TOX4 facilitates promoter-proximal pausing and C-terminal domain dephosphorylation of RNA polymerase II in human cells

The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer

(2021) Stephin J. Vervoort et al.   CELL

Protein phosphatases in the RNAPII transcription cycle: erasers, sculptors, gatekeepers, and potential drug targets

(2021) Giacomo Cossa et al.   GENES & DEVELOPMENT

DOT1L complex regulates transcriptional initiation in human erythroleukemic cells

(2021) Aiwei Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription

(2020) Giacomo Cossa et al.   MOLECULAR CELL

Using TTchem-seq for profiling nascent transcription and measuring transcript elongation

(2020) Lea H. Gregersen et al.   Nature Protocols

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

(2020) Michael Tellier et al.   NUCLEIC ACIDS RESEARCH

Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)

(2020) Tim-Michael Decker   JOURNAL OF MOLECULAR BIOLOGY

Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination

(2020) Kai-Lieh Huang et al.   MOLECULAR CELL

Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II

(2020) Pabitra K. Parua et al.   Nature Communications

Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase

(2020) Hai Zheng et al.   SCIENCE

WDR82/PNUTS-PP1 Prevents Transcription-Replication Conflicts by Promoting RNA Polymerase II Degradation on Chromatin

(2020) Helga B. Landsverk et al.   Cell Reports

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection

(2019) Francesca Alfei et al.   NATURE

TOX is a critical regulator of tumour-specific T cell differentiation

(2019) Andrew C. Scott et al.   NATURE

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

(2019) Michael P. Meers et al.   Epigenetics & Chromatin

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms

(2019) Robert G. Roeder   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Transcription Factor Tox2 Drives T Follicular Helper Cell Development via Regulating Chromatin Accessibility

(2019) Wei Xu et al.   IMMUNITY

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism

(2019) Michael A. Cortazar et al.   MOLECULAR CELL

OUP accepted manuscript

(2018)   BIOINFORMATICS

A Cdk9–PP1 switch regulates the elongation–termination transition of RNA polymerase II

(2018) Pabitra K. Parua et al.   NATURE

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation

(2017) Margaux Michel et al.   Molecular Systems Biology

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functional interplay between histone H1 and HMG proteins in chromatin

(2016) Yuri V. Postnikov et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates

(2016) Miriam Sansó et al.   GENES & DEVELOPMENT

The pol II CTD: new twists in the tail

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

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The pol II CTD: new twists in the tail

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

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Protein phosphatase 1 is a key player in nuclear events

(2015) Sandra Rebelo et al.   CELLULAR SIGNALLING

Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

(2015) Liv M.I. Austenaa et al.   MOLECULAR CELL

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

(2015) M. Yu et al.   SCIENCE

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Regulation of transcription factor activity by interconnected post-translational modifications

(2014) Theresa M. Filtz et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

(2014) Gilad Fuchs et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

(2013) Andreas H. Ehrensberger et al.   CELL

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

PNUTS/PP1 Regulates RNAPII-Mediated Gene Expression and Is Necessary for Developmental Growth

(2013) Anita Ciurciu et al.   PLoS Genetics

Promoter clearance by RNA polymerase II

(2012) Donal S. Luse   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fcp1 Dephosphorylation of the RNA Polymerase II C-Terminal Domain Is Required for Efficient Transcription of Heat Shock Genes

(2012) N. J. Fuda et al.   MOLECULAR AND CELLULAR BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Identification and Characterization of a Novel Human PP1 Phosphatase Complex

(2010) Jeong-Heon Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Serine/Threonine Phosphatases: Mechanism through Structure

(2009) Yigong Shi   CELL

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL