Efficient RNA polymerase II pause release requires U2 snRNP function

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

Transcription and splicing: A two‐way street

(2020) Michael Tellier et al.   Wiley Interdisciplinary Reviews-RNA

Molecular architecture of the human 17S U2 snRNP

(2020) Zhenwei Zhang et al.   NATURE

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

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

Promoter-proximal pausing mediated by the exon junction complex regulates splicing

(2019) Junaid Akhtar et al.   Nature Communications

A U2-snRNP–independent role of SF3b in promoting mRNA export

(2019) Ke Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Magdalena M Maslon et al.   EMBO JOURNAL

Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction

(2019) Jason Talkish et al.   RNA

Global donor and acceptor splicing site kinetics in human cells

(2019) Leonhard Wachutka et al.   eLife

Spt5 modulates co-transcriptional spliceosome assembly in Saccharomyces cerevisiae

(2019) Isabella E Maudlin et al.   RNA

Nascent RNA and the Coordination of Splicing with Transcription

(2019) Karla M. Neugebauer   Cold Spring Harbor Perspectives in Biology

The pause-initiation limit restricts transcription activation in human cells

(2019) Saskia Gressel et al.   Nature Communications

Exon-Mediated Activation of Transcription Starts

(2019) Ana Fiszbein et al.   CELL

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler et al.   MOLECULAR CELL

Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds

(2018) Constantin Cretu et al.   MOLECULAR CELL

Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

(2018) Anthony C. Chiu et al.   MOLECULAR CELL

A Novel Alternative Splicing Mechanism That Enhances Human 5-HT1A Receptor RNA Stability Is Altered in Major Depression

(2018) Brice Le François et al.   JOURNAL OF NEUROSCIENCE

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface

(2018) Sarah Loerch et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

(2017) Vahid Aslanzadeh et al.   GENOME RESEARCH

Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

(2017) Margarita Schlackow et al.   MOLECULAR CELL

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

(2017) Lydia Herzel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

(2017) Edward W.J. Wallace et al.   RNA

Splicing modulators act at the branch point adenosine binding pocket defined by the PHF5A–SF3b complex

(2017) Teng Teng et al.   Nature Communications

U1 snRNP telescripting regulates a size–function-stratified human genome

(2017) Jung-Min Oh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Co-transcriptional splicing and the CTD code

(2016) Noélia Custódio et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

(2016) Tassa Saldi et al.   JOURNAL OF MOLECULAR BIOLOGY

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide

(2016) Takayuki Nojima et al.   Nature Protocols

Interchangeable SF3B1 inhibitors interfere with pre-mRNA splicing at multiple stages

(2016) Kerstin A. Effenberger et al.   RNA

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

(2016) Kevin M. Harlen et al.   Cell Reports

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

(2015) Takayuki Nojima et al.   CELL

The core spliceosome as target and effector of non-canonical ATM signalling

(2015) Maria Tresini et al.   NATURE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

(2014) Marco Saponaro et al.   CELL

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

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate

(2014) Gilad Fuchs et al.   GENOME RESEARCH

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation

(2014) Keerthi T. Chathoth et al.   MOLECULAR CELL

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

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

(2014) Iris Jonkers et al.   eLife

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

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

Coherence between Cellular Responses andin VitroSplicing Inhibition for the Anti-tumor Drug Pladienolide B and Its Analogs

(2013) Kerstin A. Effenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The human cap-binding complex is functionally connected to the nuclear RNA exosome

(2013) Peter Refsing Andersen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Spt4 Is Selectively Required for Transcription of Extended Trinucleotide Repeats

(2012) Chia-Rung Liu et al.   CELL

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

The RNA polymerase II CTD coordinates transcription and RNA processing

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo

(2012) Bo Gu et al.   NUCLEIC ACIDS RESEARCH

First Exon Length Controls Active Chromatin Signatures and Transcription

(2012) Nicole I. Bieberstein et al.   Cell Reports

DSIF Restricts NF-κB Signaling by Coordinating Elongation with mRNA Processing of Negative Feedback Genes

(2012) Gil Diamant et al.   Cell Reports

Biological validation that SF3b is a target of the antitumor macrolide pladienolide

(2011) Akira Yokoi et al.   FEBS Journal

Reduced fidelity of branch point recognition and alternative splicing induced by the anti-tumor drug spliceostatin A

(2011) A. Corrionero et al.   GENES & DEVELOPMENT

Semiquantitative Proteomic Analysis of the Human Spliceosome via a Novel Two-Dimensional Gel Electrophoresis Method

(2011) D. E. Agafonov et al.   MOLECULAR AND CELLULAR BIOLOGY

Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes

(2011) Sandra Bento Martins et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Splicing-independent recruitment of U1 snRNP to a transcription unit in living cells

(2010) B. Spiluttini et al.   JOURNAL OF CELL SCIENCE

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Spliceostatin A inhibits spliceosome assembly subsequent to prespliceosome formation

(2010) Gabriel A. Roybal et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation

(2009) Y. Chen et al.   GENES & DEVELOPMENT

A 5′ Splice Site Enhances the Recruitment of Basal Transcription Initiation Factors In Vivo

(2008) Christian Kroun Damgaard et al.   MOLECULAR CELL

Isolation of an active step I spliceosome and composition of its RNP core

(2008) Sergey Bessonov et al.   NATURE

The splicing factor SC35 has an active role in transcriptional elongation

(2008) Shengrong Lin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA