An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long‐range loop formation

The Mediator complex regulates enhancer-promoter interactions

(2023) Shyam Ramasamy et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Coming full circle: On the origin and evolution of the looping model for enhancer–promoter communication

(2022) Tessa M. Popay et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Factors and Mechanisms That Influence Chromatin-Mediated Enhancer–Promoter Interactions and Transcriptional Regulation

(2022) Shinsuke Ito et al.   Cancers

Enhancer redundancy in development and disease

(2021) Evgeny Z. Kvon et al.   NATURE REVIEWS GENETICS

ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function

(2021) Qiling Zhou et al.   Nature Communications

Alteration of active and repressive histone marks during adipogenic differentiation of porcine mesenchymal stem cells

(2021) Joanna Stachecka et al.   Scientific Reports

Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4

(2021) Lei Chen et al.   Cell Reports

Ultraconserved enhancer function does not require perfect sequence conservation

(2021) Valentina Snetkova et al.   NATURE GENETICS

Genome folding through loop extrusion by SMC complexes

(2021) Iain F. Davidson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone modifications centric-regulation in osteogenic differentiation

(2021) Kun Li et al.   Cell Death Discovery

Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

(2021) Karolina Stępniak et al.   Nature Communications

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

Landscape of cohesin-mediated chromatin loops in the human genome

(2020) Fabian Grubert et al.   NATURE

Enhancer RNAs Mediate Estrogen-Induced Decommissioning of Selective Enhancers by Recruiting ERα and Its Cofactor

(2020) Mei Yang et al.   Cell Reports

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

(2019) Shi Hao Tan et al.   BLOOD

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

(2019) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

4C-seq from start to end: a detailed protocol for sample preparation and data analysis

(2019) Peter H.L. Krijger et al.   METHODS

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation

(2018) Xiao-Feng Chen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

BET bromodomain proteins regulate enhancer function during adipogenesis

(2018) Jonathan D. Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks

(2018) Mun-Kit Choy et al.   Nature Communications

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

Genome-Wide Chromatin Structure Changes During Adipogenesis and Myogenesis

(2018) Mengnan He 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

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

(2018) Hui Hu et al.   NUCLEIC ACIDS RESEARCH

An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3

(2018) Yuri S. Odaka et al.   Scientific Reports

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties

(2018) Ling Chen et al.   PLoS Computational Biology

Unraveling the transcriptional regulation of TWIST1 in limb development

(2018) Naama Hirsch et al.   PLoS Genetics

Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

(2017) Avital Sarusi Portuguez et al.   FEBS Journal

Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans

(2017) Aaron C. Daugherty et al.   GENOME RESEARCH

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

NFIA co-localizes with PPARγ and transcriptionally controls the brown fat gene program

(2017) Yuta Hiraike et al.   NATURE CELL BIOLOGY

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure

(2017) Sergey V. Ulianov et al.   Epigenetics & Chromatin

Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis

(2017) Ji-Eun Lee et al.   Nature Communications

Promoter–enhancer looping at the PPARγ2 locus during adipogenic differentiation requires the Prmt5 methyltransferase

(2016) Scott E. LeBlanc et al.   NUCLEIC ACIDS RESEARCH

Fasting induces a subcutaneous-to-visceral fat switch mediated by microRNA-149-3p and suppression of PRDM16

(2016) Hanying Ding et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation: Fig. 1.

(2015) Honglei Liu et al.   BIOINFORMATICS

WGE: a CRISPR database for genome engineering: Fig. 1.

(2015) Alex Hodgkins et al.   BIOINFORMATICS

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Identification and functional characterization of novel transcriptional enhancers involved in regulating humanGLI3expression during early development

(2015) Saneela Anwar et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Structural mechanism for signal transduction in RXR nuclear receptor heterodimers

(2015) Douglas J. Kojetin et al.   Nature Communications

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

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 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

Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers

(2014) Rasmus Siersbæk et al.   Cell Reports

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

(2013) Supat Thongjuea et al.   NUCLEIC ACIDS RESEARCH

Prolonged Induction Activates Cebpα Independent Adipogenesis in NIH/3T3 Cells

(2013) Hsiao-Yun Shao et al.   PLoS One

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

(2012) Natalia Naumova et al.   METHODS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Retinaldehyde dehydrogenase 1 regulates a thermogenic program in white adipose tissue

(2012) Florian W Kiefer et al.   NATURE MEDICINE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

A gene variation (rs12691) in the CCAT/enhancer binding protein α modulates glucose metabolism in metabolic syndrome

(2012) J. Delgado-Lista et al.   NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES

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

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

(2011) Rasmus Siersbaek et al.   EMBO JOURNAL

Cohesin Mediates Chromatin Interactions That Regulate Mammalian β-globin Expression

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

An Evolutionarily Conserved TNF- -Responsive Enhancer in the Far Upstream Region of Human CCL2 Locus Influences Its Gene Expression

(2011) G. B. Bonello et al.   JOURNAL OF IMMUNOLOGY

Adipose tissue stem cells meet preadipocyte commitment: going back to the future

(2011) William P. Cawthorn et al.   JOURNAL OF LIPID RESEARCH

Forming functional fat: a growing understanding of adipocyte differentiation

(2011) Ana G. Cristancho et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcriptional networks and chromatin remodeling controlling adipogenesis

(2011) Rasmus Siersbæk et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation

(2011) Hironori Waki et al.   PLoS Genetics

CCAAT/enhancer binding protein α, β and δ gene variants: associations with obesity related phenotypes in the Leeds Family Study

(2010) Claire E Bennett et al.   Diabetes & Vascular Disease Research

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

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

The Role of ATF-2 Family Transcription Factors in Adipocyte Differentiation: Antiobesity Effects of p38 Inhibitors

(2009) T. Maekawa et al.   MOLECULAR AND CELLULAR BIOLOGY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

The emerging role of nuclear architecture in DNA repair and genome maintenance

(2009) Tom Misteli et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

New developments in adipogenesis

(2009) Martina I. Lefterova et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

New insights into the functions and regulation of the transcriptional corepressors SMRT and N-CoR

(2009) Kristopher J Stanya et al.   Cell Division

CCAAT/Enhancer Binding Protein α (C/EBPα) in Adipose Tissue Regulates Genes in Lipid and Glucose Metabolism and a Genetic Variation in C/EBPα Is Associated with Serum Levels of Triglycerides

(2008) Louise E. Olofsson et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

Identification of a novel distal enhancer in human adiponectin gene

(2008) Katsumori Segawa et al.   JOURNAL OF ENDOCRINOLOGY

Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA

(2008) Vikas Chandra et al.   NATURE

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

(2008) Leighton J. Core et al.   SCIENCE