The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin

Mechanisms Underlying Nucleosome Positioning In Vivo

(2014) Amanda L. Hughes et al.   Annual Review of Biophysics

Mediator, TATA-binding Protein, and RNA Polymerase II Contribute to Low Histone Occupancy at Active Gene Promoters in Yeast

(2014) Suraiya A. Ansari et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The RSC chromatin remodeling complex has a crucial role in the complete remodeler set for yeast PHO5 promoter opening

(2014) Sanja Musladin et al.   NUCLEIC ACIDS RESEARCH

Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity

(2014) E. C. Small et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intra- and inter-nucleosome interactions of the core histone tail domains in higher-order chromatin structure

(2013) Sharon Pepenella et al.   CHROMOSOMA

Mapping the fine structure of a eukaryotic promoter input-output function

(2013) Arun S Rajkumar et al.   NATURE GENETICS

Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions

(2013) Stephanie A Morris et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosome sliding mechanisms: new twists in a looped history

(2013) Felix Mueller-Planitz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Determinants of nucleosome positioning

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

Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae

(2013) Stephan Hamperl et al.   NUCLEIC ACIDS RESEARCH

A Histone Acetylation Switch Regulates H2A.Z Deposition by the SWR-C Remodeling Enzyme

(2013) S. Watanabe et al.   SCIENCE

Nucleosome Remodeling and Epigenetics

(2013) P. B. Becker et al.   Cold Spring Harbor Perspectives in Biology

Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression

(2013) Christopher R. Brown et al.   PLOS BIOLOGY

Active nucleosome positioning beyond intrinsic biophysics is revealed byin vitroreconstitution

(2012) Philipp Korber   BIOCHEMICAL SOCIETY TRANSACTIONS

Transcription-associated histone modifications and cryptic transcription

(2012) Michaela Smolle et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Making sense of transcribing chromatin

(2012) Tom Owen-Hughes et al.   CURRENT OPINION IN CELL BIOLOGY

Chromatin and Transcription in Yeast

(2012) Oliver J. Rando et al.   GENETICS

Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators

(2012) D. J. Huebert et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2012) Ho Sung Rhee et al.   NATURE

Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler

(2012) Ashok Patel et al.   NUCLEIC ACIDS RESEARCH

Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response

(2012) Assaf Weiner et al.   PLOS BIOLOGY

The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes

(2011) Christian J Wippo et al.   EMBO JOURNAL

Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

(2011) Steven Hahn et al.   GENETICS

In VivoRole for the Chromatin-remodeling Enzyme SWI/SNF in the Removal of Promoter Nucleosomes by Disassembly Rather Than Sliding

(2011) Christopher R. Brown et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Histone H3 Lysine 4 Hypermethylation Prevents Aberrant Nucleosome Remodeling at the PHO5 Promoter

(2011) S.-S. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

Integrated Approaches Reveal Determinants of Genome-wide Binding and Function of the Transcription Factor Pho4

(2011) Xu Zhou et al.   MOLECULAR CELL

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex

(2011) Yahli Lorch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes

(2011) Hope A. Cole et al.   NUCLEIC ACIDS RESEARCH

Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes

(2011) Jason M. Rizzo et al.   NUCLEIC ACIDS RESEARCH

Occlusion of Regulatory Sequences by Promoter Nucleosomes In Vivo

(2011) Changhui Mao et al.   PLoS One

Isolation of an activator-dependent, promoter-specific chromatin remodeling factor

(2011) A. H. Ehrensberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast

(2011) Marta Radman-Livaja et al.   PLOS BIOLOGY

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

(2010) Maud Marques et al.   Epigenetics

Nucleosome dynamics and epigenetic stability

(2010) Philipp Korber et al.   Essays in Biochemistry

In Vitro Reconstitution of PHO5 Promoter Chromatin Remodeling Points to a Role for Activator-Nucleosome Competition In Vivo

(2010) F. Ertel et al.   MOLECULAR AND CELLULAR BIOLOGY

SWI/SNF Has Intrinsic Nucleosome Disassembly Activity that Is Dependent on Adjacent Nucleosomes

(2010) Mekonnen Lemma Dechassa et al.   MOLECULAR CELL

Quantitative analysis of the transcription control mechanism

(2010) Changhui Mao et al.   Molecular Systems Biology

Inducible gene expression: diverse regulatory mechanisms

(2010) Vikki M. Weake et al.   NATURE REVIEWS GENETICS

Remosomes: RSC generated non-mobilized particles with approximately 180 bp DNA loosely associated with the histone octamer

(2010) M. S. Shukla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Biology of Chromatin Remodeling Complexes

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

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

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

FACT and the Proteasome Promote Promoter Chromatin Disassembly and Transcriptional Initiation

(2009) Monica Ransom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Coupling Phosphate Homeostasis to Cell Cycle-Specific Transcription: Mitotic Activation of Saccharomyces cerevisiae PHO5 by Mcm1 and Forkhead Proteins

(2009) S. Pondugula et al.   MOLECULAR AND CELLULAR BIOLOGY

Differential Cofactor Requirements for Histone Eviction from Two Nucleosomes at the Yeast PHO84 Promoter Are Determined by Intrinsic Nucleosome Stability

(2009) C. J. Wippo et al.   MOLECULAR AND CELLULAR BIOLOGY

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

(2009) Karl A. Zawadzki et al.   MOLECULAR BIOLOGY OF THE CELL

The logic of chromatin architecture and remodelling at promoters

(2009) Bradley R. Cairns   NATURE

Nucleosomes can invade DNA territories occupied by their neighbors

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

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

Dissection of Coactivator Requirement atRNR3Reveals Unexpected Contributions from TFIID and SAGA

(2008) Hesheng Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chromatin decouples promoter threshold from dynamic range

(2008) Felix H. Lam et al.   NATURE

A quantitative model of transcription factor–activated gene expression

(2008) Harold D Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation

(2008) Stephanie K. Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Sushma Shivaswamy et al.   PLOS BIOLOGY