RNAPII driven post-translational modifications of nucleosomal histones

Transcription by RNA polymerase II and the CTD-chromatin crosstalk

(2022) Neha Singh et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A high-resolution protein architecture of the budding yeast genome

(2021) Matthew J. Rossi et al.   NATURE

Role of CxxC-finger protein 1 in establishing mouse oocyte epigenetic landscapes

(2021) Qian-Qian Sha et al.   NUCLEIC ACIDS RESEARCH

Depletion of H3K36me2 recapitulates epigenomic and phenotypic changes induced by the H3.3K36M oncohistone mutation

(2021) Kartik N. Rajagopalan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin

(2021) Alex M. Francette et al.   JOURNAL OF MOLECULAR BIOLOGY

The transcription factor code: a beacon for histone methyltransferase docking

(2021) Guillem Torcal Garcia et al.   TRENDS IN CELL BIOLOGY

Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo

(2021) Kristina Žumer et al.   MOLECULAR CELL

Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene

(2021) Linda S. Forero-Quintero et al.   Nature Communications

Interplay among transacting factors around promoter in the initial phases of transcription

(2021) Amarjeet Kumar et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

(2021) Ko Sato et al.   Nature Communications

Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome

(2020) Evan J Worden et al.   eLife

H3K36 Methylation in Neural Development and Associated Diseases

(2020) Mattia Zaghi et al.   Frontiers in Genetics

H2B ubiquitylation enhances H3K4 methylation activities of human KMT2 family complexes

(2020) Minjung Kwon et al.   NUCLEIC ACIDS RESEARCH

The Set1 N-terminal domain and Swd2 interact with RNA polymerase II CTD to recruit COMPASS

(2020) Hyun Jin Bae et al.   Nature Communications

The roles of histone variants in fine-tuning chromatin organization and function

(2020) Sara Martire et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

(2020) Michael Tellier et al.   NUCLEIC ACIDS RESEARCH

Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions

(2020) Julia V. DiFiore et al.   Cell Reports

Coordinated regulation of cellular identity–associated H3K4me3 breadth by the COMPASS family

(2020) Christie C. Sze et al.   Science Advances

Nucleosomes and Epigenetics from a Chemical Perspective

(2020) Yihong Feng et al.   CHEMBIOCHEM

An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation

(2020) Andrew M. Lerner et al.   GENOME RESEARCH

Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases

(2020) Wanqiu Li et al.   NATURE

Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3

(2020) Ksenia Finogenova et al.   eLife

A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation

(2019) Rajaraman Gopalakrishnan et al.   NUCLEIC ACIDS RESEARCH

Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally

(2019) Huilin Huang et al.   NATURE

In vitro analysis of RNA polymerase II elongation complex dynamics

(2019) Yoo Jin Joo et al.   GENES & DEVELOPMENT

Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription

(2019) Claire E. Barnes et al.   Essays in Biochemistry

Histone H3 tail binds a unique sensing pocket in EZH2 to activate the PRC2 methyltransferase

(2019) Krupa S. Jani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing

(2019) Hagar F. Moussa et al.   Nature Communications

The transcription factor OsSUF4 interacts with SDG725 in promoting H3K36me3 establishment

(2019) Bing Liu et al.   Nature Communications

Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications

(2019) Célia Jeronimo et al.   Cell Reports

Normal transcription of cellulolytic enzyme genes relies on the balance between the methylation of H3K36 and H3K4 in Penicillium oxalicum

(2019) Yanan Li et al.   Biotechnology for Biofuels

Structural basis of nucleosome recognition and modification by MLL methyltransferases

(2019) Han Xue et al.   NATURE

Histone lysine methyltransferases in biology and disease

(2019) Dylan Husmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans

(2019) Flore Beurton et al.   NUCLEIC ACIDS RESEARCH

Nucleosome and ubiquitin position Set2 to methylate H3K36

(2019) Silvija Bilokapic et al.   Nature Communications

Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS

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

PRC1 Catalytic Activity Is Central to Polycomb System Function

(2019) Neil P. Blackledge et al.   MOLECULAR CELL

The Biogenesis and Precise Control of RNA m6A Methylation

(2019) Huilin Huang et al.   TRENDS IN GENETICS

Cryo-EM structure of the human MLL1 core complex bound to the nucleosome

(2019) Sang Ho Park et al.   Nature Communications

Transcription through the nucleosome

(2019) Tomoya Kujirai et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Arabidopsis Histone Reader EMSY-LIKE 1 Binds H3K36 and Suppresses Geminivirus Infection

(2018) Tami Coursey et al.   JOURNAL OF VIROLOGY

DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants

(2018) Chao Xu et al.   STRUCTURE

Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants

(2018) Felix Wojcik et al.   Nature Communications

ChIP-seq and ChIP-exo profiling of Pol II, H2A.Z, and H3K4me3 in human K562 cells

(2018) Zenab F. Mchaourab et al.   Scientific Data

Histone Lysine and Genomic Targets of Histone Acetyltransferases in Mammals

(2018) Anne K. Voss et al.   BIOESSAYS

Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies

(2018) Rohan N. Shah et al.   MOLECULAR CELL

RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast

(2018) Sandipan Brahma et al.   MOLECULAR CELL

Histone H3K4 methylation-dependent and -independent functions of Set1A/COMPASS in embryonic stem cell self-renewal and differentiation

(2017) Christie C. Sze et al.   GENES & DEVELOPMENT

Paf1 Has Distinct Roles in Transcription Elongation and Differential Transcript Fate

(2017) Harry Fischl et al.   MOLECULAR CELL

RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction

(2017) Nova Fong et al.   MOLECULAR CELL

Determinants of Histone H3K4 Methylation Patterns

(2017) Luis M. Soares et al.   MOLECULAR CELL

The ATP-dependent chromatin remodeler Chd1 is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes

(2017) Yaelim Lee et al.   NUCLEIC ACIDS RESEARCH

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

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

H3K36 Methylation Regulates Nutrient Stress Response in Saccharomyces cerevisiae by Enforcing Transcriptional Fidelity

(2017) Stephen L. McDaniel et al.   Cell Reports

Is H3K4me3 instructive for transcription activation?

(2016) Françoise S. Howe et al.   BIOESSAYS

Epigenetic Mechanisms of Longevity and Aging

(2016) Payel Sen et al.   CELL

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

Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a

(2016) Alexandros Strikoudis et al.   NATURE CELL BIOLOGY

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast

(2016) Shota Suzuki et al.   NUCLEIC ACIDS RESEARCH

Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape

(2016) C. Lu et al.   SCIENCE

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural and Functional Analysis of the Cdk13/Cyclin K Complex

(2016) Ann Katrin Greifenberg et al.   Cell Reports

H3K36 methylation promotes longevity by enhancing transcriptional fidelity

(2015) Payel Sen et al.   GENES & DEVELOPMENT

Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex

(2015) Qing-Fu Cao et al.   MOLECULAR AND CELLULAR BIOLOGY

High-Resolution Chromatin Dynamics during a Yeast Stress Response

(2015) Assaf Weiner et al.   MOLECULAR CELL

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

(2015) Kaifu Chen et al.   NATURE GENETICS

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

RNA polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II

(2015) M. Yu et al.   SCIENCE

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

(2015) Chun Ruan et al.   Cell Reports

Context dependency of Set1/COMPASS-mediated histone H3 Lys4 trimethylation

(2014) J. L. Thornton et al.   GENES & DEVELOPMENT

A PWWP Domain-Containing Protein Targets the NuA3 Acetyltransferase Complex via Histone H3 Lysine 36 trimethylation to Coordinate Transcriptional Elongation at Coding Regions

(2014) Tonya M. Gilbert et al.   MOLECULAR & CELLULAR PROTEOMICS

Regulation of histone H3K4 methylation in brain development and disease

(2014) E. Shen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Divergence and Selectivity of Expression-Coupled Histone Modifications in Budding Yeasts

(2014) Yaron Mosesson et al.   PLoS One

The structure and substrate specificity of human Cdk12/Cyclin K

(2014) Christian A. Bösken et al.   Nature Communications

Feedback Control of Set1 Protein Levels Is Important for Proper H3K4 Methylation Patterns

(2014) Luis M. Soares et al.   Cell Reports

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

Precision Mapping of Coexisting Modifications in Histone H3 Tails from Embryonic Stem Cells by ETD-MS/MS

(2013) Hye Ryung Jung et al.   ANALYTICAL CHEMISTRY

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

(2013) Shannon M. Lauberth et al.   CELL

The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code

(2013) Célia Jeronimo et al.   CHEMICAL REVIEWS

Histone H2A Ubiquitination Inhibits the Enzymatic Activity of H3 Lysine 36 Methyltransferases

(2013) Gang Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

The n-SET Domain of Set1 Regulates H2B Ubiquitylation-Dependent H3K4 Methylation

(2013) Jaehoon Kim et al.   MOLECULAR CELL

The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells

(2013) Deqing Hu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

The PAF Complex and Prf1/Rtf1 Delineate Distinct Cdk9-Dependent Pathways Regulating Transcription Elongation in Fission Yeast

(2013) Jean Mbogning et al.   PLoS Genetics

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription

(2012) Martin Heidemann et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Pol II CTD kinases Bur1 and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex

(2012) Hongfang Qiu et al.   EMBO JOURNAL

Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells

(2012) T. Clouaire et al.   GENES & DEVELOPMENT

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin et al.   GENES & DEVELOPMENT

Histone H3 Lysine 36 Methylation Targets the Isw1b Remodeling Complex to Chromatin

(2012) V. E. Maltby et al.   MOLECULAR AND CELLULAR BIOLOGY

A Universal RNA Polymerase II CTD Cycle Is Orchestrated by Complex Interplays between Kinase, Phosphatase, and Isomerase Enzymes along Genes

(2012) Alain R. Bataille et al.   MOLECULAR CELL

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 adjustable nucleosome: an epigenetic signaling module

(2012) Bryan M. Turner   TRENDS IN GENETICS

Multiple exposures to drought 'train' transcriptional responses in Arabidopsis

(2012) Yong Ding et al.   Nature Communications

Two Distinct Repressive Mechanisms for Histone 3 Lysine 4 Methylation through Promoting 3′-End Antisense Transcription

(2012) Thanasis Margaritis et al.   PLoS Genetics

Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation

(2011) Chuanbing Bian et al.   EMBO JOURNAL

Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks

(2011) Frank W. Schmitges et al.   MOLECULAR CELL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

From Waddington’s epigenetic landscape to small noncoding RNA: some important milestones in the history of epigenetics research

(2011) Supratim Choudhuri   TOXICOLOGY MECHANISMS AND METHODS

Structural Basis for Assembly and Activation of the Heterotetrameric SAGA Histone H2B Deubiquitinase Module

(2010) Alwin Köhler et al.   CELL

Methylation of H3K4 Is Required for Inheritance of Active Transcriptional States

(2010) Tetsuya Muramoto et al.   CURRENT BIOLOGY

A Nucleosome Surface Formed by Histone H4, H2A, and H3 Residues Is Needed for Proper Histone H3 Lys36Methylation, Histone Acetylation, and Repression of Cryptic Transcription

(2010) Hai-Ning Du et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Chromatin Signaling Pathway: Diverse Mechanisms of Recruitment of Histone-Modifying Enzymes and Varied Biological Outcomes

(2010) Edwin Smith et al.   MOLECULAR CELL

Chemical-genomic dissection of the CTD code

(2010) Joshua R Tietjen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Uniform transitions of the general RNA polymerase II transcription complex

(2010) Andreas Mayer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural Insights into the Assembly and Function of the SAGA Deubiquitinating Module

(2010) N. L. Samara et al.   SCIENCE

Histone H3 Lysine 36 Dimethylation (H3K36me2) Is Sufficient to Recruit the Rpd3s Histone Deacetylase Complex and to Repress Spurious Transcription

(2009) Bing Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Global Analysis of H3K4 Methylation Defines MLL Family Member Targets and Points to a Role for MLL1-Mediated H3K4 Methylation in the Regulation of Transcriptional Initiation by RNA Polymerase II

(2009) P. Wang et al.   MOLECULAR AND CELLULAR BIOLOGY

Set2-Dependent K36 Methylation Is Regulated by Novel Intratail Interactions within H3

(2009) J. N. Psathas et al.   MOLECULAR AND CELLULAR BIOLOGY

Phosphorylation of the Pol II CTD by KIN28 Enhances BUR1/BUR2 Recruitment and Ser2 CTD Phosphorylation Near Promoters

(2009) Hongfang Qiu et al.   MOLECULAR CELL

Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

(2009) K. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites

(2008) Valérie Borde et al.   EMBO JOURNAL

Histone H3 K36 methylation is mediated by a trans-histone methylation pathway involving an interaction between Set2 and histone H4

(2008) H.-N. Du et al.   GENES & DEVELOPMENT

Roles for Ctk1 and Spt6 in Regulating the Different Methylation States of Histone H3 Lysine 36

(2008) M. L. Youdell et al.   MOLECULAR AND CELLULAR BIOLOGY