Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation

Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells

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

Forged by DXZ4, FIRRE, and ICCE: How Tandem Repeats Shape the Active and Inactive X Chromosome

(2020) Prakhar Bansal et al.   Frontiers in Cell and Developmental Biology

Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA

(2020) Ke Zhang et al.   MOLECULAR CELL

Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

(2020) He Fang et al.   Nature Communications

Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X

(2019) David Colognori et al.   MOLECULAR CELL

PRC1 collaborates with SMCHD1 to fold the X-chromosome and spread Xist RNA between chromosome compartments

(2019) Chen-Yu Wang et al.   Nature Communications

Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells

(2019) Ana Cuadrado et al.   Cell Reports

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

DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency

(2019) Katy McLaughlin et al.   Cell Reports

The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes

(2019) Nathan D. Elrod et al.   MOLECULAR CELL

SMCHD1 Merges Chromosome Compartments and Assists Formation of Super-Structures on the Inactive X

(2018) Chen-Yu Wang et al.   CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome

(2018) G. Bonora et al.   Nature Communications

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Organizational principles of 3D genome architecture

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

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome

(2018) Michal R. Gdula et al.   Nature Communications

Megadomains and superloops form dynamically but are dispensable for X-chromosome inactivation and gene escape

(2018) John E. Froberg et al.   Nature Communications

Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock

(2017) Jacqueline Deschamps et al.   GENES & DEVELOPMENT

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

(2017) Sharmistha Kundu et al.   MOLECULAR CELL

Transcription control by the ENL YEATS domain in acute leukaemia

(2017) Michael A. Erb et al.   NATURE

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

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

(2017) Takashi Nagano et al.   NATURE

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

Structural organization of the inactive X chromosome in the mouse

(2016) Luca Giorgetti et al.   NATURE

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Deletion ofDXZ4on the human inactive X chromosome alters higher-order genome architecture

(2016) Emily M. Darrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dosage compensation of the sex chromosomes and autosomes

(2016) Christine M. Disteche   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

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

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

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

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency

(2015) Onkar Joshi et al.   Cell Stem Cell

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

(2015) James Fraser et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

(2015) Johnny T. Kung et al.   MOLECULAR CELL

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

(2015) Stefan Schoenfelder et al.   NATURE GENETICS

Clustering of mammalianHoxgenes with other H3K27me3 targets within an active nuclear domain

(2015) Maxence Vieux-Rochas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

Single-Step Generation of Conditional Knockout Mouse Embryonic Stem Cells

(2015) Matyas Flemr et al.   Cell Reports

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

(2014) Suhas S.P. Rao et al.   CELL

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

(2014) Ezgi Hacisuleyman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Characterization of a DNA exit gate in the human cohesin ring

(2014) P. J. Huis in 't Veld et al.   SCIENCE

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

(2013) Warren A. Whyte et al.   CELL

Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

(2013) Matthew Denholtz et al.   Cell Stem Cell

Prophase pathway-dependent removal of cohesin from human chromosomes requires opening of the Smc3–Scc1 gate

(2013) Johannes Buheitel et al.   EMBO JOURNAL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

(2013) Matthew D. Simon et al.   NATURE

Wapl is an essential regulator of chromatin structure and chromosome segregation

(2013) Antonio Tedeschi et al.   NATURE

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Cohesin’s DNA Exit Gate Is Distinct from Its Entrance Gate and Is Regulated by Acetylation

(2012) Kok-Lung Chan et al.   CELL

The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome

(2012) Andrea H. Horakova et al.   HUMAN MOLECULAR GENETICS

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA

(2011) E. Splinter et al.   GENES & DEVELOPMENT

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control

(2011) Jeannie T. Lee   NATURE REVIEWS MOLECULAR CELL BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Cohesin: Its Roles and Mechanisms

(2009) Kim Nasmyth et al.   Annual Review of Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A new model for random X chromosome inactivation

(2008) J. Starmer et al.   DEVELOPMENT

The cohesin complex and its roles in chromosome biology

(2008) J.-M. Peters et al.   GENES & DEVELOPMENT

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation

(2008) Marnie E Blewitt et al.   NATURE GENETICS

Intersection of the RNA Interference and X-Inactivation Pathways

(2008) Y. Ogawa et al.   SCIENCE

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE