Looping the Genome with SMC Complexes

The Smc5/6 complex is a DNA loop-extruding motor

(2023) Biswajit Pradhan et al.   NATURE

CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion

(2023) Iain F. Davidson et al.   NATURE

A loop extrusion–independent mechanism contributes to condensin I–mediated chromosome shaping

(2022) Kazuhisa Kinoshita et al.   JOURNAL OF CELL BIOLOGY

Spatial organization of transcribed eukaryotic genes

(2022) Susanne Leidescher et al.   NATURE CELL BIOLOGY

Mediator recruits the cohesin loader Scc2 to RNA Pol II-transcribed genes and promotes sister chromatid cohesion

(2022) Mark Mattingly et al.   CURRENT BIOLOGY

A walk through the SMC cycle: From catching DNAs to shaping the genome

(2022) Roel Oldenkamp et al.   MOLECULAR CELL

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

MCM complexes are barriers that restrict cohesin-mediated loop extrusion

(2022) Bart J. H. Dequeker et al.   NATURE

DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations

(2022) Stefanos K Nomidis et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes

(2022) You Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A hold-and-feed mechanism drives directional DNA loop extrusion by condensin

(2022) Indra A. Shaltiel et al.   SCIENCE

Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

(2022) Michele Gabriele et al.   SCIENCE

Implications of Dosage Deficiencies in CTCF and Cohesin on Genome Organization, Gene Expression, and Human Neurodevelopment

(2022) Christopher T. Cummings et al.   Genes

Cohesin-mediated loop anchors confine the locations of human replication origins

(2022) Daniel J. Emerson et al.   NATURE

Condensin-driven loop extrusion on supercoiled DNA

(2022) Eugene Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding

(2022) Mattia Conte et al.   Nature Communications

Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks

(2022) Kristian Jeppsson et al.   Science Advances

CTCF–CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity

(2022) Yu Liu et al.   NATURE CELL BIOLOGY

SMC complexes can traverse physical roadblocks bigger than their ring size

(2022) Biswajit Pradhan et al.   Cell Reports

XerD unloads bacterial SMC complexes at the replication terminus

(2021) Xheni Karaboja et al.   MOLECULAR CELL

Loop extrusion as a mechanism for formation of DNA damage repair foci

(2021) Coline Arnould et al.   NATURE

Cohesin architecture and clustering in vivo

(2021) Siheng Xiang et al.   eLife

Bridging-induced phase separation induced by cohesin SMC protein complexes

(2021) Je-Kyung Ryu et al.   Science Advances

How DNA loop extrusion mediated by cohesin enables V(D)J recombination

(2021) Jan-Michael Peters   CURRENT OPINION IN CELL BIOLOGY

DNA-loop-extruding SMC complexes can traverse one another in vivo

(2021) Hugo B. Brandão et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Brownian ratchet model for DNA loop extrusion by the cohesin complex

(2021) Torahiko L Higashi et al.   eLife

A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis

(2021) Anna Anchimiuk et al.   eLife

Mechanisms for Chromosome Segregation in Bacteria

(2021) Christos Gogou et al.   Frontiers in Microbiology

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

(2021) Benedikt W. Bauer et al.   CELL

Cohesin regulates homology search during recombinational DNA repair

(2021) Aurèle Piazza et al.   NATURE CELL BIOLOGY

Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events

(2021) Je-Kyung Ryu et al.   NUCLEIC ACIDS RESEARCH

CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates

(2021) Ryanggeun Lee et al.   NUCLEIC ACIDS RESEARCH

Organization of the Escherichia coli Chromosome by a MukBEF Axial Core

(2020) Jarno Mäkelä et al.   MOLECULAR CELL

DNA-loop extruding condensin complexes can traverse one another

(2020) Eugene Kim et al.   NATURE

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li 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

Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA

(2020) Muwen Kong et al.   MOLECULAR CELL

Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA

(2020) Hai Pan et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM structure of the human cohesin-NIPBL-DNA complex

(2020) Zhubing Shi et al.   SCIENCE

Chromosome organization by one-sided and two-sided loop extrusion

(2020) Edward J Banigan et al.   eLife

Cohesin and condensin extrude DNA loops in a cell-cycle dependent manner

(2020) Stefan Golfier et al.   eLife

Loop extrusion: theory meets single-molecule experiments

(2020) Edward J. Banigan et al.   CURRENT OPINION IN CELL BIOLOGY

A Structure-Based Mechanism for DNA Entry into the Cohesin Ring

(2020) Torahiko L. Higashi et al.   MOLECULAR CELL

Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes

(2020) Jennifer M. Luppino et al.   NATURE GENETICS

Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism

(2020) Byung-Gil Lee et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cohesion is established during DNA replication utilising chromosome associated cohesin rings as well as those loaded de novo onto nascent DNAs

(2020) Madhusudhan Srinivasan et al.   eLife

The condensin holocomplex cycles dynamically between open and collapsed states

(2020) Je-Kyung Ryu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Purified Smc5/6 Complex Exhibits DNA Substrate Recognition and Compaction

(2020) Pilar Gutierrez-Escribano et al.   MOLECULAR CELL

Nucleosome Clutches are Regulated by Chromatin Internal Parameters

(2020) Stephanie Portillo-Ledesma et al.   JOURNAL OF MOLECULAR BIOLOGY

A Role for Chromatin Remodeling in Cohesin Loading onto Chromosomes

(2019) Sofía Muñoz et al.   MOLECULAR CELL

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

(2019) Jeffrey M Alexander et al.   eLife

Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis

(2019) Thomas M. Guérin et al.   MOLECULAR CELL

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

(2019) Yad Ghavi-Helm et al.   NATURE GENETICS

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

(2019) John F Marko et al.   NUCLEIC ACIDS RESEARCH

Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo

(2019) Jason Otterstrom et al.   NUCLEIC ACIDS RESEARCH

Determining cellular CTCF and cohesin abundances to constrain 3D genome models

(2019) Claudia Cattoglio et al.   eLife

Developmentally regulated Shh expression is robust to TAD perturbations

(2019) Iain Williamson et al.   DEVELOPMENT

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

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

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

A conserved ATP- and Scc2/4-dependent activity for cohesin in tethering DNA molecules

(2019) Pilar Gutierrez-Escribano et al.   Science Advances

Establishment of DNA-DNA Interactions by the Cohesin Ring

(2018) Yasuto Murayama et al.   CELL

The Cohesin Ring Uses Its Hinge to Organize DNA Using Non-topological as well as Topological Mechanisms

(2018) Madhusudhan Srinivasan et al.   CELL

A quantitative map of human Condensins provides new insights into mitotic chromosome architecture

(2018) Nike Walther et al.   JOURNAL OF CELL BIOLOGY

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

MCM2–7-dependent cohesin loading during S phase promotes sister-chromatid cohesion

(2018) Ge Zheng et al.   eLife

Evolutionary stability of topologically associating domains is associated with conserved gene regulation

(2018) Jan Krefting et al.   BMC BIOLOGY

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

In Vivo Evidence for ATPase-Dependent DNA Translocation by the Bacillus subtilis SMC Condensin Complex

(2018) Xindan Wang et al.   MOLECULAR CELL

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

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

Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization

(2017) Marie-Laure Diebold-Durand 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

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

(2017) Xindan Wang et al.   SCIENCE

The condensin complex is a mechanochemical motor that translocates along DNA

(2017) Tsuyoshi Terakawa et al.   SCIENCE

Specialized interfaces of Smc5/6 control hinge stability and DNA association

(2017) Aaron Alt et al.   Nature Communications

SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription

(2017) Ngat T. Tran et al.   Cell Reports

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

(2016) Emily M. Smith et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

Sororin actively maintains sister chromatid cohesion

(2016) Rene Ladurner et al.   EMBO JOURNAL

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

(2016) Iain F Davidson et al.   EMBO JOURNAL

Crystal structure of the cohesin loader Scc2 and insight into cohesinopathy

(2016) Sotaro Kikuchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation

(2016) Sophie Nolivos et al.   Nature Communications

Condensin Smc2-Smc4 Dimers Are Flexible and Dynamic

(2016) Jorine M. Eeftens et al.   Cell Reports

Single-Molecule Imaging Reveals a Collapsed Conformational State for DNA-Bound Cohesin

(2016) Johannes Stigler et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Compaction and segregation of sister chromatids via active loop extrusion

(2016) Anton Goloborodko et al.   eLife

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Dynamic enhancer–gene body contacts during transcription elongation

(2015) Kiwon Lee et al.   GENES & DEVELOPMENT

Condensin promotes the juxtaposition of DNA flanking its loading site inBacillus subtilis

(2015) Xindan Wang et al.   GENES & DEVELOPMENT

Interallelic complementation provides functional evidence for cohesin–cohesin interactions on DNA

(2015) Thomas Eng et al.   MOLECULAR BIOLOGY OF THE CELL

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

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

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan 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

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

(2014) Boryana Doyle et al.   PLoS Computational Biology

YY1 controls Igκ repertoire and B-cell development, and localizes with condensin on the Igκ locus

(2013) Xuan Pan et al.   EMBO JOURNAL

Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect

(2013) Gordon M. Bennett et al.   Genome Biology and Evolution

Biochemical reconstitution of topological DNA binding by the cohesin ring

(2013) Yasuto Murayama et al.   NATURE

Wapl is an essential regulator of chromatin structure and chromosome segregation

(2013) Antonio Tedeschi et al.   NATURE

Genome-Wide Control of RNA Polymerase II Activity by Cohesin

(2013) Cheri A. Schaaf et al.   PLoS Genetics

The Prereplication Complex Recruits XEco2 to Chromatin to Promote Cohesin Acetylation in Xenopus Egg Extracts

(2012) Torahiko L. Higashi et al.   CURRENT BIOLOGY

Cohesin Acetylation Promotes Sister Chromatid Cohesion Only in Association with the Replication Machinery

(2012) Jianhua Song et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

Sister Chromatid Cohesion

(2012) J.-M. Peters et al.   Cold Spring Harbor Perspectives in Biology

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

A new family of bacterial condensins

(2011) Zoya M. Petrushenko et al.   MOLECULAR MICROBIOLOGY

Cohesin: a catenase with separate entry and exit gates?

(2011) Kim Nasmyth   NATURE CELL BIOLOGY

The largest eukaryotic genome of them all?

(2010) JAUME PELLICER et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Sororin Mediates Sister Chromatid Cohesion by Antagonizing Wapl

(2010) Tomoko Nishiyama et al.   CELL

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Recruitment of Condensin to Replication Origin Regions by ParB/SpoOJ Promotes Chromosome Segregation in B. subtilis

(2009) Stephan Gruber et al.   CELL

Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus

(2009) Suzana Hadjur et al.   NATURE

Sister Chromatid Cohesion: A Simple Concept with a Complex Reality

(2008) Itay Onn et al.   Annual Review of Cell and Developmental Biology

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

Cdc7-Drf1 kinase links chromosome cohesion to the initiation of DNA replication in Xenopus egg extracts

(2008) T. S. Takahashi et al.   GENES & DEVELOPMENT

Acetylation of Smc3 by Eco1 Is Required for S Phase Sister Chromatid Cohesion in Both Human and Yeast

(2008) Jinglan Zhang et al.   MOLECULAR CELL

The cohesin ring concatenates sister DNA molecules

(2008) Christian H. Haering et al.   NATURE

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Molecular Determinant for the Establishment of Sister Chromatid Cohesion

(2008) E. U nal et al.   SCIENCE

Eco1-Dependent Cohesin Acetylation During Establishment of Sister Chromatid Cohesion

(2008) T. R. Ben-Shahar et al.   SCIENCE