Mechanisms Underlying Nucleosome Positioning In Vivo

A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription

(2013) Harm van Bakel et al.   PLoS Genetics

ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies

(2013) Gabriel E. Zentner et al.   PLoS Genetics

Genetic Landscape of Open Chromatin in Yeast

(2013) Kibaick Lee et al.   PLoS Genetics

Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers

(2012) Kuangyu Yen et al.   CELL

The unconventional structure of centromeric nucleosomes

(2012) Steven Henikoff et al.   CHROMOSOMA

Combinatorial complexity in chromatin structure and function: revisiting the histone code

(2012) Oliver J Rando   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromatin and Transcription in Yeast

(2012) Oliver J. Rando et al.   GENETICS

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Electrostatic Interactions between Arginines and the Minor Groove in the Nucleosome

(2012) Sean M. West et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Nucleosome Organization Affects the Sensitivity of Gene Expression to Promoter Mutations

(2012) Gil Hornung et al.   MOLECULAR CELL

A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern

(2012) Amanda L. Hughes et al.   MOLECULAR CELL

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

(2012) Ho Sung Rhee et al.   NATURE

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Promoter Nucleosome Organization Shapes the Evolution of Gene Expression

(2012) Dalia Rosin et al.   PLoS Genetics

In Vivo Effects of Histone H3 Depletion on Nucleosome Occupancy and Position in Saccharomyces cerevisiae

(2012) Andrea J. Gossett et al.   PLoS Genetics

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

Human genes with CpG island promoters have a distinct transcription-associated chromatin organization

(2012) Tanya Vavouri et al.   GENOME BIOLOGY

Working the kinks out of nucleosomal DNA

(2011) Wilma K Olson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization

(2011) Marta Radman-Livaja et al.   EMBO JOURNAL

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

(2011) A. Tsankov et al.   GENOME RESEARCH

Dynamics of Nucleosome Invasion by DNA Binding Proteins

(2011) Hannah S. Tims et al.   JOURNAL OF MOLECULAR BIOLOGY

Remodelers Organize Cellular Chromatin by Counteracting Intrinsic Histone-DNA Sequence Preferences in a Class-Specific Manner

(2011) Y. M. Moshkin et al.   MOLECULAR AND CELLULAR BIOLOGY

Histone Occupancy In Vivo at the 601 Nucleosome Binding Element Is Determined by Transcriptional History

(2011) R. Perales et al.   MOLECULAR AND CELLULAR BIOLOGY

Extranucleosomal DNA Binding Directs Nucleosome Sliding by Chd1

(2011) J. N. McKnight et al.   MOLECULAR AND CELLULAR BIOLOGY

Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters

(2011) Denis Tolkunov et al.   MOLECULAR BIOLOGY OF THE CELL

Multiple Sequence-Specific Factors Generate the Nucleosome-Depleted Region on CLN2 Promoter

(2011) Lu Bai et al.   MOLECULAR CELL

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Signal-dependent dynamics of transcription factor translocation controls gene expression

(2011) Nan Hao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization

(2011) T. Gkikopoulos et al.   SCIENCE

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Nucleosome-Depleted Regions in Cell-Cycle-Regulated Promoters Ensure Reliable Gene Expression in Every Cell Cycle

(2010) Lu Bai et al.   DEVELOPMENTAL CELL

p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy

(2010) E. Lidor Nili et al.   GENOME RESEARCH

Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing

(2010) Oliver Bell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

(2010) Jing Jin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

The Role of Nucleosome Positioning in the Evolution of Gene Regulation

(2010) Alexander M. Tsankov et al.   PLOS BIOLOGY

Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites

(2010) Wolfram Möbius et al.   PLoS Computational Biology

Capturing the dynamic epigenome

(2010) Roger B Deal et al.   GENOME BIOLOGY

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

G+C content dominates intrinsic nucleosome occupancy

(2009) Desiree Tillo et al.   BMC BIOINFORMATICS

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

A novel strategy of transcription regulation by intragenic nucleosome ordering

(2009) C. Vaillant et al.   GENOME RESEARCH

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

(2009) A. Weiner et al.   GENOME RESEARCH

A Novel Mechanism of Antagonism between ATP-Dependent Chromatin Remodeling Complexes Regulates RNR3 Expression

(2009) R. S. Tomar et al.   MOLECULAR AND CELLULAR BIOLOGY

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization

(2009) Yair Field et al.   NATURE GENETICS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

(2009) Yong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Analysis of individual remodeled nucleosomes reveals decreased histone–DNA contacts created by hSWI/SNF

(2009) Karim Bouazoune et al.   NUCLEIC ACIDS RESEARCH

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

(2009) C. Hodges et al.   SCIENCE

Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability

(2009) M. D. Vinces et al.   SCIENCE

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription

(2008) Hinrich Boeger et al.   CELL

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

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

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

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

(2008) Gwenael Badis et al.   MOLECULAR CELL

Chromatin decouples promoter threshold from dynamic range

(2008) Felix H. Lam et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion

(2008) Guo-Cheng Yuan et al.   PLoS Computational Biology

Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites

(2008) S. Sasaki et al.   SCIENCE

Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

(2008) Sushma Shivaswamy et al.   PLOS BIOLOGY

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology

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

(2008) Yutao Fu et al.   PLoS Genetics