Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells

CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

(2019) Marlies E. Oomen et al.   GENOME RESEARCH

H2A.Z facilitates licensing and activation of early replication origins

(2019) Haizhen Long et al.   NATURE

Functions of FACT in Breaking the Nucleosome and Maintaining Its Integrity at the Single-Nucleosome Level

(2018) Ping Chen et al.   MOLECULAR CELL

Histone variants H2A.Z and H3.3 coordinately regulate PRC2-dependent H3K27me3 deposition and gene expression regulation in mES cells

(2018) Yan Wang et al.   BMC BIOLOGY

UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells

(2018) Chaoyang Xiong et al.   BMC BIOLOGY

Structural basis of the nucleosome transition during RNA polymerase II passage

(2018) Tomoya Kujirai et al.   SCIENCE

Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates

(2017) Srinivas Ramachandran et al.   MOLECULAR CELL

Variants of core histones and their roles in cell fate decisions, development and cancer

(2017) Marcus Buschbeck et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

(2017) Daiki Kato et al.   SCIENCE

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

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

(2016) Lilien N. Voong et al.   CELL

Transcriptional Regulators Compete with Nucleosomes Post-replication

(2016) Srinivas Ramachandran et al.   CELL

Histone variants on the move: substrates for chromatin dynamics

(2016) Paul B. Talbert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility

(2015) Thuy T.M. Ngo et al.   CELL

Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

(2015) Sarah J. Hainer et al.   GENES & DEVELOPMENT

A simple method for generating high-resolution maps of genome-wide protein binding

(2015) Peter J Skene et al.   eLife

Replicating nucleosomes

(2015) S. Ramachandran et al.   Science Advances

Subnucleosomal Structures and Nucleosome Asymmetry across a Genome

(2014) Ho Sung Rhee et al.   CELL

High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and Sperm

(2014) Benjamin R. Carone et al.   DEVELOPMENTAL CELL

Nucleosome Positioning, Nucleosome Spacing and the Nucleosome Code

(2014) David J. Clark   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

(2014) Christopher M. Weber et al.   MOLECULAR CELL

Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data

(2014) Weizhong Chen et al.   Nature Communications

The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1

(2014) Peter J Skene et al.   eLife

H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin

(2013) P. Chen et al.   GENES & DEVELOPMENT

Histone Variants in Development and Diseases

(2013) Ping Chen et al.   Journal of Genetics and Genomics

Chromatin and DNA Replication

(2013) D. M. MacAlpine et al.   Cold Spring Harbor Perspectives in Biology

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

(2012) Karolin Luger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide nucleosome positioning during embryonic stem cell development

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

Histone H2A variants in nucleosomes and chromatin: more or less stable?

(2012) C. Bonisch et al.   NUCLEIC ACIDS RESEARCH

CTCF, cohesin, and histone variants: connecting the genome

(2011) Jean-François Millau et al.   Biochemistry and Cell Biology

Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

(2011) Y. Xi et al.   GENOME RESEARCH

The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes

(2011) Lacramioara Bintu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Reconciling the positive and negative roles of histone H2A.Z in gene transcription

(2010) Maud Marques et al.   Epigenetics

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

H2A.Z nucleosomes enriched over active genes are homotypic

(2010) Christopher M Weber et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing

(2010) N. A. Kent et al.   NUCLEIC ACIDS RESEARCH

Transcriptional and epigenetic functions of histone variant H2A.ZThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

(2009) Ryan Draker et al.   Biochemistry and Cell Biology

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

(2009) M. Y. Tolstorukov et al.   GENOME RESEARCH

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

(2009) A. Weiner et al.   GENOME RESEARCH

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

Nucleosomes can invade DNA territories occupied by their neighbors

(2009) Maik Engeholm et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The LPS-Induced Transcriptional Upregulation of the Chicken Lysozyme Locus Involves CTCF Eviction and Noncoding RNA Transcription

(2008) Pascal Lefevre et al.   MOLECULAR CELL

On the nature of human housekeeping genes

(2008) Jiang Zhu et al.   TRENDS IN GENETICS

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

(2008) Yutao Fu et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY