chromatin accessibility

(2013) Kurinji Pandiyan et al.   NUCLEIC ACIDS RESEARCH

Durable tumor regression in genetically altered malignant rhabdoid tumors by inhibition of methyltransferase EZH2

(2013) S. K. Knutson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin

(2013) Baoxu Pang et al.   Nature Communications

The G4 Genome

(2013) Nancy Maizels et al.   PLoS Genetics

Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells

(2013) Deborah A Sanders et al.   GENOME BIOLOGY

Identification and Characterization of Small Molecule Inhibitors of a Plant Homeodomain Finger

(2012) Elise K. Wagner et al.   BIOCHEMISTRY

Inhibition of BRCT(BRCA1)-phosphoprotein interaction enhances the cytotoxic effect of olaparib in breast cancer cells: a proof of concept study for synthetic lethal therapeutic option

(2012) Ziyan Yuan Pessetto et al.   BREAST CANCER RESEARCH AND TREATMENT

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

Small-Molecule Inhibition of BRDT for Male Contraception

(2012) Martin M. Matzuk et al.   CELL

Guiding the Design of Synthetic DNA-Binding Molecules with Massively Parallel Sequencing

(2012) Jordan L. Meier et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Forkhead Transcription Factor FOXM1 Controls Cell Cycle-Dependent Gene Expression through an Atypical Chromatin Binding Mechanism

(2012) X. Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response

(2012) Laurens Kruidenier et al.   NATURE

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

(2012) Michael T. McCabe et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Menin-MLL inhibitors reverse oncogenic activity of MLL fusion proteins in leukemia

(2012) Jolanta Grembecka et al.   Nature Chemical Biology

Small-molecule–induced DNA damage identifies alternative DNA structures in human genes

(2012) Raphaël Rodriguez et al.   Nature Chemical Biology

Epigenetic protein families: a new frontier for drug discovery

(2012) Cheryl H. Arrowsmith et al.   NATURE REVIEWS DRUG DISCOVERY

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Histone methylation: a dynamic mark in health, disease and inheritance

(2012) Eric L. Greer et al.   NATURE REVIEWS GENETICS

DNA secondary structures: stability and function of G-quadruplex structures

(2012) Matthew L. Bochman et al.   NATURE REVIEWS GENETICS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Perceiving the epigenetic landscape through histone readers

(2012) Catherine A Musselman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Targeting Epigenetic Readers in Cancer

(2012) Mark A. Dawson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Model for MLL translocations in therapy-related leukemia involving topoisomerase II -mediated DNA strand breaks and gene proximity

(2012) I. G. Cowell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selective Killing of Mixed Lineage Leukemia Cells by a Potent Small-Molecule DOT1L Inhibitor

(2011) Scott R. Daigle et al.   CANCER CELL

MLL-Rearranged Leukemia Is Dependent on Aberrant H3K79 Methylation by DOT1L

(2011) Kathrin M. Bernt et al.   CANCER CELL

Combination Therapy with Vidaza and Entinostat Suppresses Tumor Growth and Reprograms the Epigenome in an Orthotopic Lung Cancer Model

(2011) Steven A. Belinsky et al.   CANCER RESEARCH

Validation of the histone methyltransferase EZH2 as a therapeutic target for various types of human cancer and as a prognostic marker

(2011) Masashi Takawa et al.   CANCER SCIENCE

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

(2011) Jake E. Delmore et al.   CELL

Nucleotide Deficiency Promotes Genomic Instability in Early Stages of Cancer Development

(2011) Assaf C. Bester et al.   CELL

Selective and Cell-Active Inhibitors of the USP1/ UAF1 Deubiquitinase Complex Reverse Cisplatin Resistance in Non-small Cell Lung Cancer Cells

(2011) Junjun Chen et al.   CHEMISTRY & BIOLOGY

Discovery of Potent and Selective Inhibitors of Ataxia Telangiectasia Mutated and Rad3 Related (ATR) Protein Kinase as Potential Anticancer Agents

(2011) Jean-Damien Charrier et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery and Characterization of Small Molecule Inhibitors of the BET Family Bromodomains

(2011) Chun-wa Chung et al.   JOURNAL OF MEDICINAL CHEMISTRY

Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons

(2011) Hsien-Sung Huang et al.   NATURE

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

(2011) Ryan D. Morin et al.   NATURE

RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia

(2011) Johannes Zuber et al.   NATURE

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

(2011) Mark A. Dawson et al.   NATURE

The transcription factor FOXM1 is a cellular target of the natural product thiostrepton

(2011) Nagaratna S. Hegde et al.   Nature Chemistry

Analysis of the coding genome of diffuse large B-cell lymphoma

(2011) Laura Pasqualucci et al.   NATURE GENETICS

Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?

(2011) Shankar Balasubramanian et al.   NATURE REVIEWS DRUG DISCOVERY

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

Azacytidine and Decitabine Induce Gene-Specific and Non-Random DNA Demethylation in Human Cancer Cell Lines

(2011) Sabine Hagemann et al.   PLoS One

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

Inhibition of helicase activity by a small molecule impairs Werner syndrome helicase (WRN) function in the cellular response to DNA damage or replication stress

(2011) M. Aggarwal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Angelman syndrome: insights into genomic imprinting and neurodevelopmental phenotypes

(2011) Angela M. Mabb et al.   TRENDS IN NEUROSCIENCES

G-quadruplexes: selective DNA targeting for cancer therapeutics?

(2011) Kyle M Miller et al.   Expert Review of Clinical Pharmacology

Targeting RNA Polymerase I with an Oral Small Molecule CX-5461 Inhibits Ribosomal RNA Synthesis and Solid Tumor Growth

(2010) Denis Drygin et al.   CANCER RESEARCH

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

Virtual Ligand Screening of the p300/CBP Histone Acetyltransferase: Identification of a Selective Small Molecule Inhibitor

(2010) Erin M. Bowers et al.   CHEMISTRY & BIOLOGY

Suppression of inflammation by a synthetic histone mimic

(2010) Edwige Nicodeme et al.   NATURE

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

Epigenetic modifications as therapeutic targets

(2010) Theresa K Kelly et al.   NATURE BIOTECHNOLOGY

Small-molecule-mediated G-quadruplex isolation from human cells

(2010) Sebastian Müller et al.   Nature Chemistry

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

(2010) Ryan D Morin et al.   NATURE GENETICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements

(2010) Michael C Haffner et al.   NATURE GENETICS

Chromatin structure and the inheritance of epigenetic information

(2010) Raphaël Margueron et al.   NATURE REVIEWS GENETICS

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining

(2010) Kyle M Miller et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones

(2010) R. B. Deal et al.   SCIENCE

JAK2 phosphorylates histone H3Y41 and excludes HP1α from chromatin

(2009) Mark A. Dawson et al.   NATURE

The DNA-damage response in human biology and disease

(2009) Stephen P. Jackson et al.   NATURE

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Epigenetic inheritance during the cell cycle

(2009) Aline V. Probst et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

G-quadruplex structures: in vivo evidence and function

(2009) Hans J. Lipps et al.   TRENDS IN CELL BIOLOGY

Histones: Annotating Chromatin

(2008) Eric I. Campos et al.   Annual Review of Genetics

Histone deacetylase inhibitors: Anticancer compounds

(2008) Karen T. Smith et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

A Novel Small Molecule That Alters Shelterin Integrity and Triggers a DNA-Damage Response at Telomeres

(2008) Raphaël Rodriguez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY