Stress-induced nuclear condensation of NELF drives transcriptional downregulation

NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release

(2020) Yuki Aoi et al.   MOLECULAR CELL

Nascent-protein ubiquitination is required for heat shock–induced gene downregulation in human cells

(2019) Fernando Aprile-Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

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

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

(2019) Tobias Neumann et al.   BMC BIOINFORMATICS

Clustered telomeres in phase-separated nuclear condensates engage mitotic DNA synthesis through BLM and RAD52

(2019) Jaewon Min et al.   GENES & DEVELOPMENT

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

DDX3X acts as a live-or-die checkpoint in stressed cells by regulating NLRP3 inflammasome

(2019) Parimal Samir et al.   NATURE

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

The pause-initiation limit restricts transcription activation in human cells

(2019) Saskia Gressel et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

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

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Site-specific characterization of endogenous SUMOylation across species and organs

(2018) Ivo A. Hendriks et al.   Nature Communications

Who's In and Who's Out—Compositional Control of Biomolecular Condensates

(2018) Jonathon A. Ditlev et al.   JOURNAL OF MOLECULAR BIOLOGY

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

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

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

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

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

(2017) Ivo A Hendriks et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mitotic transcription and waves of gene reactivation during mitotic exit

(2017) Katherine C. Palozola et al.   SCIENCE

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Transcriptional response to stress is pre-wired by promoter and enhancer architecture

(2017) Anniina Vihervaara et al.   Nature Communications

Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain

(2017) Bede Portz et al.   Nature Communications

Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

(2017) Ivo A Hendriks et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation

(2016) Dig B. Mahat et al.   MOLECULAR CELL

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

(2016) Xiaodong Lu et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Architecture and RNA binding of the human negative elongation factor

(2016) Seychelle M Vos et al.   eLife

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

(2015) Fei Xavier Chen et al.   CELL

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

Getting up to speed with transcription elongation by RNA polymerase II

(2015) Iris Jonkers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A new vertebrate SUMO enzyme family reveals insights into SUMO-chain assembly

(2015) Nathalie Eisenhardt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Standardizing chromatin research: a simple and universal method for ChIP-seq

(2015) Laura Arrigoni et al.   NUCLEIC ACIDS RESEARCH

A new vertebrate SUMO enzyme family reveals insights into SUMO-chain assembly

(2015) Nathalie Eisenhardt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

Oxidative stress–induced assembly of PML nuclear bodies controls sumoylation of partner proteins

(2014) Umut Sahin et al.   JOURNAL OF CELL BIOLOGY

Control of Transcriptional Elongation

(2013) Hojoong Kwak et al.   Annual Review of Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC)

(2012) Sung-Soo Park et al.   Journal of Proteomics

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nuclear Stress Bodies

(2010) G. Biamonti et al.   Cold Spring Harbor Perspectives in Biology

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

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

Ubc9 Sumoylation Regulates SUMO Target Discrimination

(2008) Puck Knipscheer et al.   MOLECULAR CELL

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

The environmental contribution to gene expression profiles

(2008) Greg Gibson   NATURE REVIEWS GENETICS

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

(2008) Leighton J. Core et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY