Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity

MYC-driven epigenetic reprogramming favors the onset of tumorigenesis by inducing a stem cell-like state

(2018) Vittoria Poli et al.   Nature Communications

Hypermethylated LTR retrotransposon exhibits enhancer activity

(2017) Tianxiang Hu et al.   Epigenetics

Dynamic assembly and activation of estrogen receptor α enhancers through coregulator switching

(2017) Shino Murakami et al.   GENES & DEVELOPMENT

ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis

(2017) Wei Zhong Leong et al.   GENES & DEVELOPMENT

Critical threshold levels of DNA methyltransferase 1 are required to maintain DNA methylation across the genome in human cancer cells

(2017) Yi Cai et al.   GENOME RESEARCH

APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL

(2017) Z Li et al.   LEUKEMIA

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer

(2017) Alvin P Makohon-Moore et al.   NATURE GENETICS

SMARCB1 is required for widespread BAF complex–mediated activation of enhancers and bivalent promoters

(2017) Robert T Nakayama et al.   NATURE GENETICS

A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers

(2017) Dominik Glodzik et al.   NATURE GENETICS

Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis

(2017) Oliver G McDonald et al.   NATURE GENETICS

TMPRSS2–ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer

(2017) Ken J Kron et al.   NATURE GENETICS

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Variants of core histones and their roles in cell fate decisions, development and cancer

(2017) Marcus Buschbeck et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

(2017) Michael H Hauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A DNA methylation map of human cancer at single base-pair resolution

(2017) E Vidal et al.   ONCOGENE

MLL-AF9 and MLL-AF4 oncofusion proteins bind a distinct enhancer repertoire and target the RUNX1 program in 11q23 acute myeloid leukemia

(2017) K H M Prange et al.   ONCOGENE

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma

(2017) Kirsten M. Johnson et al.   PLoS One

Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer

(2017) Fátima Valdés-Mora et al.   Nature Communications

DNA methylation at enhancers identifies distinct breast cancer lineages

(2017) Thomas Fleischer et al.   Nature Communications

Small genomic insertions form enhancers that misregulate oncogenes

(2017) Brian J. Abraham et al.   Nature Communications

Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

(2017) Andrea J. Cohen et al.   Nature Communications

FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor

(2017) Leili Ran et al.   Cancer Discovery

Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex

(2017) Jon S. Zawistowski et al.   Cancer Discovery

OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma

(2017) Gaylor Boulay et al.   Cancer Discovery

Suppression of Adaptive Responses to Targeted Cancer Therapy by Transcriptional Repression

(2017) Maria Rusan et al.   Cancer Discovery

PAX3–FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability

(2017) Berkley E. Gryder et al.   Cancer Discovery

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

(2017) Michael H Hauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas

(2017) Russell J.H. Ryan et al.   Cell Reports

DNA Hypomethylating Drugs in Cancer Therapy

(2017) Takahiro Sato et al.   Cold Spring Harbor Perspectives in Medicine

SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells

(2017) Sabine Jägle et al.   PLoS Genetics

Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers

(2017) Timothy W R Kelso et al.   eLife

Enhancer deregulation in cancer and other diseases

(2016) Hans-Martin Herz   BIOESSAYS

DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias

(2016) Liubin Yang et al.   CANCER CELL

Epigenetic Perturbations by Arg882-Mutated DNMT3A Potentiate Aberrant Stem Cell Gene-Expression Program and Acute Leukemia Development

(2016) Rui Lu et al.   CANCER CELL

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility

(2016) Sarah K. Denny et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Chromatin remodeling effects on enhancer activity

(2016) Estela García-González et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Histone variants: nuclear function and disease

(2016) Lisa-Maria Zink et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Enhancer, epigenetics, and human disease

(2016) Zhuojuan Luo et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

Fox transcription factors: from development to disease

(2016) Maria L. Golson et al.   DEVELOPMENT

INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma

(2016) Bingying Zhou et al.   GENES & DEVELOPMENT

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

Monoubiquitination of Histone H2B Blocks Eviction of Histone Variant H2A.Z from Inducible Enhancers

(2016) Gregory Segala et al.   MOLECULAR CELL

Epigenome Maintenance in Response to DNA Damage

(2016) Juliette Dabin et al.   MOLECULAR CELL

The Aging Epigenome

(2016) Lauren N. Booth et al.   MOLECULAR CELL

Early dissemination seeds metastasis in breast cancer

(2016) Hedayatollah Hosseini et al.   NATURE

Metastatic colonization by circulating tumour cells

(2016) Joan Massagué et al.   NATURE

SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation

(2016) Xiaofeng Wang et al.   NATURE GENETICS

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma

(2016) Yotam Drier et al.   NATURE GENETICS

MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism

(2016) Pratiti Bandopadhayay et al.   NATURE GENETICS

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice

(2016) Radhika Mathur et al.   NATURE GENETICS

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

(2016) Xingqi Chen et al.   NATURE METHODS

Role of non-coding sequence variants in cancer

(2016) Ekta Khurana et al.   NATURE REVIEWS GENETICS

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

(2016) Elisa Fiorito et al.   NUCLEIC ACIDS RESEARCH

INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer

(2016) S Zhang et al.   ONCOGENE

SDPR functions as a metastasis suppressor in breast cancer by promoting apoptosis

(2016) Sait Ozturk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles

(2016) François Spitz   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits

(2016) Suhn Kyong Rhie et al.   Epigenetics & Chromatin

A Myc-driven self-reinforcing regulatory network maintains mouse embryonic stem cell identity

(2016) Luca Fagnocchi et al.   Nature Communications

FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells

(2016) Michèle Fournier et al.   Scientific Reports

Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism

(2016) Radhika Kandaswamy et al.   Cell Reports

FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3

(2016) Kamila M. Jozwik et al.   Cell Reports

Activation of P-TEFb by Androgen Receptor-Regulated Enhancer RNAs in Castration-Resistant Prostate Cancer

(2016) Yu Zhao et al.   Cell Reports

Integration of Signaling Pathways with the Epigenetic Machinery in the Maintenance of Stem Cells

(2016) Luca Fagnocchi et al.   Stem Cells International

Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer

(2016) H. Singhal et al.   Science Advances

Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity

(2015) Janusz Puc et al.   CELL

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Chromatin signatures of cancer

(2015) Marc A. Morgan et al.   GENES & DEVELOPMENT

EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling

(2015) Feng Liu et al.   MOLECULAR CELL

TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites to Alter the Breast Cancer Cell Transcriptome

(2015) Hector L. Franco et al.   MOLECULAR CELL

Breast Tumor Heterogeneity: Source of Fitness, Hurdle for Therapy

(2015) Shany Koren et al.   MOLECULAR CELL

YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers

(2015) Giorgio G. Galli et al.   MOLECULAR CELL

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

(2015) Denes Hnisz et al.   MOLECULAR CELL

Mediator kinase inhibition further activates super-enhancer-associated genes in AML

(2015) Henry E. Pelish et al.   NATURE

Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism

(2015) Derek A. Oldridge et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells

(2015) Devon A. Lawson et al.   NATURE

Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth

(2015) Francesca Zanconato et al.   NATURE CELL BIOLOGY

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

(2015) Mark M Pomerantz et al.   NATURE GENETICS

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Unraveling the 3D genome: genomics tools for multiscale exploration

(2015) Viviana I. Risca et al.   TRENDS IN GENETICS

Site- and allele-specific polycomb dysregulation in T-cell leukaemia

(2015) Jean-Marc Navarro et al.   Nature Communications

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

(2015) Annelien Verfaillie et al.   Nature Communications

Deregulation of the Ras-Erk Signaling Axis Modulates the Enhancer Landscape

(2015) Behnam Nabet et al.   Cell Reports

APOBEC3B-Mediated Cytidine Deamination Is Required for Estrogen Receptor Action in Breast Cancer

(2015) Manikandan Periyasamy et al.   Cell Reports

ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas

(2015) Hanseul Yang et al.   eLife

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

(2015) Lijing Yao et al.   GENOME BIOLOGY

The Four Layers of Aging

(2015) Ran Zhang et al.   Cell Systems

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

Enhancer Malfunction in Cancer

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

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor

(2014) Nicholas Kwiatkowski et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

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

(2014) Xiaoyang Zhang et al.   TRENDS IN GENETICS

Dynamics of histone variant H3.3 and its coregulation with H2A.Z at enhancers and promoters

(2014) Ping Chen et al.   Nucleus

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Chromatin Remodeling at DNA Double-Strand Breaks

(2013) Brendan D. Price 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

CTCF and BORIS in genome regulation and cancer

(2013) Amy D Marshall et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?

(2013) F. S. J. de Souza et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

FOXOs: signalling integrators for homeostasis maintenance

(2013) Astrid Eijkelenboom et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

FOXO3 Selectively Amplifies Enhancer Activity to Establish Target Gene Regulation

(2013) Astrid Eijkelenboom et al.   Cell Reports

FOXO3 Shares Common Targets with ASCL1 Genome-wide and Inhibits ASCL1-Dependent Neurogenesis

(2013) Ashley E. Webb et al.   Cell Reports

Wnt/β-Catenin Signaling and Disease

(2012) Hans Clevers et al.   CELL

Insulators, long-range interactions, and genome function

(2012) Jingping Yang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Linking disease associations with regulatory information in the human genome

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

XPG and XPF Endonucleases Trigger Chromatin Looping and DNA Demethylation for Accurate Expression of Activated Genes

(2012) Nicolas Le May et al.   MOLECULAR CELL

The landscape of cancer genes and mutational processes in breast cancer

(2012) Philip J. Stephens et al.   NATURE

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators

(2012) Akihiro Fujimoto et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

CTCF/cohesin-mediated DNA looping is required for protocadherin   promoter choice

(2012) Y. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Mapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription

(2011) Zhixiong Xu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

The Biology of Chromatin Remodeling Complexes

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

Nuclear Receptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer

(2009) Chunru Lin et al.   CELL

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

DNA Oxidation as Triggered by H3K9me2 Demethylation Drives Estrogen-Induced Gene Expression

(2008) B. Perillo et al.   SCIENCE