Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

Statistical modeling of isoform splicing dynamics from RNA-seq time series data

(2016) Yuanhua Huang et al.   BIOINFORMATICS

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

(2016) Fernando Carrillo Oesterreich et al.   CELL

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae

(2016) K. B. Hooks et al.   GENETICS

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

(2016) Tassa Saldi et al.   JOURNAL OF MOLECULAR BIOLOGY

Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin

(2016) Wai Kit Ma et al.   JOURNAL OF MOLECULAR BIOLOGY

Strand‐specific, high‐resolution mapping of modified RNA polymerase II

(2016) Laura Milligan et al.   Molecular Systems Biology

Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

(2016) P. Eser et al.   Molecular Systems Biology

Real-time selective sequencing using nanopore technology

(2016) Matthew Loose et al.   NATURE METHODS

Genome-wide quantification of 5′-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics

(2016) Vicent Pelechano et al.   Nature Protocols

Introns regulate the production of ribosomal proteins by modulating splicing of duplicated ribosomal protein genes

(2016) Cyrielle Petibon et al.   NUCLEIC ACIDS RESEARCH

Identification of new branch points and unconventional introns inSaccharomyces cerevisiae

(2016) Genevieve M. Gould et al.   RNA

Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

(2016) Kevin M. Harlen et al.   Cell Reports

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

(2016) David E. Weinberg et al.   Cell Reports

Perfect timing: splicing and transcription rates in living cells

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

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

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

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

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

(2015) Takayuki Nojima et al.   CELL

Sequencing of lariat termini inS. cerevisiaereveals 5′ splice sites, branch points, and novel splicing events

(2015) Daoming Qin et al.   RNA

Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast

(2015) Gábor Csárdi et al.   PLoS Genetics

Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast

(2015) Jeffrey A. Hussmann et al.   PLoS Genetics

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

(2014) Britta Knight et al.   GENES & DEVELOPMENT

A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation

(2014) Keerthi T. Chathoth et al.   MOLECULAR CELL

Genome-Wide Mapping of Yeast RNA Polymerase II Termination

(2014) Paul Schaughency et al.   PLoS Genetics

The DEAD-box Protein Dbp2 Functions with the RNA-Binding Protein Yra1 to Promote mRNP Assembly

(2013) Wai Kit Ma et al.   JOURNAL OF MOLECULAR BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

(2012) Y. L. Khodor et al.   RNA

Introns within Ribosomal Protein Genes Regulate the Production and Function of Yeast Ribosomes

(2011) Julie Parenteau et al.   CELL

Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

(2011) Sarah E. Munchel et al.   MOLECULAR BIOLOGY OF THE CELL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Diverse environmental stresses elicit distinct responses at the level of pre-mRNA processing in yeast

(2011) M. Bergkessel et al.   RNA

Cross-talk in transcription, splicing and chromatin: who makes the first call?

(2010) Ross Alexander et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

HITS-CLIP: panoramic views of protein-RNA regulation in living cells

(2010) Robert B. Darnell   Wiley Interdisciplinary Reviews-RNA

Growth control and ribosome biogenesis

(2009) Harri Lempiäinen et al.   CURRENT OPINION IN CELL BIOLOGY

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

(2009) S. Granneman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

L30 Binds the Nascent RPL30 Transcript to Repress U2 snRNP Recruitment

(2008) Sara Macías et al.   MOLECULAR CELL

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY