Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae

Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies

(2021) Jung-Hoon Lee et al.   Science Advances

A short guide to histone deacetylases including recent progress on class II enzymes

(2020) Suk-Youl Park et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome

(2020) Evan J Worden et al.   eLife

Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation

(2020) Seychelle M. Vos et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations

(2020) Mitchell A. Ellison et al.   G3-Genes Genomes Genetics

The role of FACT in managing chromatin: disruption, assembly, or repair?

(2020) Tim Formosa et al.   NUCLEIC ACIDS RESEARCH

Histone H2B Ubiquitylation Regulates Histone Gene Expression by Suppressing Antisense Transcription in Fission Yeast

(2019) Viviane Pagé et al.   GENETICS

High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier

(2019) Zhijie Chen et al.   eLife

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast

(2019) Wu Wei et al.   GENOME RESEARCH

Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast

(2019) So Dam Ha et al.   Nature Communications

Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases

(2019) Nicholas J Porter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Activation and regulation of H2B-Ubiquitin-dependent histone methyltransferases

(2019) Evan J Worden et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Chaperone FACT and Histone H2B Ubiquitination Maintain S. pombe Genome Architecture through Genic and Subtelomeric Functions

(2019) Magdalena Murawska et al.   MOLECULAR CELL

Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS

(2019) Peter L. Hsu et al.   MOLECULAR CELL

Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109

(2018) Lin Zhang et al.   CELL

Structural basis of the nucleosome transition during RNA polymerase II passage

(2018) Tomoya Kujirai et al.   SCIENCE

Structure of transcribing RNA polymerase II-nucleosome complex

(2018) Lucas Farnung et al.   Nature Communications

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

(2017) Benjamin J. E. Martin et al.   GENETICS

Histone chaperone networks shaping chromatin function

(2017) Colin M. Hammond et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation

(2017) S. Branden Van Oss et al.   TRENDS IN BIOCHEMICAL SCIENCES

Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress

(2017) Ana Tamarkin-Ben-Harush et al.   eLife

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

(2017) Benjamin J. E. Martin et al.   GENETICS

Combinatorial Histone Readout by the Dual Plant Homeodomain (PHD) Fingers of Rco1 Mediates Rpd3S Chromatin Recruitment and the Maintenance of Transcriptional Fidelity

(2016) Stephen L. McDaniel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6

(2016) S. Branden Van Oss et al.   MOLECULAR CELL

Lateral Thinking: How Histone Modifications Regulate Gene Expression

(2016) Moyra Lawrence et al.   TRENDS IN GENETICS

Chromatin remodelers: We are the drivers!!

(2016) Monica Tyagi et al.   Nucleus

Chromatin remodelers: We are the drivers!!

(2016) Monica Tyagi et al.   Nucleus

Histone exchange, chromatin structure and the regulation of transcription

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

Nucleosome Contact Triggers Conformational Changes of Rpd3S Driving High-Affinity H3K36me Nucleosome Engagement

(2015) Chun Ruan et al.   Cell Reports

Histone Chaperones: Assisting Histone Traffic and Nucleosome Dynamics

(2014) Zachary A. Gurard-Levin et al.   Annual Review of Biochemistry

Writing and reading H2B monoubiquitylation

(2014) Gilad Fuchs et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Replicative Stress Induces Intragenic Transcription of the ASE1 Gene that Negatively Regulates Ase1 Activity

(2014) Kelly McKnight et al.   CURRENT BIOLOGY

Writers and Readers of Histone Acetylation: Structure, Mechanism, and Inhibition

(2014) R. Marmorstein et al.   Cold Spring Harbor Perspectives in Biology

Erasers of Histone Acetylation: The Histone Deacetylase Enzymes

(2014) E. Seto et al.   Cold Spring Harbor Perspectives in Biology

The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now

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

The Recruitment of theSaccharomyces cerevisiaePaf1 Complex to Active Genes Requires a Domain of Rtf1 That Directly Interacts with the Spt4-Spt5 Complex

(2013) Manasi K. Mayekar et al.   MOLECULAR AND CELLULAR BIOLOGY

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin

(2013) A. D. Wier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Set3 HDAC Mediates Effects of Overlapping Noncoding Transcription on Gene Induction Kinetics

(2012) TaeSoo Kim et al.   CELL

Chromatin and Transcription in Yeast

(2012) Oliver J. Rando et al.   GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Perceiving the epigenetic landscape through histone readers

(2012) Catherine A Musselman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae

(2012) V. E. Maltby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast

(2012) A. S. Piro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Genome-wide function of H2B ubiquitylation in promoter and genic regions

(2011) K. Batta et al.   GENES & DEVELOPMENT

Genetic Analysis Implicates the Set3/Hos2 Histone Deacetylase in the Deposition and Remodeling of Nucleosomes Containing H2A.Z

(2011) M. Hang et al.   GENETICS

Identification of a Role for Histone H2B Ubiquitylation in Noncoding RNA 3′-End Formation Through Mutational Analysis of Rtf1 inSaccharomyces cerevisiae

(2011) Brett N. Tomson et al.   GENETICS

The Replication-independent Histone H3-H4 Chaperones HIR, ASF1, and RTT106 Co-operate to Maintain Promoter Fidelity

(2011) Andrea C. Silva et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Antagonistic Gcn5-Hda1 interactions revealed by mutations to the Anaphase Promoting Complex in yeast

(2011) Azharul Islam et al.   Cell Division

Discovery of Mutations in Saccharomyces cerevisiae by Pooled Linkage Analysis and Whole-Genome Sequencing

(2010) S. R. Birkeland et al.   GENETICS

Phosphorylated Pol II CTD Recruits Multiple HDACs, Including Rpd3C(S), for Methylation-Dependent Deacetylation of ORF Nucleosomes

(2010) Chhabi K. Govind et al.   MOLECULAR CELL

DSIF and RNA Polymerase II CTD Phosphorylation Coordinate the Recruitment of Rpd3S to Actively Transcribed Genes

(2010) Simon Drouin et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Dimethylation of H3K4 by Set1 Recruits the Set3 Histone Deacetylase Complex to 5′ Transcribed Regions

(2009) TaeSoo Kim et al.   CELL

Histone H3K4 and K36 Methylation, Chd1 and Rpd3S Oppose the Functions of Saccharomyces cerevisiae Spt4-Spt5 in Transcription

(2009) T. K. Quan et al.   GENETICS

Structural and Functional Studies of the Yeast Class II Hda1 Histone Deacetylase Complex

(2009) Jung-Hoon Lee et al.   JOURNAL OF MOLECULAR BIOLOGY

Ubiquitination of histone H2B regulates chromatin dynamics by enhancing nucleosome stability

(2009) M. B. Chandrasekharan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing Nucleosome Function: A Highly Versatile Library of Synthetic Histone H3 and H4 Mutants

(2008) Junbiao Dai et al.   CELL

H2B Ubiquitylation Plays a Role in Nucleosome Dynamics during Transcription Elongation

(2008) Alastair B. Fleming et al.   MOLECULAR CELL

Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells

(2008) Neri Minsky et al.   NATURE CELL BIOLOGY

The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men

(2008) Xiang-Jiao Yang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome

(2008) Vanessa Cheung et al.   PLOS BIOLOGY