A ubiquitous disordered protein interaction module orchestrates transcription elongation

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

(2021) Kirsten A. Reimer et al.   MOLECULAR CELL

pyGenomeTracks: reproducible plots for multivariate genomic data sets

(2020) Lucille Lopez-Delisle et al.   BIOINFORMATICS

The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae

(2020) Natalia I Reim et al.   NUCLEIC ACIDS RESEARCH

Hepatitis B Core Protein Is Post-Translationally Modified through K29-Linked Ubiquitination

(2020) Hana Langerová et al.   Cells

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

FACT caught in the act of manipulating the nucleosome

(2019) Yang Liu et al.   NATURE

Transcription elongation factor AFF2/FMR2 regulates expression of expanded GGGGCC repeat-containing C9ORF72 allele in ALS/FTD

(2019) Yeliz Yuva-Aydemir et al.   Nature Communications

LEDGF and HDGF2 relieve the nucleosome-induced barrier to transcription in differentiated cells

(2019) Gary LeRoy et al.   Science Advances

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

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation

(2018) Subhalakshmi Sharma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

HIV latency in isolated patient CD4 + T cells may be due to blocks in HIV transcriptional elongation, completion, and splicing

(2018) Steven A. Yukl et al.   Science Translational Medicine

Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation

(2018) Katerina Cermakova et al.   MOLECULES

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Casein Kinase II Phosphorylation of Spt6 Enforces Transcriptional Fidelity by Maintaining Spn1-Spt6 Interaction

(2018) Raghuvar Dronamraju et al.   Cell Reports

Solution Structure of the N-Terminal Domain of Mediator Subunit MED26 and Molecular Characterization of Its Interaction with EAF1 and TAF7

(2017) Zoé Lens et al.   JOURNAL OF MOLECULAR BIOLOGY

Transcription elongation factors represent in vivo cancer dependencies in glioblastoma

(2017) Tyler E. Miller et al.   NATURE

Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

(2017) H. Courtney Hodges et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions

(2017) Izabella Krystkowiak et al.   NUCLEIC ACIDS RESEARCH

Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers

(2017) H. Courtney Hodges et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

1H, 15N and 13C assignments of the N-terminal domain of the Mediator complex subunit MED26

(2016) Riccardo Peruzzini et al.   Biomolecular NMR Assignments

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation

(2016) B. A. Gibson et al.   SCIENCE

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin

(2015) Kosuke Izumi et al.   NATURE GENETICS

Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif

(2015) Petr Tesina et al.   Nature Communications

bwtool: a tool for bigWig files

(2014) Andy Pohl et al.   BIOINFORMATICS

Validation and Structural Characterization of the LEDGF/p75-MLL Interface as a New Target for the Treatment of MLL-Dependent Leukemia

(2014) K.  ermakova et al.   CANCER RESEARCH

Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation

(2014) Kim Van Roey et al.   CHEMICAL REVIEWS

Enhanced FASP (eFASP) to Increase Proteome Coverage and Sample Recovery for Quantitative Proteomic Experiments

(2014) Jonathan Erde et al.   JOURNAL OF PROTEOME RESEARCH

Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

(2014) Christopher M. Weber et al.   MOLECULAR CELL

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

The super elongation complex (SEC) family in transcriptional control

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

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

(2012) Norman E. Davey et al.   NUCLEIC ACIDS RESEARCH

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Human Mediator Subunit MED26 Functions as a Docking Site for Transcription Elongation Factors

(2011) Hidehisa Takahashi et al.   CELL

Attributes of short linear motifs

(2011) Norman E. Davey et al.   Molecular BioSystems

PONDR-FIT: A meta-predictor of intrinsically disordered amino acids

(2010) Bin Xue et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

TIF1γ Controls Erythroid Cell Fate by Regulating Transcription Elongation

(2010) Xiaoying Bai et al.   CELL

The structure of an Iws1/Spt6 complex reveals an interaction domain conserved in TFIIS, Elongin A and Med26

(2010) Marie-Laure Diebold et al.   EMBO JOURNAL

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

Structure and Biological Importance of the Spn1-Spt6 Interaction, and Its Regulatory Role in Nucleosome Binding

(2010) Seth M. McDonald et al.   MOLECULAR CELL

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

(2009) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

TFIIH-Associated Cdk7 Kinase Functions in Phosphorylation of C-Terminal Domain Ser7 Residues, Promoter-Proximal Pausing, and Termination by RNA Polymerase II

(2009) K. Glover-Cutter et al.   MOLECULAR AND CELLULAR BIOLOGY

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

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

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

(2009) C. Hodges et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) Leighton J. Core et al.   SCIENCE