Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

Nucleosome Positioning in Saccharomyces cerevisiae

(2011) A. Jansen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

Nucleosomes and the accessibility problem

(2011) Xin Wang et al.   TRENDS IN GENETICS

A RSC/Nucleosome Complex Determines Chromatin Architecture and Facilitates Activator Binding

(2010) Monique Floer et al.   CELL

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast

(2010) Mythily Ganapathi et al.   NUCLEIC ACIDS RESEARCH

The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data

(2010) Ho-Ryun Chung et al.   PLoS One

High-throughput sequencing reveals a simple model of nucleosome energetics

(2010) G. Locke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation

(2010) X. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

(2010) Noam Kaplan et al.   GENOME BIOLOGY

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome

(2009) B. J. Venters et al.   GENOME RESEARCH

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

Incorporating nucleosomes into thermodynamic models of transcription regulation

(2009) T. Raveh-Sadka et al.   GENOME RESEARCH

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome

(2009) R. Thomas Koerber et al.   MOLECULAR CELL

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Quantification of the yeast transcriptome by single-molecule sequencing

(2009) Doron Lipson et al.   NATURE BIOTECHNOLOGY

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

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

Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?

(2009) Arnold Stein et al.   NUCLEIC ACIDS RESEARCH

Thermodynamics of Intragenic Nucleosome Ordering

(2009) G. Chevereau et al.   PHYSICAL REVIEW LETTERS

What controls nucleosome positions?

(2009) Eran Segal et al.   TRENDS IN GENETICS

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

(2009) Piotr J Balwierz et al.   GENOME BIOLOGY

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

(2009) Cizhong Jiang et al.   GENOME BIOLOGY

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

GeneTrack--a genomic data processing and visualization framework

(2008) I. Albert et al.   BIOINFORMATICS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev 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

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Nucleosome Switches

(2008) David J. Schwab et al.   PHYSICAL REVIEW LETTERS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi 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