Regulating specificity in enhancer–promoter communication

Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements

(2021) Henry F. Thomas et al.   MOLECULAR CELL

The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes

(2021) L. S. Melnikova et al.   Acta Naturae

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development

(2021) Sergio Martin Espinola et al.   NATURE GENETICS

At the Crossroad of Gene Regulation and Genome Organization: Potential Roles for ATP-Dependent Chromatin Remodelers in the Regulation of CTCF-Mediated 3D Architecture

(2021) Aktan Alpsoy et al.   Biology-Basel

On the choreography of genome folding: A grand pas de deux of cohesin and CTCF

(2021) Marjon S. van Ruiten et al.   CURRENT OPINION IN CELL BIOLOGY

The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter–enhancer looping

(2021) Fei Sun et al.   GENES & DEVELOPMENT

Enhancer release and retargeting activates disease-susceptibility genes

(2021) Soohwan Oh et al.   NATURE

Testing the super-enhancer concept

(2021) Gerd A. Blobel et al.   NATURE REVIEWS GENETICS

A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker

(2021) Yavor K. Bozhilov et al.   Nature Communications

Cohesin mediates DNA loop extrusion by a “swing and clamp” mechanism

(2021) Benedikt W. Bauer et al.   CELL

Cell-type specialization is encoded by specific chromatin topologies

(2021) Warren Winick-Ng et al.   NATURE

CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention

(2020) Elena M. Pugacheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping

(2020) V. Loubiere et al.   Science Advances

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate

(2020) Preston R. Arnold et al.   Frontiers in Cell and Developmental Biology

Evaluating Enhancer Function and Transcription

(2020) Andrew Field et al.   Annual Review of Biochemistry

Developmental regulation of cell type-specific transcription by novel promoter-proximal sequence elements

(2020) Dan Lu et al.   GENES & DEVELOPMENT

Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Communication with a Transcription Factor and Directly Activates a Housekeeping Promoter in Drosophila

(2020) Yuankai Dong et al.   GENETICS

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Selective Mediator dependence of cell-type-specifying transcription

(2020) Martin G. Jaeger et al.   NATURE GENETICS

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

(2020) Grégoire Stik et al.   NATURE GENETICS

Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

(2020) Michiel J. Thiecke et al.   Cell Reports

Molecular Basis of the Function of Transcriptional Enhancers

(2020) Airat N. Ibragimov et al.   Cells

Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale

(2020) Ian C Tobias et al.   GENOME

A Mutation in the Drosophila melanogastereve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences

(2020) Francheska Lopez-Rivera et al.   G3-Genes Genomes Genetics

The relationship between genome structure and function

(2020) A. Marieke Oudelaar et al.   NATURE REVIEWS GENETICS

Regulation of 3D chromatin organization by CTCF

(2020) Jian-Feng Xiang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

(2019) Tsukasa Kouno et al.   Nature Communications

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

High-throughput identification of human SNPs affecting regulatory element activity

(2019) Joris van Arensbergen et al.   NATURE GENETICS

Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes

(2019) Hila Shir-Shapira et al.   PLoS One

Large distances separate coregulated genes in living Drosophila embryos

(2019) Tyler Heist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

(2019) Laila El Khattabi et al.   CELL

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts

(2019) Stephen S. Gisselbrecht et al.   MOLECULAR CELL

A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary

(2019) Rafael Galupa et al.   MOLECULAR CELL

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Deciphering Gene Regulation Using Massively Parallel Reporter Assays

(2019) Max Trauernicht et al.   TRENDS IN BIOCHEMICAL SCIENCES

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

Visualization of Transvection in Living Drosophila Embryos

(2018) Bomyi Lim et al.   MOLECULAR CELL

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin

(2018) Shraddha Shrestha et al.   PLoS One

Organizational principles of 3D genome architecture

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

Determinants of promoter and enhancer transcription directionality in metazoans

(2018) Mahmoud M. Ibrahim et al.   Nature Communications

Role of the pre-initiation complex in Mediator recruitment and dynamics

(2018) Elisabeth R Knoll et al.   eLife

Dual functionality of cis -regulatory elements as developmental enhancers and Polycomb response elements

(2017) Jelena Erceg et al.   GENES & DEVELOPMENT

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of theIl2ragene locus

(2017) Peng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Mediator Complex: At the Nexus of RNA Polymerase II Transcription

(2017) Célia Jeronimo et al.   TRENDS IN CELL BIOLOGY

High-throughput functional comparison of promoter and enhancer activities

(2016) Thomas A. Nguyen et al.   GENOME RESEARCH

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors

(2016) Muhammad A. Zabidi et al.   TRENDS IN GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

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

(2015) Darío G. Lupiáñez et al.   CELL

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

(2015) Elizabeth Ing-Simmons et al.   GENOME RESEARCH

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

(2015) Jacques P Bothma et al.   eLife

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

(2014) Suhas S.P. Rao et al.   CELL

Hormone-Responsive Enhancer-Activity Maps Reveal Predictive Motifs, Indirect Repression, and Targeting of Closed Chromatin

(2014) Daria Shlyueva et al.   MOLECULAR CELL

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

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

Architectural proteins: regulators of 3D genome organization in cell fate

(2014) Elena Gómez-Díaz et al.   TRENDS IN CELL BIOLOGY

Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome

(2014) Jutta Vogelmann et al.   PLoS Genetics

Mechanisms and proteins involved in long-distance interactions

(2014) Oksana Maksimenko et al.   Frontiers in Genetics

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

(2013) Darya Chetverina et al.   BIOESSAYS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures

(2013) R. A.- J. Chen et al.   GENOME RESEARCH

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Chromatin looping and organization at developmentally regulated gene loci

(2013) Daan Noordermeer et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

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

(2012) Stefan Bonn et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Deciphering the transcriptional cis-regulatory code

(2012) J. Omar Yáñez-Cuna et al.   TRENDS IN GENETICS

Chromatin insulator elements: establishing barriers to set heterochromatin boundaries

(2012) Gráinne Barkess et al.   Epigenomics

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

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

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Enhancer-promoter communication at the Drosophila engrailed locus

(2009) D. Kwon et al.   DEVELOPMENT

Stalled Hox promoters as chromosomal boundaries

(2009) V. S. Chopra et al.   GENES & DEVELOPMENT

Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions

(2009) A. M. Bushey et al.   GENES & DEVELOPMENT

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

(2009) N. Jiang et al.   MOLECULAR AND CELLULAR BIOLOGY

Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos

(2009) Jochen Gehrig et al.   NATURE METHODS

Global transcriptional regulation of the locus encoding the skeletal muscle determination genes Mrf4 and Myf5

(2008) J. J. Carvajal et al.   GENES & DEVELOPMENT

Caudal, a key developmental regulator, is a DPE-specific transcriptional factor

(2008) T. Juven-Gershon et al.   GENES & DEVELOPMENT

Enhancer-Promoter Communication Is Regulated by Insulator Pairing in a Drosophila Model Bigenic Locus

(2008) O. Maksimenko et al.   MOLECULAR AND CELLULAR BIOLOGY

NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila

(2008) C. Lee et al.   MOLECULAR AND CELLULAR BIOLOGY