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

Calcium signaling instructs NIPBL recruitment at active enhancers and promoters via distinct mechanisms to reconstruct genome compartmentalization

(2021) Yina Zhu et al.   GENES & DEVELOPMENT

H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization

(2021) Bobbie Pelham-Webb et al.   MOLECULAR CELL

Coolpup.py: versatile pile-up analysis of Hi-C data

(2020) Ilya M Flyamer et al.   BIOINFORMATICS

Genome anchoring to nuclear landmarks drives functional compartmentalization of the nuclear space

(2020) Antoine Canat et al.   Briefings in Functional Genomics

Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals

(2020) M Jordan Rowley et al.   GENOME RESEARCH

Pausing sites of RNA polymerase II on actively transcribed genes are enriched with DNA double-stranded breaks

(2020) Sandeep Singh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Negative supercoil at gene boundaries modulates gene topology

(2020) Yathish Jagadheesh Achar et al.   NATURE

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells

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

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

(2020) Gordana Wutz et al.   eLife

Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control

(2020) Valentina Casa et al.   GENOME RESEARCH

Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment

(2020) Celeste D. Rosencrance et al.   MOLECULAR CELL

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

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

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

(2020) Satish Sati et al.   MOLECULAR CELL

Topoisomerase IIα is essential for maintenance of mitotic chromosome structure

(2020) Christian F. Nielsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging

(2020) Bo Gu et al.   MOLECULAR CELL

Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence

(2020) Ioana Olan et al.   Nature Communications

Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture

(2020) Sjoerd JD Tjalsma et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization

(2019) M. Jordan Rowley et al.   Cell Reports

Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II

(2019) Ryosuke Nagashima et al.   JOURNAL OF CELL BIOLOGY

Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole

(2019) Aisha Yesbolatova et al.   METHODS

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

(2019) Michael P. Meers et al.   Epigenetics & Chromatin

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

(2019) Laila El Khattabi et al.   CELL

Differential contribution of steady‐state RNA and active transcription in chromatin organization

(2019) A Rasim Barutcu et al.   EMBO REPORTS

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

Control of DNA replication timing in the 3D genome

(2019) Claire Marchal et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA polymerases as moving barriers to condensin loop extrusion

(2019) Hugo B. Brandão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Forces driving the three‐dimensional folding of eukaryotic genomes

(2018) Alvaro Rada‐Iglesias et al.   Molecular Systems Biology

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes

(2018) Sheila S Teves et al.   eLife

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock

(2018) Ramon Amat et al.   GENOME RESEARCH

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

(2018) Adam Buckle et al.   MOLECULAR CELL

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

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

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

(2017) M Ryan Corces et al.   NATURE METHODS

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Recent evidence that TADs and chromatin loops are dynamic structures

(2017) Anders S. Hansen et al.   Nucleus

Recent evidence that TADs and chromatin loops are dynamic structures

(2017) Anders S. Hansen et al.   Nucleus

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

Rapid movement and transcriptional re‐localization of human cohesin on DNA

(2016) Iain F Davidson et al.   EMBO JOURNAL

A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition

(2016) Chris C.-S. Hsiung et al.   GENES & DEVELOPMENT

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

(2016) Lilija Brant et al.   Molecular Systems Biology

Structural organization of the inactive X chromosome in the mouse

(2016) Luca Giorgetti et al.   NATURE

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Cell cycle staging of individual cells by fluorescence microscopy

(2015) Vassilis Roukos et al.   Nature Protocols

iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data

(2015) Jesper Grud Skat Madsen et al.   NUCLEIC ACIDS RESEARCH

Standardizing chromatin research: a simple and universal method for ChIP-seq

(2015) Laura Arrigoni et al.   NUCLEIC ACIDS RESEARCH

Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories

(2015) Maïwen Caudron-Herger et al.   NUCLEIC ACIDS RESEARCH

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS

(2014) Jessica Zuin et al.   PLoS Genetics

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gene regulation and priming by topoisomerase IIα in embryonic stem cells

(2013) Sudhir Thakurela et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Triptolide (TPL) Inhibits Global Transcription by Inducing Proteasome-Dependent Degradation of RNA Polymerase II (Pol II)

(2011) Ying Wang et al.   PLoS One