Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing

Determination of RNA structural diversity and its role in HIV-1 RNA splicing

(2020) Phillip J. Tomezsko et al.   NATURE

Structural disruption of exonic stem–loops immediately upstream of the intron regulates mammalian splicing

(2020) Kaushik Saha et al.   NUCLEIC ACIDS RESEARCH

RNA structure maps across mammalian cellular compartments

(2019) Lei Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nascent RNA and the Coordination of Splicing with Transcription

(2019) Karla M. Neugebauer   Cold Spring Harbor Perspectives in Biology

RNA base-pairing complexity in living cells visualized by correlated chemical probing

(2019) Anthony M. Mustoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling

(2018) Weijun Chen et al.   CELL

Transcription elongation rate affects nascent histone pre-mRNA folding and 3′ end processing

(2018) Tassa Saldi et al.   GENES & DEVELOPMENT

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

(2018) Lydia Herzel et al.   GENOME RESEARCH

An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys

(2018) Marilyn Parra et al.   RNA

Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5′ Pause Release, Termination, and Transcription Elongation Rate

(2018) Ryan M. Sheridan et al.   MOLECULAR CELL

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

(2017) Vahid Aslanzadeh et al.   GENOME RESEARCH

RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction

(2017) Nova Fong et al.   MOLECULAR CELL

RNA m6A methylation regulates the ultraviolet-induced DNA damage response

(2017) Yang Xiang et al.   NATURE

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

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

Group II Intron Self-Splicing

(2016) Anna Marie Pyle   Annual Review of Biophysics

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

(2016) Fernando Carrillo Oesterreich et al.   CELL

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation

(2016) J. Matthew Taliaferro et al.   MOLECULAR CELL

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure

(2016) Jinwei Zhang et al.   TRENDS IN BIOCHEMICAL SCIENCES

Diverse regulation of 3′ splice site usage

(2015) Muhammad Sohail et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

RNA structure replaces the need for U2AF2 in splicing

(2015) Chien-Ling Lin et al.   GENOME RESEARCH

Transcriptome-wide ribonuclease-mediated protein footprinting to identify RNA–protein interaction sites

(2015) Ian M. Silverman et al.   METHODS

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes of the Arabidopsis Nucleus

(2015) Sager J. Gosai et al.   MOLECULAR CELL

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

(2015) Zohar Zafrir et al.   RNA

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

Mechanisms for U2AF to define 3′ splice sites and regulate alternative splicing in the human genome

(2014) Changwei Shao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi et al.   BIOINFORMATICS

From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase II

(2013) Hannes Braberg et al.   CELL

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

(2013) Kathi Zarnack et al.   CELL

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

(2013) L. Bazak et al.   GENOME RESEARCH

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

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

Nascent-Seq Indicates Widespread Cotranscriptional RNA Editing in Drosophila

(2012) Joseph Rodriguez et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

HEXEvent: a database of Human EXon splicing Events

(2012) Anke Busch et al.   NUCLEIC ACIDS RESEARCH

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

(2012) F. Li et al.   PLANT CELL

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

RNA structure and the mechanisms of alternative splicing

(2011) C Joel McManus et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Deciphering 3′ss Selection in the Yeast Genome Reveals an RNA Thermosensor that Mediates Alternative Splicing

(2011) Markus Meyer et al.   MOLECULAR CELL

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

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

Intronic delay is essential for oscillatory expression in the segmentation clock

(2011) Y. Takashima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for widespread association of mammalian splicing and conserved long-range RNA structures

(2011) D. D. Pervouchine et al.   RNA

Predicting sites of ADAR editing in double-stranded RNA

(2011) Julie M. Eggington et al.   Nature Communications

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

(2010) J. Y. Ip et al.   GENOME RESEARCH

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

DNA Damage Regulates Alternative Splicing through Inhibition of RNA Polymerase II Elongation

(2009) Manuel J. Muñoz et al.   CELL

Modulation of alternative splicing by long-range RNA structures in Drosophila

(2009) Veronica A. Raker et al.   NUCLEIC ACIDS RESEARCH

Role of RNA structure in regulating pre-mRNA splicing

(2009) M. Bryan Warf et al.   TRENDS IN BIOCHEMICAL SCIENCES

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

(2009) Schraga Schwartz et al.   PLoS Computational Biology

Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae

(2008) Sanja Rogic et al.   BMC GENOMICS

Alternative splicing of Alu exons—two arms are better than one

(2008) Nurit Gal-Mark et al.   NUCLEIC ACIDS RESEARCH

Conserved RNA secondary structures promote alternative splicing

(2008) P. J. Shepard et al.   RNA