Nascent RNA and the Coordination of Splicing with Transcription

Transcription elongation rate affects nascent histone pre-mRNA folding and 3′ end processing

(2018) Tassa Saldi et al.   GENES & DEVELOPMENT

The histone variant H2A.Z promotes splicing of weak introns

(2017) Kelly E. Nissen et al.   GENES & DEVELOPMENT

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

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

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

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

Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm

(2017) Mattia Brugiolo et al.   NUCLEIC ACIDS RESEARCH

Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

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

RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit

(2017) Laura Milligan et al.   eLife

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

(2016) Fernando Carrillo Oesterreich et al.   CELL

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

Strand‐specific, high‐resolution mapping of modified RNA polymerase II

(2016) Laura Milligan et al.   Molecular Systems Biology

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

(2016) P. Eser et al.   Molecular Systems Biology

Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing

(2016) Andreas Mayer et al.   Nature Protocols

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

(2016) Takayuki Nojima et al.   Nature Protocols

The pol II CTD: new twists in the tail

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

How Are Short Exons Flanked by Long Introns Defined and Committed to Splicing?

(2016) Dror Hollander et al.   TRENDS IN GENETICS

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

Perfect timing: splicing and transcription rates in living cells

(2016) Tara Alpert et al.   Wiley Interdisciplinary Reviews-RNA

The Balbiani Ring Story: Synthesis, Assembly, Processing, and Transport of Specific Messenger RNA–Protein Complexes

(2015) Petra Björk et al.   Annual Review of Biochemistry

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

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

(2015) Paul L. Boutz et al.   GENES & DEVELOPMENT

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Molecular Basis of Transcription-Coupled Pre-mRNA Capping

(2015) Fuensanta W. Martinez-Rucobo et al.   MOLECULAR CELL

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

(2015) Harold Pimentel et al.   NUCLEIC ACIDS RESEARCH

U1 snRNP is mislocalized in ALS patient fibroblasts bearing NLS mutations in FUS and is required for motor neuron outgrowth in zebrafish

(2015) Yong Yu et al.   NUCLEIC ACIDS RESEARCH

SF3B1 Association with Chromatin Determines Splicing Outcomes

(2015) Nir Kfir et al.   Cell Reports

Genetic Interaction Mapping Reveals a Role for the SWI/SNF Nucleosome Remodeler in Spliceosome Activation in Fission Yeast

(2015) Kristin L. Patrick et al.   PLoS Genetics

H2B ubiquitylation modulates spliceosome assembly and function in budding yeast

(2014) Lucas Hérissant et al.   BIOLOGY OF THE CELL

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani 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

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig 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

Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing

(2014) Jeremy C. Davis-Turak et al.   NUCLEIC ACIDS RESEARCH

Kinetic competition during the transcription cycle results in stochastic RNA processing

(2014) Antoine Coulon et al.   eLife

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

(2014) Iris Jonkers et al.   eLife

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

(2013) Hannes Braberg et al.   CELL

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

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

(2013) Xiong Ji et al.   CELL

Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation

(2013) Ignacio E Schor et al.   EMBO JOURNAL

The C-terminal domain of Brd2 is important for chromatin interaction and regulation of transcription and alternative splicing

(2013) Jarmila Hnilicová et al.   MOLECULAR BIOLOGY OF THE CELL

Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression

(2013) A. Pandya-Jones et al.   RNA

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

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

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

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

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

(2012) L. Windhager et al.   GENOME RESEARCH

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

(2012) Y. L. Khodor et al.   RNA

Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion

(2012) Cyrille Girard et al.   Nature Communications

First Exon Length Controls Active Chromatin Signatures and Transcription

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

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

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

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila

(2011) Y. L. Khodor et al.   GENES & DEVELOPMENT

Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation

(2011) Ute Schmidt et al.   JOURNAL OF CELL BIOLOGY

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli

(2011) A. Zeisel et al.   Molecular Systems Biology

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

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

Histone Deacetylase Activity Modulates Alternative Splicing

(2011) Jarmila Hnilicová et al.   PLoS One

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

The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells

(2010) Martina Huranová et al.   JOURNAL OF CELL BIOLOGY

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

Influence of secondary structure on recovery from pauses during early stages of RNA transcription

(2010) A. V. Klopper et al.   PHYSICAL REVIEW E

RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae

(2010) R. D. Alexander et al.   RNA

DNA Damage Regulates Alternative Splicing through Inhibition of RNA Polymerase II Elongation

(2009) Manuel J. Muñoz et al.   CELL

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

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

Rates of in situ transcription and splicing in large human genes

(2009) Jarnail Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

(2009) C. Hodges et al.   SCIENCE

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

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

A Single SR-like Protein, Npl3, Promotes Pre-mRNA Splicing in Budding Yeast

(2008) Tracy L. Kress et al.   MOLECULAR CELL