Eukaryotic enhancers: common features, regulation, and participation in diseases

Chromatin Contributions to the Regulation of Innate Immunity

(2014) Stephen T. Smale et al.   Annual Review of Immunology

Perinucleolar relocalization and nucleolin as crucial events in the transcriptional activation of key genes in mantle cell lymphoma

(2014) Jeanne Allinne et al.   BLOOD

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

(2014) Suhas S.P. Rao et al.   CELL

The 3D Genome in Transcriptional Regulation and Pluripotency

(2014) David U. Gorkin et al.   Cell Stem Cell

The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains

(2014) Wibke Schwarzer et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Mediator complex: a master coordinator of transcription and cell lineage development

(2014) J.-w. Yin et al.   DEVELOPMENT

Trithorax monomethylates histone H3K4 and interacts directly with CBP to promote H3K27 acetylation and antagonize Polycomb silencing

(2014) F. Tie et al.   DEVELOPMENT

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson 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

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Enhancer biology and enhanceropathies

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

Facioscapulohumeral dystrophy: the path to consensus on pathophysiology

(2014) Rabi Tawil et al.   Skeletal Muscle

Disruption of Autoregulatory Feedback by a Mutation in a Remote, Ultraconserved PAX6 Enhancer Causes Aniridia

(2013) Shipra Bhatia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Making connections: Insulators organize eukaryotic chromosomes into independent cis-regulatory networks

(2013) Darya Chetverina et al.   BIOESSAYS

GATA2 haploinsufficiency caused by mutations in a conserved intronic element leads to MonoMAC syndrome

(2013) A. P. Hsu et al.   BLOOD

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan 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

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-γ Locus

(2013) J. Antonio Gomez et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency

(2013) Zong Wei et al.   Cell Stem Cell

Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming

(2013) Effie Apostolou et al.   Cell Stem Cell

Intrachromosomal Looping Is Required for Activation of Endogenous Pluripotency Genes during Reprogramming

(2013) He Zhang et al.   Cell Stem Cell

Mechanisms of Mediator complex action in transcriptional activation

(2013) Suraiya A. Ansari et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The Mediator complex and transcription regulation

(2013) Zachary C. Poss et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Genome organization and long-range regulation of gene expression by enhancers

(2013) Andrea Smallwood et al.   CURRENT OPINION IN CELL BIOLOGY

Cohesin in development and disease

(2013) S. Remeseiro et al.   DEVELOPMENT

Chromatin insulators and long-distance interactions inDrosophila

(2013) Olga Kyrchanova et al.   FEBS LETTERS

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits

(2013) O. Corradin et al.   GENOME RESEARCH

Defective Regulation of MicroRNA Target Genes in Myoblasts from Facioscapulohumeral Dystrophy Patients

(2013) Petr Dmitriev et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

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

(2013) Eliezer Calo et al.   MOLECULAR CELL

Genome-wide analysis of FOXO3 mediated transcription regulation through RNA polymerase II profiling

(2013) A. Eijkelenboom et al.   Molecular Systems Biology

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

Pathways systematically associated to Hirschsprung’s disease

(2013) Raquel M Fernández et al.   Orphanet Journal of Rare Diseases

Transcription through enhancers suppresses their activity in Drosophila

(2013) Maksim Erokhin et al.   Epigenetics & Chromatin

Genome-Wide Control of RNA Polymerase II Activity by Cohesin

(2013) Cheri A. Schaaf et al.   PLoS Genetics

H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation

(2013) Ji-Eun Lee et al.   eLife

Computational Identification of Active Enhancers in Model Organisms

(2013) Chengqi Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A Long ncRNA Links Copy Number Variation to a Polycomb/Trithorax Epigenetic Switch in FSHD Muscular Dystrophy

(2012) Daphne S. Cabianca et al.   CELL

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4

(2012) H.-M. Herz et al.   GENES & DEVELOPMENT

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Coding exons function as tissue-specific enhancers of nearby genes

(2012) Ramon Y. Birnbaum 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

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

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

Chromatin loop formation in the β-globin locus and its role in globin gene transcription

(2012) AeRi Kim et al.   MOLECULES AND CELLS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali 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

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

(2012) Yin C Lin et al.   NATURE IMMUNOLOGY

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

A noncoding RNA regulates the neurogenin1 gene locus during mouse neocortical development

(2012) M. Onoguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted deletion of Sost distal enhancer increases bone formation and bone mass

(2012) N. M. Collette et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Human limb abnormalities caused by disruption of hedgehog signaling

