The upstream 5′ splice site remains associated to the transcription machinery during intron synthesis

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

(2021) Kirsten A. Reimer et al.   MOLECULAR CELL

Structure of a transcribing RNA polymerase II–U1 snRNP complex

(2021) Suyang Zhang et al.   SCIENCE

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

U1 snRNP regulates chromatin retention of noncoding RNAs

(2020) Yafei Yin et al.   NATURE

Global donor and acceptor splicing site kinetics in human cells

(2019) Leonhard Wachutka et al.   eLife

A unified mechanism for intron and exon definition and back-splicing

(2019) Xueni Li et al.   NATURE

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

(2019) Jernej Ule et al.   MOLECULAR CELL

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler et al.   MOLECULAR CELL

Integrating ChIP-seq with other functional genomics data

(2018) Shan Jiang et al.   Briefings in Functional Genomics

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

(2018) Lydia Herzel et al.   GENOME RESEARCH

Interactome analyses revealed that the U1 snRNP machinery overlaps extensively with the RNAP II machinery and contains multiple ALS/SMA-causative proteins

(2018) Binkai Chi et al.   Scientific Reports

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

(2018) Lorea Blazquez et al.   MOLECULAR CELL

Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity

(2018) Volker Boehm et al.   MOLECULAR CELL

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing

(2018) Takayuki Nojima et al.   MOLECULAR CELL

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

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

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

Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution

(2016) Ronen Sadeh et al.   MOLECULAR CELL

Global Mapping of Human RNA-RNA Interactions

(2016) Eesha Sharma et al.   MOLECULAR CELL

The Spliceosome: The Ultimate RNA Chaperone and Sculptor

(2016) Panagiotis Papasaikas et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2016) Dror Hollander et al.   TRENDS IN GENETICS

Perfect timing: splicing and transcription rates in living cells

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

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

Chromatin, DNA structure and alternative splicing

(2015) Nicolás Nieto Moreno et al.   FEBS LETTERS

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

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

SF3B1 Association with Chromatin Determines Splicing Outcomes

(2015) Nir Kfir et al.   Cell Reports

HP1 Is Involved in Regulating the Global Impact of DNA Methylation on Alternative Splicing

(2015) Ahuvi Yearim et al.   Cell Reports

bwtool: a tool for bigWig files

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Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

(2014) Jesse M. Engreitz et al.   CELL

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

(2014) Cem Kuscu et al.   NATURE BIOTECHNOLOGY

Insights into the U1 small nuclear ribonucleoprotein complex superfamily

(2014) J Guiro et al.   Wiley Interdisciplinary Reviews-RNA

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Pick one, but be quick: 5' splice sites and the problems of too many choices

(2013) X. Roca et al.   GENES & DEVELOPMENT

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

A Novel Intra-U1 snRNP Cross-Regulation Mechanism: Alternative Splicing Switch Links U1C and U1-70K Expression

(2013) Tanja Dorothe Rösel-Hillgärtner et al.   PLoS Genetics

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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(2012) Alexander Dobin et al.   BIOINFORMATICS

Origin and evolution of spliceosomal introns

(2012) Igor B Rogozin et al.   Biology Direct

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

Alternative splicing: decoding an expansive regulatory layer

(2012) Manuel Irimia et al.   CURRENT OPINION IN CELL BIOLOGY

The RNA polymerase II CTD coordinates transcription and RNA processing

(2012) J.-P. Hsin 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

(2012) Y. L. Khodor et al.   RNA

Exon and intron definition in pre-mRNA splicing

(2012) Laura De Conti et al.   Wiley Interdisciplinary Reviews-RNA

Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

(2011) S. Gelfman et al.   GENOME RESEARCH

The Genomic Signature of Splicing-Coupled Selection Differs between Long and Short Introns

(2011) A. Farlow et al.   MOLECULAR BIOLOGY AND EVOLUTION

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

(2011) Yehuda Brody et al.   PLOS BIOLOGY

Exon Definition Complexes Contain the Tri-snRNP and Can Be Directly Converted into B-like Precatalytic Splicing Complexes

(2010) Marc Schneider 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

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

Rates of in situ transcription and splicing in large human genes

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

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Co-transcriptional splicing of constitutive and alternative exons

(2009) A. Pandya-Jones et al.   RNA