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

Rbfox2 controls autoregulation in RNA-binding protein networks

(2014) M. Jangi et al.   GENES & DEVELOPMENT

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Identification of a BRCA1-mRNA Splicing Complex Required for Efficient DNA Repair and Maintenance of Genomic Stability

(2014) Kienan I. Savage et al.   MOLECULAR CELL

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

(2014) Reut Shalgi et al.   Cell Reports

Organizing Principles of Mammalian Nonsense-Mediated mRNA Decay

(2013) Maximilian Wei-Lin Popp et al.   Annual Review of Genetics

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

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

Regulation of splicing by SR proteins and SR protein-specific kinases

(2013) Zhihong Zhou et al.   CHROMOSOMA

Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery

(2013) M. Bezzi et al.   GENES & DEVELOPMENT

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

(2013) J. A. Hurt et al.   GENOME RESEARCH

Partitioning RS Domain Phosphorylation in an SR Protein through the CLK and SRPK Protein Kinases

(2013) Brandon E. Aubol et al.   JOURNAL OF MOLECULAR BIOLOGY

RNA splicing regulates the temporal order of TNF-induced gene expression

(2013) S. Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2012) Dev M. Bhatt et al.   CELL

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

(2012) K. Yap 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

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

(2012) L. Windhager et al.   GENOME RESEARCH

Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells

(2012) Mangmang Li et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

p53 is activated in response to disruption of the pre-mRNA splicing machinery

(2012) N Allende-Vega et al.   ONCOGENE

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

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

(2012) Minna-Liisa Änkö et al.   GENOME BIOLOGY

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

Specific CLK Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing

(2011) Oleg Fedorov et al.   CHEMISTRY & BIOLOGY

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

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

Multiple factors in the early splicing complex are involved in the nuclear retention of pre-mRNAs in mammalian cells

(2011) Reiko Takemura et al.   GENES TO CELLS

Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor

(2011) Kensuke Ninomiya et al.   JOURNAL OF CELL BIOLOGY

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

Interaction between the RNA binding domains of Ser-Arg splicing factor 1 and U1-70K snRNP protein determines early spliceosome assembly

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

Differential effect of CLK SR Kinases on HIV-1 gene expression: potential novel targets for therapy

(2011) Raymond Wong et al.   Retrovirology

Pre-mRNA splicing during transcription in the mammalian system

(2011) Amy Pandya-Jones   Wiley Interdisciplinary Reviews-RNA

Biology and prognosis by age of primary operable breast cancer.

(2010) O Brouckaert et al.   CANCER RESEARCH

Cdc2-like Kinase 2 Is an Insulin-Regulated Suppressor of Hepatic Gluconeogenesis

(2010) Joseph T. Rodgers et al.   Cell Metabolism

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

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

A role for TREX components in the release of spliced mRNA from nuclear speckle domains

(2010) Anusha P. Dias et al.   Nature Communications

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

(2009) Roberto Perales et al.   MOLECULAR CELL

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

(2009) Caroline C. Friedel et al.   NUCLEIC ACIDS RESEARCH

Co-transcriptional splicing of constitutive and alternative exons

(2009) A. Pandya-Jones et al.   RNA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Akt2 Regulation of Cdc2-Like Kinases (Clk/Sty), Serine/Arginine-Rich (SR) Protein Phosphorylation, and Insulin-Induced Alternative Splicing of PKCβII Messenger Ribonucleic Acid

(2008) Kun Jiang et al.   ENDOCRINOLOGY

Combination of Clk family kinase and SRp75 modulates alternative splicing of Adenovirus E1A

(2008) Jun-ichiro Yomoda et al.   GENES TO CELLS

Intron-3 Retention/Splicing Controls Neuronal Expression of Apolipoprotein E in the CNS

(2008) Q. Xu et al.   JOURNAL OF NEUROSCIENCE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS