The Mediator complex regulates enhancer-promoter interactions

The role of loop extrusion in enhancer-mediated gene activation

(2023) Magdalena A Karpinska et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

(2023) Viraat Y. Goel et al.   NATURE GENETICS

Enhancer–promoter contact formation requires RNAPII and antagonizes loop extrusion

(2023) Shu Zhang et al.   NATURE GENETICS

Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

(2022) Damien J. Downes et al.   Nature Protocols

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

(2022) Abrar Aljahani et al.   Nature Communications

Cohesin-dependence of neuronal gene expression relates to chromatin loop length

(2022) Lesly Calderon et al.   eLife

The Mediator complex as a master regulator of transcription by RNA polymerase II

(2022) William F. Richter et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A cohesin traffic pattern genetically linked to gene regulation

(2022) Anne-Laure Valton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

BET inhibition disrupts transcription but retains enhancer-promoter contact

(2021) Nicholas T. Crump et al.   Nature Communications

High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale

(2021) Damien J. Downes et al.   Nature Communications

Structure of the human Mediator-bound transcription preinitiation complex

(2021) R. Abdella et al.   SCIENCE

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Structure of the human Mediator–RNA polymerase II pre-initiation complex

(2021) Srinivasan Rengachari et al.   NATURE

Structures of the human Mediator and Mediator-bound preinitiation complex

(2021) Xizi Chen et al.   SCIENCE

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

(2021) Fei Sun et al.   GENES & DEVELOPMENT

Defining genome architecture at base-pair resolution

(2021) Peng Hua et al.   NATURE

Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions

(2021) Leonid Mirny et al.   Cold Spring Harbor Perspectives in Biology

How subtle changes in 3D structure can create large changes in transcription

(2021) Jordan Yupeng Xiao et al.   eLife

BRD4 orchestrates genome folding to promote neural crest differentiation

(2021) Ricardo Linares-Saldana et al.   NATURE GENETICS

RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis

(2021) Shu Zhang et al.   Science Advances

Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells

(2020) James D.P. Rhodes et al.   Cell Reports

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

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

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Selective Mediator dependence of cell-type-specifying transcription

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

Dynamics of the 4D genome during in vivo lineage specification and differentiation

(2020) A. Marieke Oudelaar et al.   Nature Communications

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

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

Structural Biology of RNA Polymerase II Transcription: 20 Years On

(2020) Sara Osman et al.   Annual Review of Cell and Developmental Biology

WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation

(2020) Ning Qing Liu et al.   NATURE GENETICS

The relationship between genome structure and function

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

CTCF: a Swiss-army knife for genome organization and transcription regulation

(2019) Luca Braccioli et al.   Essays in Biochemistry

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

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

(2019) Laila El Khattabi et al.   CELL

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

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

(2019) Haoyue Zhang et al.   NATURE

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

(2019) Kristin Abramo et al.   NATURE CELL BIOLOGY

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

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

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

(2017) Jonathan A. Beagan et al.   GENOME RESEARCH

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

(2017) Georg A. Busslinger et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A simple method for generating high-resolution maps of genome-wide protein binding

(2015) Peter J Skene et al.   eLife

Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping

(2014) Wulan Deng et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

Role of LDB1 in the transition from chromatin looping to transcription activation

(2014) I. Krivega et al.   GENES & DEVELOPMENT

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Warren A. Whyte et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

(2012) Wulan Deng et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE