Organismal benefits of transcription speed control at gene boundaries

Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation

(2019) Micaela A. Godoy Herz et al.   MOLECULAR CELL

Transcription-driven chromatin repression of Intragenic transcription start sites

(2019) Mathias Nielsen et al.   PLoS Genetics

A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes

(2019) Magdalena M Maslon et al.   EMBO JOURNAL

Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

(2019) Peter Kindgren et al.   NUCLEIC ACIDS RESEARCH

Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II

(2018) Barbara Steurer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5′ Pause Release, Termination, and Transcription Elongation Rate

(2018) Ryan M. Sheridan et al.   MOLECULAR CELL

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Comprehensive profiling of the fission yeast transcription start site activity during stress and media response

(2018) Malte Thodberg et al.   NUCLEIC ACIDS RESEARCH

Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

(2018) Peter Kindgren et al.   Nature Communications

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

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters

(2017) Arnaud R. Krebs et al.   MOLECULAR CELL

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

(2017) Runxuan Zhang et al.   NUCLEIC ACIDS RESEARCH

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation

(2016) Dig B. Mahat et al.   MOLECULAR CELL

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

(2016) Lin-Tai Da et al.   Nature Communications

High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop

(2016) Chenxi Qiu et al.   PLoS Genetics

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Plant germline formation: common concepts and developmental flexibility in sexual and asexual reproduction

(2015) A. Schmidt et al.   DEVELOPMENT

NTR1 is required for transcription elongation checkpoints at alternative exons in Arabidopsis

(2015) J. Dolata et al.   EMBO JOURNAL

Widespread Inducible Transcription Downstream of Human Genes

(2015) Anna Vilborg et al.   MOLECULAR CELL

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes

(2015) Clélia Laitem et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PlantDHS: a database for DNase I hypersensitive sites in plants

(2015) Tao Zhang et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants

(2015) Tao Zhang et al.   PLANT PHYSIOLOGY

CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II–transcribed genes

(2015) Clélia Laitem et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs

(2014) Nicholas J. Schurch et al.   PLoS One

Light-dependent expression of flg22-induced defense genes in Arabidopsis

(2014) Satoshi Sano et al.   Frontiers in Plant Science

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

(2013) Andreas H. Ehrensberger et al.   CELL

From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

(2013) Hannes Braberg et al.   CELL

RNA Polymerase II C-Terminal Domain: Tethering Transcription to Transcript and Template

(2013) Jeffry L. Corden   CHEMICAL REVIEWS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Kinetic Competition between RNA Polymerase II and Sen1-Dependent Transcription Termination

(2012) Dane Z. Hazelbaker et al.   MOLECULAR CELL

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

(2012) Alexander Sherstnev et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dissection of Pol II Trigger Loop Function and Pol II Activity–Dependent Control of Start Site Selection In Vivo

(2012) Craig D. Kaplan et al.   PLoS Genetics

Structural basis of RNA polymerase II backtracking, arrest and reactivation

(2011) Alan C. M. Cheung et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution

(2009) D. Wang et al.   SCIENCE

Sex-Biased Lethality or Transmission of Defective Transcription Machinery in Arabidopsis

(2008) Y. Onodera et al.   GENETICS

Transient Reversal of RNA Polymerase II Active Site Closing Controls Fidelity of Transcription Elongation

(2008) Maria L. Kireeva et al.   MOLECULAR CELL

The RNA Polymerase II Trigger Loop Functions in Substrate Selection and Is Directly Targeted by α-Amanitin

(2008) Craig D. Kaplan et al.   MOLECULAR CELL