Related references
Note: Only part of the references are listed.Mechanisms Underlying Nucleosome Positioning In Vivo
Amanda L. Hughes et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 43 (2014)
Chromatin as dynamic 10-nm fibers
Kazuhiro Maeshima et al.
CHROMOSOMA (2014)
Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging
Zheng Hu et al.
GENES & DEVELOPMENT (2014)
Two independent transcription initiation codes overlap on vertebrate core promoters
Vanja Haberle et al.
NATURE (2014)
A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress
Nils Elfving et al.
NUCLEIC ACIDS RESEARCH (2014)
The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin
Philipp Korber et al.
NUCLEIC ACIDS RESEARCH (2014)
Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity
Eliza C. Small et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Ubiquitous nucleosome crowding in the yeast genome
Razvan V. Chereji et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
NucleoFinder: a statistical approach for the detection of nucleosome positions
Jeremie Becker et al.
BIOINFORMATICS (2013)
Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe
Ignacio Soriano et al.
BMC GENOMICS (2013)
Nucleosome-free Region Dominates Histone Acetylation in Targeting SWR1 to Promoters for H2A.Z Replacement
Anand Ranjan et al.
CELL (2013)
SWR-C and INO80 Chromatin Remodelers Recognize Nucleosome-free Regions Near+1 Nucleosomes
Kuangyu Yen et al.
CELL (2013)
Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae
Hiromi Nishida et al.
GENE (2013)
DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
Kaifu Chen et al.
GENOME RESEARCH (2013)
Specification of DNA Replication Origins and Genomic Base Composition in Fission Yeasts
Laura Mojardin et al.
JOURNAL OF MOLECULAR BIOLOGY (2013)
Combined Micrococcal Nuclease and Exonuclease III Digestion Reveals Precise Positions of the Nucleosome Core/Linker Junctions: Implications for High-Resolution Nucleosome Mapping
Tatiana Nikitina et al.
JOURNAL OF MOLECULAR BIOLOGY (2013)
Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast
Christine M. DeGennaro et al.
MOLECULAR AND CELLULAR BIOLOGY (2013)
DNA Looping Facilitates Targeting of a Chromatin Remodeling Enzyme
Adam N. Yadon et al.
MOLECULAR CELL (2013)
Determinants of nucleosome positioning
Kevin Struhl et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)
Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning
Georgette Moyle-Heyrman et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Toward a unified physical model of nucleosome patterns flanking transcription start sites
Wolfram Moebius et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme
Shinya Watanabe et al.
SCIENCE (2013)
Nucleosome Remodeling and Epigenetics
Peter B. Becker et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2013)
Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression
Christopher R. Brown et al.
PLOS BIOLOGY (2013)
Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers
Evgeniy A. Ozonov et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription
Harm van Bakel et al.
PLOS GENETICS (2013)
ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies
Gabriel E. Zentner et al.
PLOS GENETICS (2013)
Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution
Philipp Korber
BIOCHEMICAL SOCIETY TRANSACTIONS (2012)
Perfect and imperfect nucleosome positioning in yeast
Hope A. Cole et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2012)
Standardized collection of MNase-seq experiments enables unbiased dataset comparisons
Jason M. Rizzo et al.
BMC MOLECULAR BIOLOGY (2012)
Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers
Kuangyu Yen et al.
CELL (2012)
Nucleosomal organization of replication origins and meiotic recombination hotspots in fission yeast
Elisa de Castro et al.
EMBO JOURNAL (2012)
CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe
Julia Pointner et al.
EMBO JOURNAL (2012)
Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin
Young Sam Shim et al.
EMBO JOURNAL (2012)
Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription
Bianca P. Hennig et al.
EMBO REPORTS (2012)
Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1
Jung-Shin Lee et al.
GENES & DEVELOPMENT (2012)
Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping
James Allan et al.
JOURNAL OF MOLECULAR BIOLOGY (2012)
Linker Histone Subtypes Differ in Their Effect on Nucleosomal Spacing In Vivo
Christine Oberg et al.
JOURNAL OF MOLECULAR BIOLOGY (2012)
The Linker Histone Plays a Dual Role during Gametogenesis in Saccharomyces cerevisiae
Jessica M. Bryant et al.
MOLECULAR AND CELLULAR BIOLOGY (2012)
Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators
Dana J. Huebert et al.
MOLECULAR AND CELLULAR BIOLOGY (2012)
A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern
Amanda L. Hughes et al.
MOLECULAR CELL (2012)
Genome-wide structure and organization of eukaryotic pre-initiation complexes
Ho Sung Rhee et al.
NATURE (2012)
Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
Tali Raveh-Sadka et al.
NATURE GENETICS (2012)
Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange
Michaela Smolle et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)
Chromatin architectures at fission yeast transcriptional promoters and replication origins
Robert M. Givens et al.
NUCLEIC ACIDS RESEARCH (2012)
Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing
Feng Cui et al.
NUCLEIC ACIDS RESEARCH (2012)
Conservation of Nucleosome Positions in Duplicated and Orthologous Gene Pairs
Hiromi Nishida
SCIENTIFIC WORLD JOURNAL (2012)
Nucleosome positioning: bringing order to the eukaryotic genome
Vishwanath R. Iyer
TRENDS IN CELL BIOLOGY (2012)
Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping
Hiromi Nishida et al.
OPEN BIOLOGY (2012)
In Vivo Effects of Histone H3 Depletion on Nucleosome Occupancy and Position in Saccharomyces cerevisiae
Andrea J. Gossett et al.
PLOS GENETICS (2012)
Genome-wide identification and characterization of replication origins by deep sequencing
Jia Xu et al.
GENOME BIOLOGY (2012)
nucleR: a package for non-parametric nucleosome positioning
Oscar Flores et al.
BIOINFORMATICS (2011)
High-Resolution Genome-wide Mapping of the Primary Structure of Chromatin
Zhenhai Zhang et al.
CELL (2011)
Global Regulation of H2A.Z Localization by the INO80 Chromatin-Remodeling Enzyme Is Essential for Genome Integrity
Manolis Papamichos-Chronakis et al.
CELL (2011)
Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
Ho Sung Rhee et al.
CELL (2011)
The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes
Christian J. Wippo et al.
EMBO JOURNAL (2011)
The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4
Triantaffyllos Gkikopoulos et al.
EMBO JOURNAL (2011)
Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
Alex Tsankov et al.
GENOME RESEARCH (2011)
Stable and dynamic nucleosome states during a meiotic developmental process
Liye Zhang et al.
GENOME RESEARCH (2011)
Evolution of Nucleosome Occupancy: Conservation of Global Properties and Divergence of Gene-Specific Patterns
Kyle Tsui et al.
MOLECULAR AND CELLULAR BIOLOGY (2011)
Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters
Denis Tolkunov et al.
MOLECULAR BIOLOGY OF THE CELL (2011)
Multiple Sequence-Specific Factors Generate the Nucleosome-Depleted Region on CLN2 Promoter
Lu Bai et al.
MOLECULAR CELL (2011)
Determinants of nucleosome organization in primary human cells
Anton Valouev et al.
NATURE (2011)
Structure and mechanism of the chromatin remodelling factor ISW1a
Kazuhiro Yamada et al.
NATURE (2011)
Determinants and dynamics of genome accessibility
Oliver Bell et al.
NATURE REVIEWS GENETICS (2011)
Nucleosome Positioning in Saccharomyces cerevisiae
An Jansen et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2011)
Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast
Mythily Ganapathi et al.
NUCLEIC ACIDS RESEARCH (2011)
Chromatin particle spectrum analysis: a method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing
Nicholas A. Kent et al.
NUCLEIC ACIDS RESEARCH (2011)
Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes
Hope A. Cole et al.
NUCLEIC ACIDS RESEARCH (2011)
Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes
Jason M. Rizzo et al.
NUCLEIC ACIDS RESEARCH (2011)
The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere
Hope A. Cole et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Epigenome characterization at single base-pair resolution
Jorja G. Henikoff et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization
Triantaffyllos Gkikopoulos et al.
SCIENCE (2011)
A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome
Zhenhai Zhang et al.
SCIENCE (2011)
Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast
Marta Radman-Livaja et al.
PLOS BIOLOGY (2011)
Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output
Barbara Celona et al.
PLOS BIOLOGY (2011)
A RSC/Nucleosome Complex Determines Chromatin Architecture and Facilitates Activator Binding
Monique Floer et al.
CELL (2010)
Nucleosome positioning: How is it established, and why does it matter?
Marta Radman-Livaja et al.
DEVELOPMENTAL BIOLOGY (2010)
Conserved nucleosome positioning defines replication origins
Matthew L. Eaton et al.
GENES & DEVELOPMENT (2010)
High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
Assaf Weiner et al.
GENOME RESEARCH (2010)
Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes
Carolina Kristell et al.
GENOME RESEARCH (2010)
Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae
Alexandra B. Lantermann et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2010)
Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?
Arnold Stein et al.
NUCLEIC ACIDS RESEARCH (2010)
The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data
Ho-Ryun Chung et al.
PLOS ONE (2010)
High-throughput sequencing reveals a simple model of nucleosome energetics
George Locke et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
The Role of Nucleosome Positioning in the Evolution of Gene Regulation
Alexander M. Tsankov et al.
PLOS BIOLOGY (2010)
Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites
Wolfram Moebius et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Diversity of Eukaryotic DNA Replication Origins Revealed by Genome-Wide Analysis of Chromatin Structure
Nicolas M. Berbenetz et al.
PLOS GENETICS (2010)
Widespread remodeling of mid-coding sequence nucleosomes by Isw1
Itay Tirosh et al.
GENOME BIOLOGY (2010)
Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology
Noam Kaplan et al.
GENOME BIOLOGY (2010)
The Biology of Chromatin Remodeling Complexes
Cedric R. Clapier et al.
ANNUAL REVIEW OF BIOCHEMISTRY (2009)
Mechanisms that Specify Promoter Nucleosome Location and Identity
Paul D. Hartley et al.
CELL (2009)
Poly(dA:dT) tracts: major determinants of nucleosome organization
Eran Segal et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)
Chromatin Remodelers Act Globally, Sequence Positions Nucleosomes Locally
Peretz D. Partensky et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae
Karl A. Zawadzki et al.
MOLECULAR BIOLOGY OF THE CELL (2009)
Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome
R. Thomas Koerber et al.
MOLECULAR CELL (2009)
The DNA-encoded nucleosome organization of a eukaryotic genome
Noam Kaplan et al.
NATURE (2009)
The logic of chromatin architecture and remodelling at promoters
Bradley R. Cairns
NATURE (2009)
Nucleosome positioning and gene regulation: advances through genomics
Cizhong Jiang et al.
NATURE REVIEWS GENETICS (2009)
Nucleosomes can invade DNA territories occupied by their neighbors
Maik Engeholm et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)
Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome
Folkert J. van Werven et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)
Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
Yong Zhang et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
Paul G. Giresi et al.
METHODS (2009)
Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe
Alexandra Lantermann et al.
METHODS (2009)
A translational signature for nucleosome positioning in vivo
Micaela Caserta et al.
NUCLEIC ACIDS RESEARCH (2009)
Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence
Joke J. F. A. van Vugt et al.
PLOS ONE (2009)
A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions
Pei Fen Kuan et al.
STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2009)
What controls nucleosome positions?
Eran Segal et al.
TRENDS IN GENETICS (2009)
The Schizosaccharomyces pombe JmjC-Protein, Msc1, Prevents H2A.Z Localization in Centromeric and Subtelomeric Chromatin Domains
Luke Buchanan et al.
PLOS GENETICS (2009)
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
Cizhong Jiang et al.
GENOME BIOLOGY (2009)
Dynamic regulation of nucleosome positioning in the human genome
Dustin E. Schones et al.
CELL (2008)
Two strategies for gene regulation by promoter nucleosomes
Itay Tirosh et al.
GENOME RESEARCH (2008)
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
Travis N. Mavrich et al.
GENOME RESEARCH (2008)
A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters
Gwenael Badis et al.
MOLECULAR CELL (2008)
Chromatin decouples promoter threshold from dynamic range
Felix H. Lam et al.
NATURE (2008)
Nucleosome organization in the Drosophila genome
Travis N. Mavrich et al.
NATURE (2008)
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
Sushma Shivaswamy et al.
PLOS BIOLOGY (2008)
Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
Yair Field et al.
PLOS COMPUTATIONAL BIOLOGY (2008)
RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes
Timothy J. Parnell et al.
EMBO JOURNAL (2008)
Chromatin remodelling at promoters suppresses antisense transcription
Iestyn Whitehouse et al.
NATURE (2007)
Transcription factor access to promoter elements
Randall H. Morse
JOURNAL OF CELLULAR BIOCHEMISTRY (2007)
DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes
Karsten Rippe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
A high- resolution atlas of nucleosome occupancy in yeast
William Lee et al.
NATURE GENETICS (2007)
Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3K56 acetylation and Asf1
Anne Rufiange et al.
MOLECULAR CELL (2007)
Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3
Hesheng Zhang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
Istvan Albert et al.
NATURE (2007)
Dynamics of replication-independent histone turnover in budding yeast
Michael F. Dion et al.
SCIENCE (2007)
Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication
Adil Jamai et al.
MOLECULAR CELL (2007)
Physicochemical analysis of electrostatic foundation for DNA-protein interactions in chromatin transformations
Nikolay Korolev et al.
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY (2007)
The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length sensor that regulates nucleosome spacing
Janet G. Yang et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2006)
A genomic code for nucleosome positioning
Eran Segal et al.
NATURE (2006)
Nucleosome stability at the yeast PHO5 and PHO8 promoters correlates with differential cofactor requirements for chromatin opening
CB Hertel et al.
MOLECULAR AND CELLULAR BIOLOGY (2005)
Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin
RM Raisner et al.
CELL (2005)
Domain-wide displacement of histones by activated heat shock factor occurs independently of Swi/Snf and is not correlated with RNA polymerase II density
J Zhao et al.
MOLECULAR AND CELLULAR BIOLOGY (2005)
Noise in gene expression: Origins, consequences, and control
JM Raser et al.
SCIENCE (2005)
Genome-scale identification of nucleosome positions in S-cerevisiae
GC Yuan et al.
SCIENCE (2005)
Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast
EA Sekinger et al.
MOLECULAR CELL (2005)
Identification and distinct regulation of yeast TATA box-containing genes
AD Basehoar et al.
CELL (2004)
ATP-Driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex
G Mizuguchi et al.
SCIENCE (2004)
In vitro assembly of the characteristic chromatin organization at the yeast PHO5 promoter by a replication-independent extract system
P Korber et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2004)
Control of stochasticity in eukaryotic gene expression
JM Raser et al.
SCIENCE (2004)
Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin
PL Nagy et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
The structure of DNA in the nucleosome core
TJ Richmond et al.
NATURE (2003)
DNA-dependent divalent cation binding in the nucleosome core particle
CA Davey et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Remodeling of yeast CUP1 chromatin involves activator-dependent repositioning of nucleosomes over the entire gene and flanking sequences
CH Shen et al.
MOLECULAR AND CELLULAR BIOLOGY (2001)
Share Paper
