Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

RNA–DNA and DNA–DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate

(2018) Maria KIreeva et al.   NUCLEIC ACIDS RESEARCH

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

(2017) Carrie Bernecky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of the complete elongation complex of RNA polymerase II with basal factors

(2017) Haruhiko Ehara et al.   SCIENCE

Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation

(2017) S. Branden Van Oss et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

(2017) Carrie Bernecky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2017) Sofia Battaglia et al.   eLife

A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription

(2017) Matthew A Sdano et al.   eLife

P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates

(2016) Miriam Sansó et al.   GENES & DEVELOPMENT

Gctf: Real-time CTF determination and correction

(2016) Kai Zhang   JOURNAL OF STRUCTURAL BIOLOGY

Near-atomic resolution visualization of human transcription promoter opening

(2016) Yuan He et al.   NATURE

Six alternative proteases for mass spectrometry–based proteomics beyond trypsin

(2016) Piero Giansanti et al.   Nature Protocols

Multiple P-TEFbs cooperatively regulate the release of promoter-proximally paused RNA polymerase II

(2016) Xiaodong Lu et al.   NUCLEIC ACIDS RESEARCH

NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

(2016) Matti Turtola et al.   eLife

Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

(2016) Dari Kimanius et al.   eLife

PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II

(2015) Fei Xavier Chen et al.   CELL

Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures

(2015) Jan Kosinski et al.   JOURNAL OF STRUCTURAL BIOLOGY

xiNET: Cross-link Network Maps With Residue Resolution

(2015) Colin W. Combe et al.   MOLECULAR & CELLULAR PROTEOMICS

Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex

(2015) Qing-Fu Cao et al.   MOLECULAR AND CELLULAR BIOLOGY

Architecture of the RNA polymerase II–Mediator core initiation complex

(2015) C. Plaschka et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

RNA polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II

(2015) M. Yu et al.   SCIENCE

Rpb4 Subunit Functions Mainly in mRNA Synthesis by RNA Polymerase II

(2014) Daniel Schulz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   SCIENCE

D3, the new diffractometer for the macromolecular crystallography beamlines of the Swiss Light Source

(2014) Martin R. Fuchs et al.   JOURNAL OF SYNCHROTRON RADIATION

The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex

(2013) Felix Halbach et al.   CELL

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Scalable web services for the PSIPRED Protein Analysis Workbench

(2013) Daniel W. A. Buchan et al.   NUCLEIC ACIDS RESEARCH

A feed forward circuit comprising Spt6, Ctk1 and PAF regulates Pol II CTD phosphorylation and transcription elongation

(2013) R. Dronamraju et al.   NUCLEIC ACIDS RESEARCH

Cdc73 Subunit of Paf1 Complex Contains C-terminal Ras-like Domain That Promotes Association of Paf1 Complex with Chromatin

(2012) Christopher G. Amrich et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Identification of cross-linked peptides from complex samples

(2012) Bing Yang et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Crystal Structures of the S. cerevisiae Spt6 Core and C-Terminal Tandem SH2 Domain

(2011) Devin Close et al.   JOURNAL OF MOLECULAR BIOLOGY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Structure and function of WD40 domain proteins

(2011) Chao Xu et al.   Protein & Cell

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Human PAF1 Complex Acts in Chromatin Transcription Elongation Both Independently and Cooperatively with SII/TFIIS

(2010) Jaehoon Kim et al.   CELL

Noncanonical Tandem SH2 Enables Interaction of Elongation Factor Spt6 with RNA Polymerase II

(2010) Marie-Laure Diebold 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

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Spt6 enhances the elongation rate of RNA polymerase II in vivo

(2009) M Behfar Ardehali et al.   EMBO JOURNAL

DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation

(2009) Y. Chen et al.   GENES & DEVELOPMENT

SLP-65 Phosphorylation Dynamics Reveals a Functional Basis for Signal Integration by Receptor-proximal Adaptor Proteins

(2009) Thomas Oellerich et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused RNA Polymerase II with Frayed RNA

(2009) Jasmin F. Sydow et al.   MOLECULAR CELL

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 Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation

(2008) S. M. Yoh et al.   GENES & DEVELOPMENT

Genome-associated RNA Polymerase II Includes the Dissociable Rpb4/7 Subcomplex

(2008) Anna J. Jasiak et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE