RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

(2017) Carlo Baejen et al.   MOLECULAR CELL

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

(2016) Fernando Carrillo Oesterreich et al.   CELL

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

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

Transcription initiation complex structures elucidate DNA opening

(2016) C. Plaschka et al.   NATURE

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

(2015) Yongsheng Shi et al.   GENES & DEVELOPMENT

Structures and Functions of the Multiple KOW Domains of Transcription Elongation Factor Spt5

(2015) Peter A. Meyer et al.   MOLECULAR AND CELLULAR BIOLOGY

Molecular Basis of Transcription-Coupled Pre-mRNA Capping

(2015) Fuensanta W. Martinez-Rucobo et al.   MOLECULAR CELL

High-Resolution Chromatin Dynamics during a Yeast Stress Response

(2015) Assaf Weiner et al.   MOLECULAR CELL

Structural basis of transcription initiation by RNA polymerase II

(2015) Sarah Sainsbury et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a noncanonical CTD-interacting domain fold

(2015) Wolfgang Mühlbacher et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2015) Daoming Qin et al.   RNA

Transcriptome Maps of mRNP Biogenesis Factors Define Pre-mRNA Recognition

(2014) Carlo Baejen et al.   MOLECULAR CELL

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

(2014) Nils A Kulak et al.   NATURE METHODS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

Cap Completion and C-Terminal Repeat Domain Kinase Recruitment Underlie the Initiation-Elongation Transition of RNA Polymerase II

(2013) M. Lidschreiber et al.   MOLECULAR AND CELLULAR BIOLOGY

The Recruitment of theSaccharomyces cerevisiaePaf1 Complex to Active Genes Requires a Domain of Rtf1 That Directly Interacts with the Spt4-Spt5 Complex

(2013) Manasi K. Mayekar et al.   MOLECULAR AND CELLULAR BIOLOGY

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin

(2013) A. D. Wier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Pol II CTD kinases Bur1 and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex

(2012) Hongfang Qiu et al.   EMBO JOURNAL

The Yeast Cap Binding Complex Modulates Transcription Factor Recruitment and Establishes Proper Histone H3K36 Trimethylation during Active Transcription

(2012) M. A. Hossain et al.   MOLECULAR AND CELLULAR BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

(2012) S. Luehr et al.   NUCLEIC ACIDS RESEARCH

Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity

(2011) Fuensanta W Martinez-Rucobo et al.   EMBO JOURNAL

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

Cotranscriptional Association of mRNA Export Factor Yra1 with C-terminal Domain of RNA Polymerase II

(2011) April L. MacKellar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deciphering the RNA Polymerase II CTD Code in Fission Yeast

(2011) Beate Schwer et al.   MOLECULAR CELL

The Initiation Factor TFE and the Elongation Factor Spt4/5 Compete for the RNAP Clamp during Transcription Initiation and Elongation

(2011) Dina Grohmann et al.   MOLECULAR CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Leo1 Subunit of the Yeast Paf1 Complex Binds RNA and Contributes to Complex Recruitment

(2010) Jessica L. Dermody et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Tandem SH2 Domain in Transcription Elongation Factor Spt6 Binds the Phosphorylated RNA Polymerase II C-terminal Repeat Domain (CTD)

(2010) Mai Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Uniform transitions of the general RNA polymerase II transcription complex

(2010) Andreas Mayer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA polymerase and transcription elongation factor Spt4/5 complex structure

(2010) B. J. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex

(2010) A. Missra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

(2010) Markus Hafner et al.   Jove-Journal of Visualized Experiments

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cotranslational assembly of the yeast SET1C histone methyltransferase complex

(2009) André Halbach et al.   EMBO JOURNAL

Structure and in Vivo Requirement of the Yeast Spt6 SH2 Domain

(2009) Stefan Dengl et al.   JOURNAL OF MOLECULAR BIOLOGY

Phosphorylation of the Transcription Elongation Factor Spt5 by Yeast Bur1 Kinase Stimulates Recruitment of the PAF Complex

(2009) Y. Liu et al.   MOLECULAR AND CELLULAR BIOLOGY

Phosphorylation of the Pol II CTD by KIN28 Enhances BUR1/BUR2 Recruitment and Ser2 CTD Phosphorylation Near Promoters

(2009) Hongfang Qiu et al.   MOLECULAR CELL

“Cotranscriptionality”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions

(2009) Roberto Perales et al.   MOLECULAR CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5

(2009) K. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Structure and DNA Binding of the Human Rtf1 Plus3 Domain

(2008) Rob N. de Jong et al.   STRUCTURE