Transcription and splicing: A two‐way street

Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation

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

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

(2019) Junaid Akhtar et al.   Nature Communications

U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene Regulation

(2019) Christopher C. Venters et al.   Cold Spring Harbor Perspectives in Biology

Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination

(2019) Kinga Kamieniarz-Gdula et al.   MOLECULAR CELL

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins

(2019) Lea H. Gregersen et al.   CELL

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

(2019) Magdalena M Maslon et al.   EMBO JOURNAL

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

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

XAB2 depletion induces intron retention in POLR2A to impair global transcription and promote cellular senescence

(2019) Shuai Hou et al.   NUCLEIC ACIDS RESEARCH

H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly

(2019) Calvin S. Leung et al.   Cell Reports

A unified mechanism for intron and exon definition and back-splicing

(2019) Xueni Li et al.   NATURE

Intron definition, exon definition and back-splicing revisited

(2019) Eytan Zlotorynski   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Splicing Factor hnRNP M Is a Critical Regulator of Innate Immune Gene Expression in Macrophages

(2019) Kelsi O. West et al.   Cell Reports

Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II

(2018) Christoph Engel et al.   Annual Review of Biophysics

Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation

(2018) Johanna Fitz et al.   EMBO JOURNAL

Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

(2018) Joshua D. Eaton et al.   GENES & DEVELOPMENT

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Precise temporal regulation of alternative splicing during neural development

(2018) Sebastien M. Weyn-Vanhentenryck et al.   Nature Communications

Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain

(2018) Akihide Takeuchi et al.   Cell Reports

Influenza Virus Mounts a Two-Pronged Attack on Host RNA Polymerase II Transcription

(2018) David L.V. Bauer et al.   Cell Reports

mRNA Cap Methyltransferase, RNMT-RAM, Promotes RNA Pol II-Dependent Transcription

(2018) Dhaval Varshney et al.   Cell Reports

Dynamic turnover of paused Pol II complexes at human promoters

(2018) Benjamin Erickson et al.   GENES & DEVELOPMENT

Influenza virus infection causes global RNAPII termination defects

(2018) Nan Zhao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

(2018) Takayuki Nojima 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

RBM17 Interacts with U2SURP and CHERP to Regulate Expression and Splicing of RNA-Processing Proteins

(2018) Antonia De Maio et al.   Cell Reports

The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae

(2017) Lauren T. Neves et al.   GENES & DEVELOPMENT

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

(2017) Vahid Aslanzadeh et al.   GENOME RESEARCH

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

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

Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation

(2017) Ameet Shetty et al.   MOLECULAR CELL

Subgenic Pol II interactomes identify region‐specific transcription elongation regulators

(2017) Kevin M Harlen et al.   Molecular Systems Biology

Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis

(2017) Sarah A Boswell et al.   Nature Chemical Biology

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

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

Mechanistic insights into precursor messenger RNA splicing by the spliceosome

(2017) Yigong Shi   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

ARS2 is a general suppressor of pervasive transcription

(2017) Claudia Iasillo et al.   NUCLEIC ACIDS RESEARCH

Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

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

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine

(2017) Sebastian M Fica et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

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

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

RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

(2017) Sofia Battaglia et al.   eLife

Dynamics and consequences of spliceosome E complex formation

(2017) Joshua Donald Larson et al.   eLife

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

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

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

The SNW Domain of SKIP Is Required for Its Integration into the Spliceosome and Its Interaction with the Paf1 Complex in Arabidopsis

(2016) Yan Li et al.   Molecular Plant

The pol II CTD: new twists in the tail

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

The yeast transcription elongation factor Spt4/5 is a sequence-specific RNA binding protein

(2016) Amanda J. Blythe et al.   PROTEIN SCIENCE

Histone H3K36 methylation regulates pre-mRNA splicing inSaccharomyces cerevisiae

(2016) Matthew R. Sorenson et al.   RNA Biology

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

The elongation factor Spt5 facilitates transcription initiation for rapid induction of inflammatory-response genes

(2016) Gil Diamant et al.   Nature Communications

The pol II CTD: new twists in the tail

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

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

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

PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation

(2016) Yan Yang 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

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

(2015) Yongsheng Shi 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

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

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

(2015) Bushra Raj et al.   NEURON

Splicing inhibition decreases phosphorylation level of Ser2 in Pol II CTD

(2015) Mitsunori Koga et al.   NUCLEIC ACIDS RESEARCH

High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma

(2015) T H Ho et al.   ONCOGENE

SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair

(2015) N Kanu et al.   ONCOGENE

FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP

(2015) Yong Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional control of alternative splicing along time: Ideas change, experiments remain

(2015) Alberto R. Kornblihtt   RNA

ALS-causative mutations in FUS/TLS confer gain and loss of function by altered association with SMN and U1-snRNP

(2015) Shuying Sun et al.   Nature Communications

SF3B1 Association with Chromatin Determines Splicing Outcomes

(2015) Nir Kfir et al.   Cell Reports

Human Telomerase RNA Processing and Quality Control

(2015) Chi-Kang Tseng et al.   Cell Reports

H2B ubiquitylation modulates spliceosome assembly and function in budding yeast

(2014) Lucas Hérissant et al.   BIOLOGY OF THE 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

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

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

Sudemycin E influences alternative splicing and changes chromatin modifications

(2014) Paolo Convertini et al.   NUCLEIC ACIDS RESEARCH

The timing of pre-mRNA splicing visualized in real-time

(2014) Maria Carmo-Fonseca et al.   Nucleus

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

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

A Novel Role for Cet1p mRNA 5′-Triphosphatase in Promoter Proximal Accumulation of RNA Polymerase II in Saccharomyces cerevisiase

(2013) Shweta Lahudkar et al.   GENETICS

Alternative splicing: a pivotal step between eukaryotic transcription and translation

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

CBC–ARS2 stimulates 3′-end maturation of multiple RNA families and favors cap-proximal processing

(2013) Marie Hallais et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Splicing-coupled 3′ end formation requires a terminal splice acceptor site, but not intron excision

(2013) Lee Davidson et al.   NUCLEIC ACIDS RESEARCH

Pre-mRNA Splicing Is a Determinant of Nucleosome Organization

(2013) Hadas Keren-Shaul et al.   PLoS One

The nuclear cap-binding complex interacts with the U4/U6{middle dot}U5 tri-snRNP and promotes spliceosome assembly in mammalian cells

(2013) M. Pabis et al.   RNA

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Live-Cell Visualization of Pre-mRNA Splicing with Single-Molecule Sensitivity

(2013) Robert M. Martin et al.   Cell Reports

Transcriptional elongation and alternative splicing

(2012) Gwendal Dujardin et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Microprocessor, Setx, Xrn2, and Rrp6 Co-operate to Induce Premature Termination of Transcription by RNAPII

(2012) Alexandre Wagschal et al.   CELL

Spt4 Is Selectively Required for Transcription of Extended Trinucleotide Repeats

(2012) Chia-Rung Liu et al.   CELL

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

CTCF: from insulators to alternative splicing regulation

(2012) Alberto R Kornblihtt   CELL RESEARCH

The RNA polymerase II CTD coordinates transcription and RNA processing

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

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

(2012) H. Tilgner et al.   GENOME RESEARCH

The Spt5 C-Terminal Region Recruits Yeast 3' RNA Cleavage Factor I

(2012) A. Mayer et al.   MOLECULAR AND CELLULAR BIOLOGY

SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles

(2012) Vidisha Tripathi et al.   MOLECULAR BIOLOGY OF THE CELL

Mediator Complex Regulates Alternative mRNA Processing via the MED23 Subunit

(2012) Yan Huang et al.   MOLECULAR CELL

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

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

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

(2012) Y. L. Khodor et al.   RNA

First Exon Length Controls Active Chromatin Signatures and Transcription

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

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit 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

The Yeast SR-Like Protein Npl3 Links Chromatin Modification to mRNA Processing

(2012) Erica A. Moehle et al.   PLoS Genetics

H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast

(2011) Grace S Shieh et al.   BMC GENOMICS

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex

(2011) C. J. David et al.   GENES & DEVELOPMENT

A U1-U2 snRNP Interaction Network during Intron Definition

(2011) W. Shao et al.   MOLECULAR AND CELLULAR BIOLOGY

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An Investigation of a Role for U2 snRNP Spliceosomal Components in Regulating Transcription

(2011) Susannah L. McKay et al.   PLoS One

Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner

(2011) H.-L. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements

(2011) Felizza Q. Gunderson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pre-mRNA splicing is a determinant of histone H3K36 methylation

(2011) S. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

(2011) Yehuda Brody et al.   PLOS BIOLOGY

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast

(2011) Brian T Wilhelm et al.   GENOME BIOLOGY

Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers

(2010) Michiel Vermeulen et al.   CELL

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

(2010) J. Y. Ip et al.   GENOME RESEARCH

Splicing-Dependent RNA Polymerase Pausing in Yeast

(2010) Ross D. Alexander et al.   MOLECULAR CELL

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

(2010) Fernando Carrillo Oesterreich et al.   MOLECULAR CELL

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

Reciprocal intronic and exonic histone modification regions in humans

(2010) Jason T Huff et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution

(2010) Pawandeep Dhami et al.   PLoS One

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

The carboxy terminal domain of RNA polymerase II and alternative splicing

(2010) Manuel J. Muñoz et al.   TRENDS IN BIOCHEMICAL SCIENCES

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

The Carboxyl-terminal Domain of RNA Polymerase II Is Not Sufficient to Enhance the Efficiency of Pre-mRNA Capping or Splicing in the Context of a Different Polymerase

(2009) Barbara J. Natalizio et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SR Protein Family Members Display Diverse Activities in the Formation of Nascent and Mature mRNPs In Vivo

(2009) Aparna K. Sapra et al.   MOLECULAR CELL

“Cotranscriptionality”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions

(2009) Roberto Perales et al.   MOLECULAR CELL

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing

(2009) I. E. Schor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3′ mRNA processing factors

(2009) Orit Rozenblatt-Rosen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acetylation by the Transcriptional Coactivator Gcn5 Plays a Novel Role in Co-Transcriptional Spliceosome Assembly

(2009) Felizza Q. Gunderson et al.   PLoS Genetics

SWI/SNF Associates with Nascent Pre-mRNPs and Regulates Alternative Pre-mRNA Processing

(2009) Anu Tyagi et al.   PLoS Genetics

The splicing factor SC35 has an active role in transcriptional elongation

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