On the role of transcription in positioning nucleosomes

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

(2020) Zohar Shipony et al.   NATURE METHODS

Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination

(2019) Josefina Ocampo et al.   GENOME RESEARCH

Critical role of histone tail entropy in nucleosome unwinding

(2019) Thomas Parsons et al.   JOURNAL OF CHEMICAL PHYSICS

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Biophysical regulation of local chromatin structure

(2019) Nick Gilbert   CURRENT OPINION IN GENETICS & DEVELOPMENT

Single-molecule long-read sequencing reveals the chromatin basis of gene expression

(2019) Yunhao Wang et al.   GENOME RESEARCH

Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome

(2019) Elisa Oberbeckmann et al.   GENOME RESEARCH

Theory of Active Chromatin Remodeling

(2019) Zhongling Jiang et al.   PHYSICAL REVIEW LETTERS

Major Determinants of Nucleosome Positioning

(2018) Răzvan V. Chereji et al.   BIOPHYSICAL JOURNAL

Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing

(2018) Binbin Lai et al.   NATURE

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

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

The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer

(2017) Yupeng Qiu et al.   MOLECULAR CELL

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping

(2017) Lilien N. Voong et al.   TRENDS IN GENETICS

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

(2016) Lilien N. Voong et al.   CELL

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

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

(2016) Josefina Ocampo et al.   NUCLEIC ACIDS RESEARCH

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

(2016) René Dreos et al.   NUCLEIC ACIDS RESEARCH

Genomic Organization of Human Transcription Initiation Complexes

(2016) B. Franklin Pugh et al.   PLoS One

Histone exchange, chromatin structure and the regulation of transcription

(2015) Swaminathan Venkatesh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functional roles of nucleosome stability and dynamics

(2014) R. V. Chereji et al.   Briefings in Functional Genomics

Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons

(2014) Glòria Mas Martín et al.   Epigenetics

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

(2014) René Dreos et al.   NUCLEIC ACIDS RESEARCH

DNA Shape Dominates Sequence Affinity in Nucleosome Formation

(2014) Gordon S. Freeman et al.   PHYSICAL REVIEW LETTERS

Transcribing through the nucleosome

(2014) Sheila S. Teves et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now

(2014) Stacia R. Engel et al.   G3-Genes Genomes Genetics

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

(2013) Geeta J. Narlikar et al.   CELL

ISWI Remodelers Slide Nucleosomes with Coordinated Multi-Base-Pair Entry Steps and Single-Base-Pair Exit Steps

(2013) Sebastian Deindl et al.   CELL

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence

(2013) Jyotsana J. Parmar et al.   NUCLEIC ACIDS RESEARCH

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

Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers

(2012) Kuangyu Yen et al.   CELL

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

Chromatin organization — The 30nm fiber

(2012) Sergei A. Grigoryev et al.   EXPERIMENTAL CELL RESEARCH

A map of nucleosome positions in yeast at base-pair resolution

(2012) Kristin Brogaard et al.   NATURE

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee 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

Kinetic Control of Nucleosome Displacement by ISWI/ACF Chromatin Remodelers

(2012) Ana-Maria Florescu et al.   PHYSICAL REVIEW LETTERS

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

(2012) T. van der Heijden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro

(2012) B. G. Kuryan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome spacing and chromatin higher-order folding

(2012) Sergei A. Grigoryev   Nucleus

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Nucleosome positioning in a model of active chromatin remodeling enzymes

(2011) R. Padinhateeri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome

(2011) Tanya Vavouri et al.   PLoS Genetics

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

(2010) Desiree Tillo et al.   PLoS One

A Complete Set of Nascent Transcription Rates for Yeast Genes

(2010) Vicent Pelechano et al.   PLoS One

RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones

(2010) O. I. Kulaeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene regulation by nucleosome positioning

(2010) Lu Bai et al.   TRENDS IN GENETICS

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

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

Dynamics of nucleosome remodelling by individual ACF complexes

(2009) Timothy R. Blosser et al.   NATURE

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

What controls nucleosome positions?

(2009) Eran Segal et al.   TRENDS IN GENETICS

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE