Chromatin’s thread to alternative splicing regulation

Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

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

(2013) Xiong Ji et al.   CELL

Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression

(2013) J. M. Taliaferro et al.   GENES & DEVELOPMENT

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure

(2013) S. Gelfman et al.   GENOME RESEARCH

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Alternative splicing: a pivotal step between eukaryotic transcription and translation

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

Pre-mRNA Splicing Is a Determinant of Nucleosome Organization

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

Reflections on the history of pre-mRNA processing and highlights of current knowledge: A unified picture

(2013) J. E. Darnell   RNA

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

(2013) H. Kwak et al.   SCIENCE

Co-transcriptional regulation of alternative pre-mRNA splicing

(2012) Sanjeev Shukla et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Function of alternative splicing

(2012) Olga Kelemen et al.   GENE

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

CBX3 regulates efficient RNA processing genome-wide

(2012) A. Smallwood et al.   GENOME RESEARCH

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

(2012) Pierre Close et al.   NATURE

The spliceosome as a target of novel antitumour drugs

(2012) Sophie Bonnal et al.   NATURE REVIEWS DRUG DISCOVERY

5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary

(2012) Tarang Khare et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Argonaute proteins couple chromatin silencing to alternative splicing

(2012) Maya Ameyar-Zazoua et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

(2012) Y. L. Khodor et al.   RNA

Design principles of interconnections between chromatin and pre-mRNA splicing

(2012) Sérgio F. de Almeida et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing

(2012) Madapura M. Pradeepa 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

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

PNAS-4 expression and its relationship to p53 in colorectal cancer

(2011) Bin Zhou et al.   MOLECULAR BIOLOGY REPORTS

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

(2011) Sanjeev Shukla et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes

(2011) Sandra Bento Martins et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André 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

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

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

(2010) Satu Nahkuri et al.   CELL CYCLE

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

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

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

(2010) Pawandeep Dhami et al.   PLoS One

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

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

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

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

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

(2009) E. Hodges et al.   GENOME RESEARCH

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

SR Proteins in Vertical Integration of Gene Expression from Transcription to RNA Processing to Translation

(2009) Xiang-Yang Zhong et al.   MOLECULAR CELL

Chromatin Binding of SRp20 and ASF/SF2 and Dissociation from Mitotic Chromosomes Is Modulated by Histone H3 Serine 10 Phosphorylation

(2009) Rebecca J. Loomis 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

Control of alternative splicing through siRNA-mediated transcriptional gene silencing

(2009) Mariano Alló 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

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

7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development

(2009) M. Barboric et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A human B cell methylome at 100−base pair resolution

(2009) Tibor A. Rauch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-transcriptional splicing of constitutive and alternative exons

(2009) A. Pandya-Jones et al.   RNA

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

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

Foxn1 is required to maintain the postnatal thymic microenvironment in a dosage-sensitive manner

(2008) L. Chen et al.   BLOOD

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

The splicing factor SC35 has an active role in transcriptional elongation

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

Alteration of cyclin D1 transcript elongation by a mutated transcription factor up-regulates the oncogenic D1b splice isoform in cancer

(2008) G. Sanchez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

(2008) Z. Wang et al.   RNA