Functional partitioning of transcriptional regulators by patterned charge blocks

Identification and functional characterization of transcriptional activators in human cells

(2022) Nader Alerasool et al.   MOLECULAR CELL

Differential cofactor dependencies define distinct types of human enhancers

(2022) Christoph Neumayr et al.   NATURE

Cell cycle-specific phase separation regulated by protein charge blockiness

(2022) Hiroya Yamazaki et al.   NATURE CELL BIOLOGY

The Mediator complex as a master regulator of transcription by RNA polymerase II

(2022) William F. Richter et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mutations linked to neurological disease enhance self-association of low-complexity protein sequences

(2022) Xiaoming Zhou et al.   SCIENCE

High-fidelity reconstitution of stress granules and nucleoli in mammalian cellular lysate

(2021) Brian D. Freibaum et al.   JOURNAL OF CELL BIOLOGY

Co-condensation between transcription factor and coactivator p300 modulates transcriptional bursting kinetics

(2021) Liang Ma et al.   MOLECULAR CELL

Stress-induced nuclear condensation of NELF drives transcriptional downregulation

(2021) Prashant Rawat et al.   MOLECULAR CELL

Structure of the human Mediator-bound transcription preinitiation complex

(2021) R. Abdella et al.   SCIENCE

Critical roles of transcriptional coactivator MED1 in the formation and function of mouse adipose tissues

(2021) Keiichi Ito et al.   GENES & DEVELOPMENT

Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure

(2021) Ryan J. Emenecker et al.   BIOPHYSICAL JOURNAL

Polyampholyte physics: Liquid–liquid phase separation and biological condensates

(2021) Jelena Dinic et al.   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

Liquid–Liquid Phase Separation in Chromatin

(2021) Karsten Rippe   Cold Spring Harbor Perspectives in Biology

Biophysical studies of phase separation integrating experimental and computational methods

(2021) Nicolas L. Fawzi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Phase separation in fluids with many interacting components

(2021) Krishna Shrinivas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A ubiquitous disordered protein interaction module orchestrates transcription elongation

(2021) Katerina Cermakova et al.   SCIENCE

Molecular determinants of phase separation for Drosophila DNA replication licensing factors

(2021) Matthew W Parker et al.   eLife

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

(2020) Jeong-Mo Choi et al.   Annual Review of Biophysics

A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes

(2020) Yi-Hsuan Lin et al.   JOURNAL OF CHEMICAL PHYSICS

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Transcription in Living Cells: Molecular Mechanisms of Bursting

(2020) Joseph Rodriguez et al.   Annual Review of Biochemistry

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

(2020) Sagie Brodsky et al.   MOLECULAR CELL

MeCP2 links heterochromatin condensates and neurodevelopmental disease

(2020) Charles H. Li et al.   NATURE

Biomolecular Condensates in the Nucleus

(2020) Benjamin R. Sabari et al.   TRENDS IN BIOCHEMICAL SCIENCES

Biomolecular Condensates and Gene Activation in Development and Disease

(2020) Benjamin R. Sabari   DEVELOPMENTAL CELL

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

Molecular determinants of protein-based coacervates

(2020) Rachel A. Kapelner et al.   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

(2020) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

MobiDB: intrinsically disordered proteins in 2021

(2020) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells

(2020) Li Ding et al.   Life Science Alliance

Insights into gene regulation: From regulatory genomic elements to DNA-protein and protein-protein interactions

(2020) Leonid Serebreni et al.   CURRENT OPINION IN CELL BIOLOGY

Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

(2019) Sreejith J. Nair et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The C-Terminal Domain of RNA Polymerase II Is a Multivalent Targeting Sequence that Supports Drosophila Development with Only Consensus Heptads

(2019) Feiyue Lu et al.   MOLECULAR CELL

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2

(2019) Aaron J. Plys et al.   GENES & DEVELOPMENT

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

(2019) Laila El Khattabi et al.   CELL

Enhancer Features that Drive Formation of Transcriptional Condensates

(2019) Krishna Shrinivas et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

(2019) Alicia V. Zamudio et al.   MOLECULAR CELL

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

50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms

(2019) Robert G. Roeder   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The liquid nucleome – phase transitions in the nucleus at a glance

(2019) Amy R. Strom et al.   JOURNAL OF CELL SCIENCE

Binding without folding – the biomolecular function of disordered polyelectrolyte complexes

(2019) Benjamin Schuler et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Theories for Sequence-Dependent Phase Behaviors of Biomolecular Condensates

(2018) Yi-Hsuan Lin et al.   BIOCHEMISTRY

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

(2018) Jie Wang et al.   CELL

Sequence charge decoration dictates coil-globule transition in intrinsically disordered proteins

(2018) Taylor Firman et al.   JOURNAL OF CHEMICAL PHYSICS

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

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

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

(2018) Robert McCoy Vernon et al.   eLife

Protein motion in the nucleus: from anomalous diffusion to weak interactions

(2018) Maxime Woringer et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

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

(2018) Ann Boija et al.   CELL

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

(2018) Mustafa Mir et al.   eLife

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins

(2017) A. Hongjun Wang et al.   MOLECULAR CELL

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation

(2017) Rasmus Siersbæk et al.   MOLECULAR CELL

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Transcription regulation by the Mediator complex

(2017) Julie Soutourina   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Biomolecular condensates: organizers of cellular biochemistry

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

Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

(2017) Yi-Hsuan Lin et al.   NEW JOURNAL OF PHYSICS

Nuclear microenvironments modulate transcription from low-affinity enhancers

(2017) Albert Tsai et al.   eLife

Compositional Control of Phase-Separated Cellular Bodies

(2016) Salman F. Banani et al.   CELL

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

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

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

The Mediator complex: a central integrator of transcription

(2015) Benjamin L. Allen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

The Mediator complex: a master coordinator of transcription and cell lineage development

(2014) J.-w. Yin et al.   DEVELOPMENT

Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers

(2014) Rasmus Siersbæk et al.   Cell Reports

Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus

(2014) Ignacio Izeddin et al.   eLife

Control of Transcriptional Elongation

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

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

(2013) R. K. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

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

(2012) Johannes Schindelin et al.   NATURE METHODS

D2P2: database of disordered protein predictions

(2012) Matt E. Oates et al.   NUCLEIC ACIDS RESEARCH

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparing Models of Evolution for Ordered and Disordered Proteins

(2009) C. J. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genome-wide profiling of PPAR :RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

(2008) R. Nielsen et al.   GENES & DEVELOPMENT

Malleable machines take shape in eukaryotic transcriptional regulation

(2008) Monika Fuxreiter et al.   Nature Chemical Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY