Enhancer RNAs in cancer: regulation, mechanisms and therapeutic potential

The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia

(2019) Shi Hao Tan et al.   BLOOD

Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription

(2019) Rui Xiao et al.   CELL

Inflammation and Cancer: Triggers, Mechanisms, and Consequences

(2019) Florian R. Greten et al.   IMMUNITY

A Non-canonical Role of YAP/TEAD Is Required for Activation of Estrogen-Regulated Enhancers in Breast Cancer

(2019) Chi Zhu et al.   MOLECULAR CELL

Chromatin-associated RNAs as facilitators of functional genomic interactions

(2019) Xiao Li et al.   NATURE REVIEWS GENETICS

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

(2018) Han Chen et al.   CELL

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

The Role of RNA in Biological Phase Separations

(2018) Marta M. Fay et al.   JOURNAL OF MOLECULAR BIOLOGY

A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans

(2018) Pei-Fang Tsai et al.   MOLECULAR CELL

HPSE enhancer RNA promotes cancer progression through driving chromatin looping and regulating hnRNPU/p300/EGR1/HPSE axis

(2018) Wanju Jiao et al.   ONCOGENE

Sex reversal following deletion of a single distal enhancer ofSox9

(2018) Nitzan Gonen et al.   SCIENCE

Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function

(2018) Yifei Miao et al.   Nature Communications

Enhancer RNA - P2RY2e induced by estrogen promotes malignant behaviors of bladder cancer

(2018) Mengting Ding et al.   International Journal of Biological Sciences

A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies

(2018) Carsten Bahr et al.   NATURE

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation

(2018) Homa Rahnamoun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enhancer RNA and NFκB-dependent P300 regulation of ADAMDEC1

(2018) Lihua Shi et al.   MOLECULAR IMMUNOLOGY

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

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

(2017) Shino Murakami et al.   GENES & DEVELOPMENT

SERPINB2 is regulated by dynamic interactions with pause-release proteins and enhancer RNAs

(2017) Lihua Shii et al.   MOLECULAR IMMUNOLOGY

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

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6

(2017) Ru-Juan Liu et al.   NUCLEIC ACIDS RESEARCH

On the Origin of lncRNAs: Missing Link Found

(2017) Joaquín M. Espinosa   TRENDS IN GENETICS

Mutant p53 shapes the enhancer landscape of cancer cells in response to chronic immune signaling

(2017) Homa Rahnamoun et al.   Nature Communications

Mechanisms of Hippo pathway regulation

(2016) Zhipeng Meng et al.   GENES & DEVELOPMENT

CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer

(2016) Mark L. McCleland et al.   JOURNAL OF CLINICAL INVESTIGATION

Revisiting lncRNAs: How Do You Know Yours Is Not an eRNA?

(2016) Joaquín M. Espinosa   MOLECULAR CELL

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

Unlinking an lncRNA from Its Associated cis Element

(2016) Vikram R. Paralkar et al.   MOLECULAR CELL

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

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

(2016) Andrew P. Feinberg et al.   NATURE REVIEWS GENETICS

The regulation and functions of the nuclear RNA exosome complex

(2016) Cornelia Kilchert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epstein–Barr virus super-enhancer eRNAs are essential for MYC oncogene expression and lymphoblast proliferation

(2016) Jun Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

(2016) Yasuhiro Murakawa et al.   TRENDS IN GENETICS

Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer

(2016) Steffen Grampp et al.   Nature Communications

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

(2016) Yu Zhao et al.   Cell Reports

Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α

(2016) Francesca Aguilo et al.   Cell Reports

The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers

(2015) Leng Han et al.   CANCER CELL

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

(2015) Evangelos Pefanis et al.   CELL

Chromatin signatures at Notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation

(2015) L. Skalska et al.   EMBO JOURNAL

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

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

Integrator mediates the biogenesis of enhancer RNAs

(2015) Fan Lai et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

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

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs

(2015) Nasun Hah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

(2015) Nicolas Léveillé et al.   Nature Communications

The Human Nuclear Exosome Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis

(2015) Michal Lubas et al.   Cell Reports

Regulation of Transcription by Long Noncoding RNAs

(2014) Roberto Bonasio et al.   Annual Review of Genetics

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

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

m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem Cell

Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease

(2014) Samir Ounzain et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

(2014) Jonathan D. Brown et al.   MOLECULAR CELL

Enhancer Malfunction in Cancer

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

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway

(2014) Xi Chen et al.   NATURE

BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2

(2014) Vaibhav Bhatia et al.   NATURE

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

(2014) Leighton J Core et al.   NATURE GENETICS

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

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

(2014) M. R. Mansour et al.   SCIENCE

Enhancer RNAs and regulated transcriptional programs

(2014) Michael T.Y. Lam et al.   TRENDS IN BIOCHEMICAL SCIENCES

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms

(2014) Mary Ann Allen et al.   eLife

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

(2013) J. R. Alvarez-Dominguez et al.   BLOOD

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Posttranslational Modification of the Androgen Receptor in Prostate Cancer

(2013) Travis Van der Steen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

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

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

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers

(2013) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

Estrogen and Cancer

(2012) Jing Liang et al.   Annual Review of Physiology

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases

(2012) B. Zamft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The tRNA methyltransferase NSun2 stabilizes p16INK4 mRNA by methylating the 3′-untranslated region of p16

(2012) Xiaotian Zhang et al.   Nature Communications

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

R-loop-mediated genomic instability is caused by impairment of replication fork progression

(2011) W. Gan et al.   GENES & DEVELOPMENT

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

(2011) Kevin C. Wang et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

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

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

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability

(2009) Renee D. Paulsen et al.   MOLECULAR CELL

Molecular Biology of Head and Neck Cancer: Risks and Pathways

(2008) Michael E. Stadler et al.   HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA

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

(2008) Leighton J. Core et al.   SCIENCE