Nutrient-dependent control of RNA polymerase II elongation rate regulates specific gene expression programs by alternative polyadenylation

iREAD: a tool for intron retention detection from RNA-seq data

(2020) Hong-Dong Li et al.   BMC GENOMICS

Short-Homology-Mediated CRISPR/Cas9-Based Method for Genome Editing in Fission Yeast

(2019) Aki Hayashi et al.   G3-Genes Genomes Genetics

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

(2019) Jason N. Kuehner et al.   MOLECULAR CELL

Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism

(2019) Michael A. Cortazar et al.   MOLECULAR CELL

Repression of Cell Differentiation by a cis -Acting lincRNA in Fission Yeast

(2018) Sylvain Fauquenoy et al.   CURRENT BIOLOGY

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

(2018) Tassa Saldi et al.   GENES & DEVELOPMENT

Polymerase pausing induced by sequence-specific RNA-binding protein drives heterochromatin assembly

(2018) Jahan-Yar Parsa et al.   GENES & DEVELOPMENT

A long noncoding (lnc)RNA governs expression of the phosphate transporter Pho84 in fission yeast and has cascading effects on the flankingprtlncRNA andpho1genes

(2018) Angad Garg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Emerging Roles of Non-Coding RNA Transcription

(2018) Minna U. Kaikkonen et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

RNA polymerase II CTD interactome with 3′ processing and termination factors in fission yeast and its impact on phosphate homeostasis

(2018) Ana M. Sanchez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast

(2018) Marc Larochelle et al.   Nature Communications

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

(2017) Vahid Aslanzadeh et al.   GENOME RESEARCH

Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe

(2017) Xiaochuan Liu et al.   GENOME RESEARCH

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster

(2017) Xiaochuan Liu et al.   RNA

Poly(A) site choice and Pol2 CTD Serine-5 status govern lncRNA control of phosphate-responsive tgp1 gene expression in fission yeast

(2017) Ana M. Sanchez et al.   RNA

Architecture of eukaryotic mRNA 3′-end processing machinery

(2017) Ana Casañal et al.   SCIENCE

Defining the DNA Binding Site Recognized by the Fission Yeast Zn 2 Cys 6 Transcription Factor Pho7 and Its Role in Phosphate Homeostasis

(2017) Beate Schwer et al.   mBio

Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation

(2017) Adrien Chauvier et al.   Nature Communications

The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA

(2017) Sina Wittmann et al.   Nature Communications

The Nrd1-like protein Seb1 coordinates cotranscriptional 3′ end processing and polyadenylation site selection

(2016) Jean-François Lemay et al.   GENES & DEVELOPMENT

Alternative polyadenylation of mRNA precursors

(2016) Bin Tian et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference

(2016) Ryan Ard et al.   NUCLEIC ACIDS RESEARCH

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Evolution and Biological Roles of Alternative 3′UTRs

(2016) Christine Mayr   TRENDS IN CELL BIOLOGY

Transcription Termination: Variations on Common Themes

(2016) Odil Porrua et al.   TRENDS IN GENETICS

Use of a fluoride channel as a new selection marker for fission yeast plasmids and application to fast genome editing with CRISPR/Cas9

(2016) Ronan Fernandez et al.   YEAST

The pol II CTD: new twists in the tail

(2016) Justyna Zaborowska et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

(2015) Nova Fong et al.   MOLECULAR CELL

AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast

(2015) Danny A. Bitton et al.   Frontiers in Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Dissection of the PHO pathway in Schizosaccharomyces pombe using epistasis and the alternate repressor adenine

(2014) Molly Estill et al.   CURRENT GENETICS

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

lncRNA recruits RNAi and the exosome to dynamically regulate pho1 expression in response to phosphate levels in fission yeast

(2014) S. Shah et al.   GENES & DEVELOPMENT

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

The RNA exosome promotes transcription termination of backtracked RNA polymerase II

(2014) Jean-François Lemay et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long non-coding RNA-mediated transcriptional interference of a permease gene confers drug tolerance in fission yeast

(2014) Ryan Ard et al.   Nature Communications

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

(2014) Iris Jonkers et al.   eLife

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe

(2012) Ian Carter-O’Connell et al.   BMC GENOMICS

One step back before moving forward: Regulation of transcription elongation by arrest and backtracking

(2012) Fernando Gómez-Herreros et al.   FEBS LETTERS

Regulation of Amino Acid, Nucleotide, and Phosphate Metabolism in Saccharomyces cerevisiae

(2012) P. O. Ljungdahl et al.   GENETICS

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

(2012) M. Sun et al.   GENOME RESEARCH

The Fidelity of Transcription

(2012) Jeffrey Strathern et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Kinetic Competition between RNA Polymerase II and Sen1-Dependent Transcription Termination

(2012) Dane Z. Hazelbaker et al.   MOLECULAR CELL

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

RNA polymerase II kinetics inpolopolyadenylation signal selection

(2011) Pedro A B Pinto et al.   EMBO JOURNAL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

The Yeast 5′-3′ Exonuclease Rat1p Functions during Transcription Elongation by RNA Polymerase II

(2010) Silvia Jimeno-González et al.   MOLECULAR CELL

Splicing-Dependent RNA Polymerase Pausing in Yeast

(2010) Ross D. Alexander et al.   MOLECULAR CELL

Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain

(2010) Bradley M Lunde et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations

(2009) Viktor M. Boer et al.   MOLECULAR BIOLOGY OF THE CELL

Key Function for the CCAAT-Binding Factor Php4 To Regulate Gene Expression in Response to Iron Deficiency in Fission Yeast

(2008) Alexandre Mercier et al.   EUKARYOTIC CELL

Futile Cycle of Transcription Initiation and Termination Modulates the Response to Nucleotide Shortage in S. cerevisiae

(2008) Marilyne Thiebaut et al.   MOLECULAR CELL

Co-regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations

(2008) Sébastien Gauthier et al.   MOLECULAR MICROBIOLOGY

Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs

(2008) Kouji Hirota et al.   NATURE