(2012) Eve Anderson et al.   TRENDS IN GENETICS

Enhancers as information integration hubs in development: lessons from genomics

(2012) Christa Buecker et al.   TRENDS IN GENETICS

Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos

(2012) Per-Henrik Holmqvist et al.   PLoS Genetics

abd-A Regulation by the iab-8 Noncoding RNA

(2012) Maheshwar Gummalla et al.   PLoS Genetics

Long non-coding RNA modifies chromatin

(2011) Alka Saxena et al.   BIOESSAYS

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

(2011) Nasun Hah et al.   CELL

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Cohesin: genomic insights into controlling gene transcription and development

(2011) Dale Dorsett   CURRENT OPINION IN GENETICS & DEVELOPMENT

DrosophilaSet1 is the major histone H3 lysine 4 trimethyltransferase with role in transcription

(2011) M Behfar Ardehali et al.   EMBO JOURNAL

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

dSet1 Is the Main H3K4 Di- and Tri-Methyltransferase ThroughoutDrosophilaDevelopment

(2011) Graham Hallson et al.   GENETICS

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

(2011) O. Hakim et al.   GENOME RESEARCH

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

(2011) A. A. Serandour et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Distant cis-regulatory elements in human skeletal muscle differentiation

(2011) Rachel Patton McCord et al.   GENOMICS

Cohesin Mediates Chromatin Interactions That Regulate Mammalian β-globin Expression

(2011) Richard Chien et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The COMPASS Family of H3K4 Methylases in Drosophila

(2011) M. Mohan et al.   MOLECULAR AND CELLULAR BIOLOGY

RETRACTED: The Noncoding RNA Mistral Activates Hoxa6 and Hoxa7 Expression and Stem Cell Differentiation by Recruiting MLL1 to Chromatin

(2011) Stéphane Bertani et al.   MOLECULAR CELL

SAGA and ATAC Histone Acetyl Transferase Complexes Regulate Distinct Sets of Genes and ATAC Defines a Class of p300-Independent Enhancers

(2011) Arnaud R. Krebs et al.   MOLECULAR CELL

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

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

(2011) Olivier Harismendy et al.   NATURE

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Deletion of a remote enhancer near ATOH7 disrupts retinal neurogenesis, causing NCRNA disease

(2011) Noor M Ghiasvand et al.   NATURE NEUROSCIENCE

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

Epigenetic Priming of a Pre-B Cell-Specific Enhancer through Binding of Sox2 and Foxd3 at the ESC Stage

(2010) Daniel Liber et al.   Cell Stem Cell

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

(2010) Qihuang Jin et al.   EMBO JOURNAL

Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases

(2010) David C. Bedford et al.   Epigenetics

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

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

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

Genome-wide assessment of differential roles for p300 and CBP in transcription regulation

(2010) Y. F. M. Ramos et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Activator-Mediator binding regulates Mediator-cofactor interactions

(2010) C. C. Ebmeier 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

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

A Comprehensive Map of Insulator Elements for the Drosophila Genome

(2010) Nicolas Nègre et al.   PLoS Genetics

Early chromatin unfolding by RUNX1: a molecular explanation for differential requirements during specification versus maintenance of the hematopoietic gene expression program

(2009) M. Hoogenkamp et al.   BLOOD

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang 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

Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells

(2009) J. Xu et al.   GENES & DEVELOPMENT

Paused Pol II captures enhancer activity and acts as a potent insulator

(2009) L. J. Core et al.   GENES & DEVELOPMENT

Long-range oncogenic activation of Igh–c-myc translocations by the Igh 3′ regulatory region

(2009) Monica Gostissa et al.   NATURE

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

(2009) Jasmina Ponjavic et al.   PLoS Genetics

Structure and chemistry of the p300/CBP and Rtt109 histone acetyltransferases: implications for histone acetyltransferase evolution and function

(2008) Ling Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells

(2008) D. N. Levasseur et al.   GENES & DEVELOPMENT

Molecular Regulation of H3K4 Trimethylation by Wdr82, a Component of Human Set1/COMPASS

(2008) M. Wu et al.   MOLECULAR AND CELLULAR BIOLOGY

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Pearls in the junk: Dissecting the molecular pathogenesis of facioscapulohumeral muscular dystrophy

(2008) Petr Dmitriev et al.   NEUROMUSCULAR DISORDERS

Facioscapulohumeral muscular dystrophy

(2008) Rabi Tawil   Neurotherapeutics