Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress

RNA interactome capture in yeast

(2017) Benedikt M. Beckmann   METHODS

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

(2016) Laura Milligan et al.   Molecular Systems Biology

irCLIP platform for efficient characterization of protein–RNA interactions

(2016) Brian J Zarnegar et al.   NATURE METHODS

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Functions of Ribosomal Proteins in Assembly of Eukaryotic Ribosomes In Vivo

(2015) Jesús de la Cruz et al.   Annual Review of Biochemistry

Transcription termination and the control of the transcriptome: why, where and how to stop

(2015) Odil Porrua et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

(2015) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli

(2014) Jai J. Tree et al.   MOLECULAR CELL

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress

(2014) Samuel Marguerat et al.   RNA Biology

Dissecting noncoding and pathogen RNA–protein interactomes

(2014) Ryan A. Flynn et al.   RNA

Genome-Wide Mapping of Yeast RNA Polymerase II Termination

(2014) Paul Schaughency et al.   PLoS Genetics

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast

(2014) Shaun Webb et al.   GENOME BIOLOGY

A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs

(2013) Alex Charles Tuck et al.   CELL

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

(2013) Daniel Schulz et al.   CELL

RNAi function, diversity, and loss in the fungal kingdom

(2013) R. Blake Billmyre et al.   CHROMOSOME RESEARCH

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Complex Degradation Processes Lead to Non-Exponential Decay Patterns and Age-Dependent Decay Rates of Messenger RNA

(2013) Carlus Deneke et al.   PLoS One

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

Set3 HDAC Mediates Effects of Overlapping Noncoding Transcription on Gene Induction Kinetics

(2012) TaeSoo Kim et al.   CELL

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

The Saccharomyces cerevisiae Nrd1-Nab3 Transcription Termination Pathway Acts in Opposition to Ras Signaling and Mediates Response to Nutrient Depletion

(2012) M. M. Darby et al.   MOLECULAR AND CELLULAR BIOLOGY

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

Genome-wide studies of mRNA synthesis and degradation in eukaryotes

(2011) José E. Pérez-Ortín et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

(2011) Wiebke Wlotzka et al.   EMBO JOURNAL

A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease

(2011) Sander Granneman et al.   EMBO JOURNAL

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

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing

(2011) N. Jamonnak et al.   RNA

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Gene-specific RNA polymerase II phosphorylation and the CTD code

(2010) Hyunmin Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

(2010) Moran Yassour et al.   GENOME BIOLOGY

Transposable elements: powerful facilitators of evolution

(2009) Keith R. Oliver et al.   BIOESSAYS

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

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

Regulation of a Eukaryotic Gene by GTP-Dependent Start Site Selection and Transcription Attenuation

(2008) Jason N. Kuehner et al.   MOLECULAR CELL

The Anchor-Away Technique: Rapid, Conditional Establishment of Yeast Mutant Phenotypes

(2008) Hirohito Haruki et al.   MOLECULAR CELL

Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice

(2008) Rajani Kanth Gudipati et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain

(2008) Lidia Vasiljeva et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY