Allosteric transcription stimulation by RNA polymerase II super elongation complex

Acute perturbation strategies in interrogating RNA polymerase II elongation factor function in gene expression

(2021) Bin Zheng et al.   GENES & DEVELOPMENT

Structural and functional insight into the effect of AFF4 dimerization on activation of HIV-1 proviral transcription

(2020) Dan Tang et al.   Cell Discovery

Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation

(2020) Seychelle M. Vos et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure of the super-elongation complex subunit AFF4 C-terminal homology domain reveals requirements for AFF homo- and heterodimerization

(2019) Ying Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural basis of TFIIH activation for nucleotide excision repair

(2019) Goran Kokic et al.   Nature Communications

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

(2019) Zhen-Lin Chen et al.   Nature Communications

Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

(2019) Rune Thomas Kidmose et al.   IUCrJ

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

DALI and the persistence of protein shape

(2019) Liisa Holm   PROTEIN SCIENCE

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Real-space refinement in PHENIX for cryo-EM and crystallography

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

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

(2018) Seychelle M. Vos et al.   NATURE

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani 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

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Structural basis for ELL2 and AFF4 activation of HIV-1 proviral transcription

(2017) Shiqian Qi et al.   Nature Communications

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 transcribing mammalian RNA polymerase II

(2016) Carrie Bernecky et al.   NATURE

Near-atomic resolution visualization of human transcription promoter opening

(2016) Yuan He et al.   NATURE

Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb

(2016) Alexandre J. C. Quaresma et al.   NUCLEIC ACIDS RESEARCH

Architecture and RNA binding of the human negative elongation factor

(2016) Seychelle M Vos et al.   eLife

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

(2016) Ursula Schulze-Gahmen et al.   eLife

Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide

(2015) Fei Chen et al.   GENES & DEVELOPMENT

xiNET: Cross-link Network Maps With Residue Resolution

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

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

AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation

(2014) Yuanyuan Li et al.   CELL

Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4

(2014) Jianyou Gu et al.   CELL CYCLE

Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation

(2014) Friederike Itzen et al.   NUCLEIC ACIDS RESEARCH

A series of PDB-related databanks for everyday needs

(2014) Wouter G. Touw et al.   NUCLEIC ACIDS RESEARCH

Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms

(2014) V. Schweikhard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter

(2014) Ursula Schulze-Gahmen et al.   eLife

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

(2014) Iris Jonkers et al.   eLife

Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals

(2013) Telmo Henriques et al.   MOLECULAR CELL

Structural insights into Paf1 complex assembly and histone binding

(2013) Xinlei Chu et al.   NUCLEIC ACIDS RESEARCH

AFF1 is a ubiquitous P-TEFb partner to enable Tat extraction of P-TEFb from 7SK snRNP and formation of SECs for HIV transactivation

(2013) H. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat

(2013) Ursula Schulze-Gahmen et al.   eLife

The Super Elongation Complex Family of RNA Polymerase II Elongation Factors: Gene Target Specificity and Transcriptional Output

(2012) Z. Luo et al.   MOLECULAR AND CELLULAR BIOLOGY

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex

(2012) Sarah Sainsbury et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

The super elongation complex (SEC) family in transcriptional control

(2012) Zhuojuan Luo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold

(2012) S. Chou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Leukemia Fusion Target AF9 Is an Intrinsically Disordered Transcriptional Regulator that Recruits Multiple Partners via Coupled Folding and Binding

(2012) Benjamin I. Leach et al.   STRUCTURE

Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC)

(2011) C. Lin et al.   GENES & DEVELOPMENT

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

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

A Higher-Order Complex Containing AF4 and ENL Family Proteins with P-TEFb Facilitates Oncogenic and Physiologic MLL-Dependent Transcription

(2010) Akihiko Yokoyama et al.   CANCER CELL

RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex

(2010) Sebastian R. Geiger et al.   MOLECULAR CELL

HIV-1 Tat and Host AFF4 Recruit Two Transcription Elongation Factors into a Bifunctional Complex for Coordinated Activation of HIV-1 Transcription

(2010) Nanhai He et al.   MOLECULAR CELL

AFF4, a Component of the ELL/P-TEFb Elongation Complex and a Shared Subunit of MLL Chimeras, Can Link Transcription Elongation to Leukemia

(2010) Chengqi Lin et al.   MOLECULAR CELL

HIV-1 Tat Assembles a Multifunctional Transcription Elongation Complex and Stably Associates with the 7SK snRNP

(2010) Bijan Sobhian et al.   MOLECULAR CELL

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

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

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

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

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE