Long-read sequencing of nascent RNA reveals coupling among RNA processing events

Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution

(2018) Jordan E. Burke et al.   CELL

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

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

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

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

(2017) Hagen Tilgner et al.   GENOME RESEARCH

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

Widespread intra-dependencies in the removal of introns from human transcripts

(2017) Seong Won Kim et al.   NUCLEIC ACIDS RESEARCH

Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

(2017) Anna Vilborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

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

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

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

Control of Gene Expression in Senescence through Transcriptional Read-Through of Convergent Protein-Coding Genes

(2017) Lisa Muniz et al.   Cell Reports

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

(2016) Fernando Carrillo Oesterreich et al.   CELL

The power of fission: yeast as a tool for understanding complex splicing

(2016) Benjamin Jung Fair et al.   CURRENT GENETICS

The dynamic landscape of fission yeast meiosis alternative-splice isoforms

(2016) Zheng Kuang et al.   GENOME RESEARCH

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

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

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

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

The regulation and functions of the nuclear RNA exosome complex

(2016) Cornelia Kilchert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

(2016) Maliheh Movassat et al.   RNA Biology

The Meaning of NMD: Translate or Perish

(2016) Saverio Brogna et al.   TRENDS IN GENETICS

Perfect timing: splicing and transcription rates in living cells

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

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Intron retention in mRNA: No longer nonsense

(2015) Justin J.-L. Wong et al.   BIOESSAYS

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

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

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

Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast

(2015) Danny A. Bitton et al.   GENOME RESEARCH

Quantification of co-transcriptional splicing from RNA-Seq data

(2015) Lydia Herzel et al.   METHODS

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

(2015) Hagen Tilgner et al.   NATURE BIOTECHNOLOGY

SR protein kinases promote splicing of nonconsensus introns

(2015) Jesse J Lipp et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The fission yeast MTREC complex targets CUTs and unspliced pre-mRNAs to the nuclear exosome

(2015) Yang Zhou et al.   Nature Communications

SR protein kinases promote splicing of nonconsensus introns

(2015) Jesse J Lipp et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

(2014) Nova Fong et al.   GENES & DEVELOPMENT

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

The translational landscape of fission-yeast meiosis and sporulation

(2014) Caia D S Duncan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Quantification of pre-mRNA escape rate and synergy in splicing

(2014) Marie Mi Bonde et al.   NUCLEIC ACIDS RESEARCH

Endogenous U2{middle dot}U5{middle dot}U6 snRNA complexes in S. pombe are intron lariat spliceosomes

(2014) W. Chen et al.   RNA

A global non-coding RNA system modulates fission yeast protein levels in response to stress

(2014) Hui Sun Leong et al.   Nature Communications

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

(2014) Reut Shalgi et al.   Cell Reports

Competition between Pre-mRNAs for the Splicing Machinery Drives Global Regulation of Splicing

(2013) Elizabeth M. Munding et al.   MOLECULAR CELL

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Co-transcriptional degradation of aberrant pre-mRNA by Xrn2

(2012) Lee Davidson et al.   EMBO JOURNAL

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

NMD: a multifaceted response to premature translational termination

(2012) Stephanie Kervestin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang et al.   NUCLEIC ACIDS RESEARCH

Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing

(2012) Anita Nag et al.   RNA Biology

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

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

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

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

A U1-U2 snRNP Interaction Network during Intron Definition

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

Intragenic alternative splicing coordination is essential for Caenorhabditis elegans slo-1 gene function

(2011) D. A. Glauser 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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genomic mRNA Profiling Reveals Compensatory Mechanisms for the Requirement of the Essential Splicing Factor U2AF

(2010) V. Sridharan et al.   MOLECULAR AND CELLULAR BIOLOGY

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

(2010) Fernando Carrillo Oesterreich et al.   MOLECULAR CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

First come, first served revisited: Factors affecting the same alternative splicing event have different effects on the relative rates of intron removal

(2010) M. de la Mata et al.   RNA

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

Retention of spliceosomal components along ligated exons ensures efficient removal of multiple introns

(2010) T. L. Crabb et al.   RNA

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

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

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

The Evolutionarily Conserved Core Design of the Catalytic Activation Step of the Yeast Spliceosome

(2009) Patrizia Fabrizio et al.   MOLECULAR CELL

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

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

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE