CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays

(2019) Mikhail V. Bass et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups

(2019) Katherine A. Giles et al.   Epigenetics & Chromatin

Nucleosome positioning and spacing: from genome-wide maps to single arrays

(2019) Sandro Baldi   Essays in Biochemistry

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries

(2019) Laura Wiehle et al.   GENOME RESEARCH

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

Dynamic chromatin organization without the 30-nm fiber

(2019) Kazuhiro Maeshima et al.   CURRENT OPINION IN CELL BIOLOGY

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

(2019) Christopher Barrington et al.   Nature Communications

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Opposing chromatin remodelers control transcription initiation frequency and start site selection

(2019) Slawomir Kubik et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CTCF confers local nucleosome resiliency after DNA replication and during mitosis

(2019) Nick Owens et al.   eLife

Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells

(2018) Ioanna Pavlaki et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression

(2018) Susanne Bornelöv et al.   MOLECULAR CELL

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus

(2018) A. Rasim Barutcu et al.   Nature Communications

Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing

(2018) Sandro Baldi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods

(2018) Fei Sun et al.   MOLECULAR CELL

Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion

(2017) Gavin D Bascom et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Potential energy landscapes identify the information-theoretic nature of the epigenome

(2017) Garrett Jenkinson et al.   NATURE GENETICS

Understanding nucleosome dynamics and their links to gene expression and DNA replication

(2017) William K. M. Lai et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Discovering a binary CTCF code with a little help from BORIS

(2017) Victor V. Lobanenkov et al.   Nucleus

The connection between BRG1, CTCF and topoisomerases at TAD boundaries

(2017) A. Rasim Barutcu et al.   Nucleus

Discovering a binary CTCF code with a little help from BORIS

(2017) Victor V. Lobanenkov et al.   Nucleus

The connection between BRG1, CTCF and topoisomerases at TAD boundaries

(2017) A. Rasim Barutcu et al.   Nucleus

DNA topology in chromatin is defined by nucleosome spacing

(2017) Tatiana Nikitina et al.   Science Advances

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

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

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

(2016) Ge Tan et al.   BIOINFORMATICS

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

(2016) Lilien N. Voong et al.   CELL

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

(2016) Matthew W. Snyder et al.   CELL

CTCF: making the right connections

(2016) Rodolfo Ghirlando et al.   GENES & DEVELOPMENT

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

(2016) Maud de Dieuleveult et al.   NATURE

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

(2016) Viviana I. Risca et al.   NATURE

The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacingin vivo

(2016) Josefina Ocampo et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

(2016) Nicola Wiechens et al.   PLoS Genetics

Functional diversity of CTCFs is encoded in their binding motifs

(2015) Rongxin Fang et al.   BMC GENOMICS

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

(2014) Vladimir B. Teif et al.   GENOME RESEARCH

Protein−DNA binding in the absence of specific base-pair recognition

(2014) Ariel Afek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions

(2014) Daria A. Beshnova et al.   PLoS Computational Biology

Toward a unified physical model of nucleosome patterns flanking transcription start sites

(2013) W. Mobius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription

(2012) Bianca P Hennig et al.   EMBO REPORTS

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

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

(2012) Yin Shen et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genome-wide nucleosome positioning during embryonic stem cell development

(2012) Vladimir B Teif et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

(2012) Hebing Chen et al.   PLoS One

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(2011) David Martin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells

(2011) Lucie Carrière et al.   NUCLEIC ACIDS RESEARCH

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

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

Poly(dA:dT) tracts: major determinants of nucleosome organization

(2009) Eran Segal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TFIIIC Binding Sites Function as both Heterochromatin Barriers and Chromatin Insulators inSaccharomyces cerevisiae

(2008) Tiffany A. Simms et al.   EUKARYOTIC CELL

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

(2008) Andrew Routh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics