Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver

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

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

(2017) Tim J. Stevens et al.   NATURE

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells

(2017) M. Willi et al.   Nature Communications

CTCF-mediated chromatin loops enclose inducible gene regulatory domains

(2016) Martin Oti et al.   BMC GENOMICS

A benchmark of gene expression tissue-specificity metrics

(2016) Nadezda Kryuchkova-Mostacci et al.   BRIEFINGS IN BIOINFORMATICS

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

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

(2016) Iain F Davidson et al.   EMBO JOURNAL

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer

(2016) Akihiro Fujimoto et al.   NATURE GENETICS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

(2016) Ramya Raviram et al.   PLoS Computational Biology

Identification of hierarchical chromatin domains

(2015) Caleb Weinreb et al.   BIOINFORMATICS

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

(2015) Zhonghui Tang et al.   CELL

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

Hepatic lincRNAs: high promoter conservation and dynamic, sex-dependent transcriptional regulation by growth hormone

(2015) Tisha Melia et al.   MOLECULAR AND CELLULAR BIOLOGY

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

(2015) Carlos Gómez-Marín et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

(2015) Paul Martin et al.   Nature Communications

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

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

(2015) Matteo Vietri Rudan et al.   Cell Reports

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang 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

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53

(2014) R. Saldana-Meyer et al.   GENES & DEVELOPMENT

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

(2013) Elphège P. Nora et al.   BIOESSAYS

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

(2013) Warren A. Whyte et al.   CELL

Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes

(2013) Jacqueline K. White et al.   CELL

Jpx RNA Activates Xist by Evicting CTCF

(2013) Sha Sun et al.   CELL

Cohesin-mediated interactions organize chromosomal domain architecture

(2013) Sevil Sofueva et al.   EMBO JOURNAL

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

(2013) V. C. Seitan et al.   GENOME RESEARCH

Genome-Wide Analysis of Chromatin States Reveals Distinct Mechanisms of Sex-Dependent Gene Regulation in Male and Female Mouse Liver

(2013) A. Sugathan et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2013) Takashi Nagano et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

(2013) Supat Thongjuea et al.   NUCLEIC ACIDS RESEARCH

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi et al.   Cell Reports

Cohesin-SA1 deficiency drives aneuploidy and tumourigenesis in mice due to impaired replication of telomeres

(2012) Silvia Remeseiro et al.   EMBO JOURNAL

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen 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

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

Loss of Maternal CTCF Is Associated with Peri-Implantation Lethality of Ctcf Null Embryos

(2012) James M. Moore et al.   PLoS One

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

A co-ordinated interaction between CTCF and ER in breast cancer cells

(2011) Caryn S Ross-Innes et al.   BMC GENOMICS

Specific Sites in the C Terminus of CTCF Interact with the SA2 Subunit of the Cohesin Complex and Are Required for Cohesin-Dependent Insulation Activity

(2011) T. Xiao et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2011) Sanjeev Shukla et al.   NATURE

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression

(2010) G. Ling et al.   MOLECULAR AND CELLULAR BIOLOGY

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Rad21-Cohesin Haploinsufficiency Impedes DNA Repair and Enhances Gastrointestinal Radiosensitivity in Mice

(2010) Huiling Xu et al.   PLoS One

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

CTCF regulates cell cycle progression of αβ T cells in the thymus

(2008) Helen Heath et al.   EMBO JOURNAL

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS