4.5 Article

A cohesin traffic pattern genetically linked to gene regulation

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Inference of CRISPR Edits from Sanger Trace Data

David Conant et al.

Summary: ICE is a tool for analyzing CRISPR edits using Sanger data, providing a fast, accurate, and affordable way to assess the genotype after editing. It proposes potential editing outcomes and determines the data-supported results through regression analysis. ICE can analyze CRISPR experiments within days after transfection and produces accurate estimates of editing outcomes in various benchmarks and existing tools.

CRISPR JOURNAL (2022)

Article Multidisciplinary Sciences

Nonlinear control of transcription through enhancer-promoter interactions

Jessica Zuin et al.

Summary: This study reveals a nonlinear relationship between the contact probabilities of an enhancer with a promoter and its transcriptional effect. Mathematical modeling suggests that this nonlinearity arises from transient enhancer-promoter interactions being translated into slower promoter bursting dynamics. Additionally, the study shows that enhancer strength determines transcription levels and the sensitivity of a promoter to transcriptional insulation mediated by CTCF.

NATURE (2022)

Article Biochemistry & Molecular Biology

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

Niels J. Rinzema et al.

Summary: Developmental gene expression is controlled by enhancers, which form structural chromosomal domains with the help of CTCF boundaries and cohesin. Enhancers recruit cohesin to stimulate domain formation and engage with CTCF sites, thereby activating distal target genes.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Ctcfhaploinsufficiency mediates intron retention in a tissue-specific manner

Adel B. Alharbi et al.

Summary: CTCF acts as a master regulator of gene transcription and chromatin organisation, with haploinsufficiency linked to tumor development and hypermethylation. Reduced levels of CTCF in different tissues led to tissue-specific differences in gene expression and alternative splicing. In liver and kidney, CTCF haploinsufficiency resulted in increased intron retention, particularly affecting genes related to cytoskeletal organization, splicing, and metabolism.

RNA BIOLOGY (2021)

Article Genetics & Heredity

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

Ning Qing Liu et al.

Summary: WAPL generates a pool of free cohesin through cohesin turnover, which reloads it to cell-type-specific binding sites. The binding of cohesin to cell-type-specific sites is dependent on the pioneer transcription factors OCT4 and SOX2.

NATURE GENETICS (2021)

Article Biochemistry & Molecular Biology

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Naoki Kubo et al.

Summary: CTCF, together with the cohesin complex, drives chromatin loops and topologically associating domains formation. Acute loss of CTCF affects transcription of genes that display promoter-proximal CTCF binding and are dependent on long-distance enhancers. Promoter-proximal CTCF binding is correlated with transcription of over 2,000 genes across diverse adult tissues.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Article Cell Biology

Distinct properties and functions of CTCF revealed by a rapidly inducible degron system

Jing Luan et al.

Summary: CTCF, a conserved zinc finger transcription factor implicated in genome organization and transcription regulation, displays variable resistance to degradation at different binding sites. Motif sequence does not significantly predict degradation behavior, but location at chromatin boundaries and co-occupancy with cohesin are associated with delayed degradation. Single-molecule tracking experiments link chromatin residence time to CTCF degradation kinetics, providing insights into architectural CTCF functions.

CELL REPORTS (2021)

Article Biology

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

Jordan Yupeng Xiao et al.

Summary: Animal genomes are organized into topologically associated domains (TADs), which contribute to gene regulation by facilitating enhancer-promoter (E-P) contacts within a TAD and preventing these contacts across TAD borders. Existing models fail to explain the hypersensitive response when disruptions occur at TAD boundaries. A futile cycle model of enhancer-mediated regulation is proposed to explain this hypersensitivity through bistability and hysteresis, showing that E-P biochemical specificity may be an illusion and emphasizing the importance of weak TAD boundaries.

ELIFE (2021)

Review Genetics & Heredity

DEAD-Box RNA Helicases and Genome Stability

Michael Cargill et al.

Summary: DEAD-box RNA helicases are crucial regulators of RNA metabolism and are linked to genome stability and cancer development. They play important roles by regulating the expression of factors related to genome stability and repairing DNA damage.

GENES (2021)

Article Biochemistry & Molecular Biology

DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

Vishal Nanavaty et al.

MOLECULAR CELL (2020)

Article Biochemistry & Molecular Biology

Exploring the Interaction between the SWI/SNF Chromatin Remodeling Complex and the Zinc Finger Factor CTCF

Mariangela Valletta et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Review Multidisciplinary Sciences

Principles of genome folding into topologically associating domains

Quentin Szabo et al.

SCIENCE ADVANCES (2019)

Article Biochemistry & Molecular Biology

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

Anders S. Hansen et al.

MOLECULAR CELL (2019)

Article Multidisciplinary Sciences

RNA polymerases as moving barriers to condensin loop extrusion

Hugo B. Brandao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation

Antoine Campagne et al.

NATURE COMMUNICATIONS (2019)

Review Genetics & Heredity

Human gene essentiality

Istvan Bartha et al.

NATURE REVIEWS GENETICS (2018)

Article Multidisciplinary Sciences

Chromatin organization by an interplay of loop extrusion and compartmental segregation

Johannes Nuebler et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

Two independent modes of chromatin organization revealed by cohesin removal

Wibke Schwarzer et al.

NATURE (2017)

Article Multidisciplinary Sciences

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

Georg A. Busslinger et al.

NATURE (2017)

Article Genetics & Heredity

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

Traver Hart et al.

G3-GENES GENOMES GENETICS (2017)

Article Biochemistry & Molecular Biology

CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals

Mariana Ruiz-Velasco et al.

CELL SYSTEMS (2017)

Article Biochemistry & Molecular Biology

A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture

Johanna Gassler et al.

EMBO JOURNAL (2017)

Article Biochemistry & Molecular Biology

Multiscale 3D Genome Rewiring during Mouse Neural Development

Boyan Bonev et al.

Article Biochemistry & Molecular Biology

Cohesin Loss Eliminates All Loop Domains

Suhas S. P. Rao et al.

Article Biochemistry & Molecular Biology

The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension

Judith H. I. Haarhuis et al.

Article Multidisciplinary Sciences

Insulator dysfunction and oncogene activation in IDH mutant gliomas

William A. Flavahan et al.

NATURE (2016)

Article Biochemical Research Methods

BAGEL: a computational framework for identifying essential genes from pooled library screens

Traver Hart et al.

BMC BIOINFORMATICS (2016)

Article Cell Biology

TAD disruption as oncogenic driver

Anne-Laure Valton et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2016)

Article Biochemistry & Molecular Biology

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

Lionel A. Sanz et al.

MOLECULAR CELL (2016)

Article Multidisciplinary Sciences

Formation of new chromatin domains determines pathogenicity of genomic duplications

Martin Franke et al.

NATURE (2016)

Article Multidisciplinary Sciences

Activation of proto-oncogenes by disruption of chromosome neighborhoods

Denes Hnisz et al.

SCIENCE (2016)

Review Genetics & Heredity

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

Dario G. Lupianez et al.

TRENDS IN GENETICS (2016)

Article Cell Biology

Formation of Chromosomal Domains by Loop Extrusion

Geoffrey Fudenberg et al.

CELL REPORTS (2016)

Article Biotechnology & Applied Microbiology

Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders

Liis Uuskula-Reimand et al.

GENOME BIOLOGY (2016)

Article Biochemistry & Molecular Biology

CTCF Binding Polarity Determines Chromatin Looping

Elzo de Wit et al.

MOLECULAR CELL (2015)

Article Multidisciplinary Sciences

Condensin-driven remodelling of X chromosome topology during dosage compensation

Emily Crane et al.

NATURE (2015)

Article Multidisciplinary Sciences

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Adrian L. Sanborn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemistry & Molecular Biology

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

Suhas S. P. Rao et al.

Article Biochemistry & Molecular Biology

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

Traver Hart et al.

MOLECULAR SYSTEMS BIOLOGY (2014)

Article Biochemistry & Molecular Biology

dREAM co-operates with insulator-binding proteins and regulates expression at divergently paired genes

Michael Korenjak et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

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

Jennifer E. Phillips-Cremins et al.

Article Biochemical Research Methods

Genome engineering using the CRISPR-Cas9 system

F. Ann Ran et al.

NATURE PROTOCOLS (2013)

Article Biochemistry & Molecular Biology

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

Tom Sexton et al.

Article Multidisciplinary Sciences

The long-range interaction landscape of gene promoters

Amartya Sanyal et al.

NATURE (2012)

Article Multidisciplinary Sciences

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Jesse R. Dixon et al.

NATURE (2012)

Article Multidisciplinary Sciences

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

Elphege P. Nora et al.

NATURE (2012)

Article Biochemistry & Molecular Biology

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

Elnaz Alipour et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3

Zhe Liu et al.

Article Multidisciplinary Sciences

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

Sanjeev Shukla et al.

NATURE (2011)

Article Multidisciplinary Sciences

Mediator and cohesin connect gene expression and chromatin architecture

Michael H. Kagey et al.

NATURE (2010)

Review Biochemistry & Molecular Biology

The SAGA continues: expanding the cellular role of a transcriptional co-activator complex

S. P. Baker et al.

ONCOGENE (2007)

Article Genetics & Heredity

RNA interference machinery influences the nuclear organization of a chromatin insulator

Elissa P. Lei et al.

NATURE GENETICS (2006)

Article Biochemistry & Molecular Biology

Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae

EF Glynn et al.

PLOS BIOLOGY (2004)