Orphan CpG islands define a novel class of highly active enhancers

Frequent hypermethylation of orphan CpG islands with enhancer activity in cancer

(2016) Min Gyun Bae et al.   BMC Medical Genomics

Abstract 1508: Integration of transcriptomic and metabolomic data reveals a central role for EGR1 in regulating survival and cellular metabolism in endocrine-resistant breast cancer

(2016) Ayesha N. Shajahan-Haq et al.   CANCER RESEARCH

Factors affecting the persistence of drug-induced reprogramming of the cancer methylome

(2016) Joshua S. K. Bell et al.   Epigenetics

Enhancer methylation dynamics contribute to cancer plasticity and patient mortality

(2016) Rachel E. Bell et al.   GENOME RESEARCH

Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations

(2016) Phillippa C. Taberlay et al.   GENOME RESEARCH

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

(2016) Fumitaka Inoue et al.   GENOME RESEARCH

Plasma cell differentiation is coupled to division-dependent DNA hypomethylation and gene regulation

(2016) Benjamin G Barwick et al.   NATURE IMMUNOLOGY

MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma

(2016) Dongxue Wang et al.   NUCLEIC ACIDS RESEARCH

5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients

(2016) Kevin C. Johnson et al.   Nature Communications

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Sp1 and the ‘hallmarks of cancer’

(2015) Kate Beishline et al.   FEBS Journal

Loss ofTET2in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis

(2015) Kasper D. Rasmussen et al.   GENES & DEVELOPMENT

GC skew defines distinct RNA polymerase pause sites in CpG island promoters

(2015) Wendy A. Kellner et al.   GENOME RESEARCH

Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation

(2015) Isabel Mendizabal et al.   HUMAN MOLECULAR GENETICS

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

SEA: a super-enhancer archive

(2015) Yanjun Wei et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Disruption of CTCF/cohesin-mediated high-order chromatin structures by DNA methylation downregulates PTGS2 expression

(2015) J Y Kang et al.   ONCOGENE

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi–Goutières syndrome

(2015) Yoong Wearn Lim et al.   eLife

The Transcription Factor Titration Effect Dictates Level of Gene Expression

(2014) Robert C. Brewster et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Recurrent epimutations activate gene body promoters in primary glioblastoma

(2014) R. P. Nagarajan et al.   GENOME RESEARCH

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation

(2014) Gary C. Hon et al.   MOLECULAR CELL

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones

(2014) Tomohiko Kanno et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA Methylation of Transcriptional Enhancers and Cancer Predisposition

(2013) Dvir Aran 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

Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release

(2013) Wen Liu et al.   CELL

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

(2013) Cornelia G. Spruijt et al.   CELL

The role of chromatin insulators in nuclear architecture and genome function

(2013) Kevin Van Bortle et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency

(2013) Tao Wang et al.   NATURE CELL BIOLOGY

A common mode of recognition for methylated CpG

(2013) Yiwei Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

Macrohistone Variants Preserve Cell Identity by Preventing the Gain of H3K4me2 during Reprogramming to Pluripotency

(2013) María J. Barrero et al.   Cell Reports

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

(2013) Dvir Aran et al.   GENOME BIOLOGY

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Human LSD2/KDM1b/AOF1 Regulates Gene Transcription by Modulating Intragenic H3K4me2 Methylation

(2010) Rui Fang et al.   MOLECULAR CELL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

SLC45A3-ELK4 Is a Novel and Frequent Erythroblast Transformation-Specific Fusion Transcript in Prostate Cancer

(2009) D. S. Rickman et al.   CANCER RESEARCH

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Cancer DNA Methylation: Molecular Mechanisms and Clinical Implications

(2009) M. T. McCabe et al.   CLINICAL CANCER RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Transcription factors mediate long-range enhancer-promoter interactions

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

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE