Enhancer alterations in cancer: a source for a cell identity crisis

The lncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer

(2015) John R. Prensner et al.   Oncotarget

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

(2014) M. Ronnerblad et al.   BLOOD

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

(2014) V. R. Paralkar et al.   BLOOD

GATA3mutations define a unique subtype of luminal-like breast cancer with improved survival

(2014) Yi-Zhou Jiang et al.   CANCER

Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

(2014) Jian-Feng Xiang et al.   CELL RESEARCH

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

Identification of cellular and genetic drivers of breast cancer heterogeneity in genetically engineered mouse tumour models

(2014) Lorenzo Melchor et al.   JOURNAL OF PATHOLOGY

Enhancer Malfunction in Cancer

(2014) Hans-Martin Herz et al.   MOLECULAR CELL

A Role for H3K4 Monomethylation in Gene Repression and Partitioning of Chromatin Readers

(2014) Jemmie Cheng et al.   MOLECULAR CELL

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Integrated genomic characterization of adrenocortical carcinoma

(2014) Guillaume Assié et al.   NATURE GENETICS

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

(2014) Kai Wang et al.   NATURE GENETICS

An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia

(2014) Birgit Knoechel et al.   NATURE GENETICS

Enhancer biology and enhanceropathies

(2014) Edwin Smith et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation

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

Laying a solid foundation for Manhattan – ‘setting the functional basis for the post-GWAS era’

(2014) Xiaoyang Zhang et al.   TRENDS IN GENETICS

DNA Methylation is Developmentally Regulated for Genes Essential for Cardiogenesis

(2014) Alyssa A. Chamberlain et al.   Journal of the American Heart Association

High Incidence of ActivatingTERTPromoter Mutations in Meningiomas Undergoing Malignant Progression

(2013) Stéphane Goutagny et al.   BRAIN PATHOLOGY

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

(2013) Bjoern Chapuy et al.   CANCER CELL

Androgen Receptor-Independent Function of FoxA1 in Prostate Cancer Metastasis

(2013) H.-J. Jin et al.   CANCER RESEARCH

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

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

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Long non-coding RNAs: modulators of nuclear structure and function

(2013) Jan H Bergmann et al.   CURRENT OPINION IN CELL BIOLOGY

Highly prevalent TERT promoter mutations in aggressive thyroid cancers

(2013) Xiaoli Liu et al.   ENDOCRINE-RELATED CANCER

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Long noncoding RNA HOTTIP/HOXA13 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients

(2013) Luca Quagliata et al.   HEPATOLOGY

The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers

(2013) D. Hu et al.   MOLECULAR AND CELLULAR BIOLOGY

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs

(2013) Liuqing Yang et al.   NATURE

Tumour heterogeneity and cancer cell plasticity

(2013) Corbin E. Meacham et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation

(2013) Guangwu Guo et al.   NATURE GENETICS

Frequent truncating mutations of STAG2 in bladder cancer

(2013) David A Solomon et al.   NATURE GENETICS

Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

(2013) Michael N Weedon et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Stem Cell-Like Gene Expression in Ovarian Cancer Predicts Type II Subtype and Prognosis

(2013) Matthew Schwede et al.   PLoS One

Genome-wide reprogramming of the chromatin landscape underlies endocrine therapy resistance in breast cancer

(2013) L. Magnani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TERT promoter mutations in bladder cancer affect patient survival and disease recurrence through modification by a common polymorphism

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

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

(2013) Dvir Aran et al.   GENOME BIOLOGY

GATA3 Mutations Found in Breast Cancers May Be Associated with Aberrant Nuclear Localization, Reduced Transactivation and Cell Invasiveness

(2013) Katherine U. Gaynor et al.   Hormones & Cancer

FOXA1 mutations in hormone-dependent cancers

(2013) Jessica L. L. Robinson et al.   Frontiers in Oncology

Long Intergenic Noncoding RNA HOTAIR Is Overexpressed and Regulates PTEN Methylation in Laryngeal Squamous Cell Carcinoma

(2012) Dandan Li et al.   AMERICAN JOURNAL OF PATHOLOGY

High frequency of GATA2 mutations in patients with mild chronic neutropenia evolving to MonoMac syndrome, myelodysplasia, and acute myeloid leukemia

(2012) M. Pasquet et al.   BLOOD

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

(2012) X. Zhang et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease

(2012) Scott Smemo et al.   HUMAN MOLECULAR GENETICS

Bromodomain-containing Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells

(2012) Weishi Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes

(2012) Deborah I. Ritter et al.   PLoS One

Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer

(2012) B. Akhtar-Zaidi et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

(2011) Srinivasan Yegnasubramanian et al.   BMC GENOMICS

A Comprehensive View of Nuclear Receptor Cancer Cistromes

(2011) Q. Tang et al.   CANCER RESEARCH

Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers

(2011) R. Kogo et al.   CANCER RESEARCH

Genetic Predisposition Directs Breast Cancer Phenotype by Dictating Progenitor Cell Fate

(2011) Theresa A. Proia et al.   Cell Stem Cell

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

RUNX1 and RUNX1-ETO: roles in hematopoiesis and leukemogenesis

(2011) Kentson Lam   Frontiers in Bioscience-Landmark

Colon cancer associated transcript-1: A novel RNA expressed in malignant and pre-malignant human tissues

(2011) Aviram Nissan et al.   INTERNATIONAL JOURNAL OF CANCER

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation

(2011) Vlad C. Seitan et al.   NATURE

Initial genome sequencing and analysis of multiple myeloma

(2011) Michael A. Chapman et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MED12, the Mediator Complex Subunit 12 Gene, Is Mutated at High Frequency in Uterine Leiomyomas

(2011) N. Makinen et al.   SCIENCE

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

BRCA1 Basal-like Breast Cancers Originate from Luminal Epithelial Progenitors and Not from Basal Stem Cells

(2010) Gemma Molyneux et al.   Cell Stem Cell

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Transcription control of early B cell differentiation

(2010) Elizabeth M Mandel et al.   CURRENT OPINION IN IMMUNOLOGY

Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation

(2010) Qihuang Jin et al.   EMBO JOURNAL

Upregulation of c-MYC in cis through a Large Chromatin Loop Linked to a Cancer Risk-Associated Single-Nucleotide Polymorphism in Colorectal Cancer Cells

(2010) J. B. Wright et al.   MOLECULAR AND CELLULAR BIOLOGY

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

(2010) Shinsuke Ito et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

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

DNMT3AMutations in Acute Myeloid Leukemia

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

Long-range enhancers on 8q24 regulate c-Myc

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

8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC

(2010) N. Ahmadiyeh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Sickle cell disease caused by heterozygosity for Hb S and novel LCR deletion: Report of two patients

(2009) Sara C. Koenig et al.   AMERICAN JOURNAL OF HEMATOLOGY

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Finding distal regulatory elements in the human genome

(2009) Nathaniel D Heintzman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing

(2009) F. Tie et al.   DEVELOPMENT

Long-range regulation at the SOX9 locus in development and disease

(2009) C T Gordon et al.   JOURNAL OF MEDICAL GENETICS

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

(2009) Sari Tuupanen et al.   NATURE GENETICS

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

(2009) Elgene Lim et al.   NATURE MEDICINE

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Mutation inTET2in Myeloid Cancers

(2009) François Delhommeau et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Chromatin conformation signatures of cellular differentiation

(2009) James Fraser et al.   GENOME BIOLOGY

Conserved features of cohesin binding along fission yeast chromosomes

(2009) Christine K Schmidt et al.   GENOME BIOLOGY

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

An embryonic stem cell–like gene expression signature in poorly differentiated aggressive human tumors

(2008) Ittai Ben-Porath et al.   NATURE GENETICS

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA