Intron retention as a component of regulated gene expression programs

A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages

(2016) C. R. Edwards et al.   BLOOD

Intron retention resulting from a silent mutation in the VWF gene that structurally influences the 5' splice site

(2016) H. Yadegari et al.   BLOOD

The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress

(2016) Jessica Tsalikis et al.   BMC GENOMICS

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

(2016) Xinping Yang et al.   CELL

Preferential binding of a stable G3BP ribonucleoprotein complex to intron-retaining transcripts in mouse brain and modulation of their expression in the cerebellum

(2016) Sophie Martin et al.   JOURNAL OF NEUROCHEMISTRY

Cryptic splicing events in the iron transporter ABCB7 and other key target genes in SF3B1-mutant myelodysplastic syndromes

(2016) H Dolatshad et al.   LEUKEMIA

An NXF1 mRNA with a retained intron is expressed in hippocampal and neocortical neurons and is translated into a protein that functions as an Nxf1 cofactor

(2016) Ying Li et al.   MOLECULAR BIOLOGY OF THE CELL

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Targeted Intron Retention and Excision for Rapid Gene Regulation in Response to Neuronal Activity

(2016) Oriane Mauger et al.   NEURON

The bromodomain protein BRD4 regulates splicing during heat shock

(2016) Michelle Hussong et al.   NUCLEIC ACIDS RESEARCH

The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

(2016) Miriam Llorian et al.   NUCLEIC ACIDS RESEARCH

Global intron retention mediated gene regulation during CD4+T cell activation

(2016) Ting Ni et al.   NUCLEIC ACIDS RESEARCH

An Ultraconserved Element (UCE) controls homeostatic splicing of ARGLU1 mRNA

(2016) Stephan P. Pirnie et al.   NUCLEIC ACIDS RESEARCH

Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2

(2016) Soroush Tahmasebi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation

(2016) Julie Rodor et al.   RNA

Splicing-factor alterations in cancers

(2016) Olga Anczuków et al.   RNA

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Antisense Oligonucleotides Modulating Activation of a Nonsense-Mediated RNA Decay Switch Exon in theATMGene

(2016) Jana Kralovicova et al.   Nucleic Acid Therapeutics

A new view of transcriptome complexity and regulation through the lens of local splicing variations

(2016) Jorge Vaquero-Garcia et al.   eLife

Hypoxia-driven splicing into noncoding isoforms regulates the DNA damage response

(2016) Danish Memon et al.   npj Genomic Medicine

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

(2015) Shiran Naftelberg et al.   Annual Review of Biochemistry

Intron retention in mRNA: No longer nonsense

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

Biochemical identification of new proteins involved in splicing repression at theDrosophilaP-element exonic splicing silencer

(2015) Lucas Horan et al.   GENES & DEVELOPMENT

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

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

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity

(2015) Yamile Marquez et al.   GENOME RESEARCH

Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

(2015) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

Regulated Intron Retention and Nuclear Pre-mRNA Decay Contribute toPABPN1Autoregulation

(2015) Danny Bergeron et al.   MOLECULAR AND CELLULAR BIOLOGY

Functional Splicing Network Reveals Extensive Regulatory Potential of the Core Spliceosomal Machinery

(2015) Panagiotis Papasaikas et al.   MOLECULAR CELL

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

(2015) Harrison W. Gabel et al.   NATURE

Recursive splicing in long vertebrate genes

(2015) Christopher R. Sibley et al.   NATURE

The spliceosome is a therapeutic vulnerability in MYC-driven cancer

(2015) Tiffany Y.-T. Hsu et al.   NATURE

Intron retention is a widespread mechanism of tumor-suppressor inactivation

(2015) Hyunchul Jung et al.   NATURE GENETICS

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

(2015) Harold Pimentel et al.   NUCLEIC ACIDS RESEARCH

Epigenetic and transcriptional determinants of the human breast

(2015) Philippe Gascard et al.   Nature Communications

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

Building Robust Transcriptomes with Master Splicing Factors

(2014) Mohini Jangi et al.   CELL

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

Lipopolysaccharide Is a Direct Agonist for Platelet RNA Splicing

(2014) P. N. Shashkin et al.   JOURNAL OF IMMUNOLOGY

BS69/ZMYND11 Reads and Connects Histone H3.3 Lysine 36 Trimethylation-Decorated Chromatin to Regulated Pre-mRNA Processing

(2014) Rui Guo et al.   MOLECULAR CELL

Context-dependent control of alternative splicing by RNA-binding proteins

(2014) Xiang-Dong Fu et al.   NATURE REVIEWS GENETICS

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis

(2014) Harold Pimentel et al.   NUCLEIC ACIDS RESEARCH

Optimal antisense target reducingINSintron 1 retention is adjacent to a parallel G quadruplex

(2014) Jana Kralovicova et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Reut Shalgi et al.   Cell Reports

The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA

(2014) Vicky Cho et al.   GENOME BIOLOGY

The functional consequences of intron retention: Alternative splicing coupled to NMD as a regulator of gene expression

(2013) Ying Ge et al.   BIOESSAYS

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

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

Regulation of Axon Guidance by Compartmentalized Nonsense-Mediated mRNA Decay

(2013) Dilek Colak et al.   CELL

Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW

(2013) A. Graindorge et al.   GENES & DEVELOPMENT

Frac-seq reveals isoform-specific recruitment to polyribosomes

(2013) T. Sterne-Weiler et al.   GENOME RESEARCH

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

Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis

(2013) Peter T. Buckley et al.   Wiley Interdisciplinary Reviews-RNA

Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2

(2012) Niroshika Keppetipola et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

(2012) Marija Buljan et al.   MOLECULAR CELL

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Alternative splicing in plants – coming of age

(2012) Naeem H. Syed et al.   TRENDS IN PLANT SCIENCE

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

(2012) Maayan Amit et al.   Cell Reports

Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

(2012) Joachim Weischenfeldt et al.   GENOME BIOLOGY

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

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

U1 snRNA Directly Interacts with Polypyrimidine Tract-Binding Protein during Splicing Repression

(2011) Shalini Sharma et al.   MOLECULAR CELL

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Pioneer Round of Translation: Features and Functions

(2010) Lynne E. Maquat et al.   CELL

Sam68 regulates EMT through alternative splicing–activated nonsense-mediated mRNA decay of the SF2/ASF proto-oncogene

(2010) Cristina Valacca et al.   JOURNAL OF CELL BIOLOGY

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

SF2/ASF autoregulation involves multiple layers of post-transcriptional and translational control

(2010) Shuying Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Intron retention facilitates splice variant diversity in calcium-activated big potassium channel populations

(2010) T. J. Bell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear Stress Bodies

(2010) G. Biamonti et al.   Cold Spring Harbor Perspectives in Biology

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

(2009) Mo Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Co-transcriptional splicing of constitutive and alternative exons

(2009) A. Pandya-Jones et al.   RNA

Cellular stress and RNA splicing

(2009) Giuseppe Biamonti et al.   TRENDS IN BIOCHEMICAL SCIENCES

Altered splicing in exon 8 of the DNA replication factor CIZ1 affects subnuclear distribution and is associated with Alzheimer's disease

(2008) Christina Mackeprang Dahmcke et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Alternative Splicing of the Robo3 Axon Guidance Receptor Governs the Midline Switch from Attraction to Repulsion

(2008) Zhe Chen et al.   NEURON

Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?

(2008) Nicholas J. McGlincy et al.   TRENDS IN BIOCHEMICAL SCIENCES