Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response

Chaperones directly and efficiently disperse stress-triggered biomolecular condensates

(2022) Haneul Yoo et al.   MOLECULAR CELL

Reversible phase separation of HSF1 is required for an acute transcriptional response during heat shock

(2022) Hongchen Zhang et al.   NATURE CELL BIOLOGY

Sequence grammar underlying the unfolding and phase separation of globular proteins

(2022) Kiersten M. Ruff et al.   MOLECULAR CELL

1,6-Hexanediol, commonly used to dissolve liquid-liquid phase separated condensates, directly impairs kinase and phosphatase activities

(2021) Robert Düster et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stress-induced nuclear condensation of NELF drives transcriptional downregulation

(2021) Prashant Rawat et al.   MOLECULAR CELL

1,6-hexanediol rapidly immobilizes and condenses chromatin in living human cells

(2021) Yuji Itoh et al.   Life Science Alliance

Primordial super-enhancers: heat shock-induced chromatin organization in yeast

(2021) Amoldeep S. Kainth et al.   TRENDS IN CELL BIOLOGY

Mediator subunit Med15 dictates the conserved “fuzzy” binding mechanism of yeast transcription activators Gal4 and Gcn4

(2021) Lisa M. Tuttle et al.   Nature Communications

Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology

(2021) Rohini R Nair et al.   eLife

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

(2021) Adrian L Sanborn et al.   eLife

Single-molecule studies reveal branched pathways for activator-dependent assembly of RNA polymerase II pre-initiation complexes

(2021) Inwha Baek et al.   MOLECULAR CELL

Glucocorticoid receptor condensates link DNA-dependent receptor dimerization and transcriptional transactivation

(2021) Filipp Frank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mediator dynamics during heat shock in budding yeast

(2021) Debasish Sarkar et al.   GENOME RESEARCH

HSF1 phase transition mediates stress adaptation and cell fate decisions

(2020) Giorgio Gaglia et al.   NATURE CELL BIOLOGY

Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization

(2020) David W. Sanders et al.   CELL

Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression

(2020) Yi Lu et al.   NATURE CELL BIOLOGY

Feedback regulation of heat shock factor 1 (Hsf1) activity by Hsp70‐mediated trimer unzipping and dissociation from DNA

(2020) Szymon W Kmiecik et al.   EMBO JOURNAL

Nucleated transcriptional condensates amplify gene expression

(2020) Ming-Tzo Wei et al.   NATURE CELL BIOLOGY

RNA-Mediated Feedback Control of Transcriptional Condensates

(2020) Jonathan E. Henninger et al.   CELL

Heat Shock Factor 1 Drives Intergenic Association of Its Target Gene Loci upon Heat Shock

(2019) Surabhi Chowdhary et al.   Cell Reports

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

A ribosome assembly stress response regulates transcription to maintain proteome homeostasis

(2019) Benjamin Albert et al.   eLife

Regulation of the Hsf1-dependent transcriptome via conserved bipartite contacts with Hsp70 promotes survival in yeast

(2019) Sara Peffer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chromosome conformation capture that detects novel cis- and trans-interactions in budding yeast

(2019) Surabhi Chowdhary et al.   METHODS

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

Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1

(2019) Anna E Masser et al.   eLife

A Solid-State Conceptualization of Information Transfer from Gene to Message to Protein

(2018) Masato Kato et al.   Annual Review of Biochemistry

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

Dissecting super-enhancer hierarchy based on chromatin interactions

(2018) Jialiang Huang et al.   Nature Communications

Hsf1 Phosphorylation Generates Cell-to-Cell Variation in Hsp90 Levels and Promotes Phenotypic Plasticity

(2018) Xu Zheng et al.   Cell Reports

Hsf1 and Hsp70 constitute a two-component feedback loop that regulates the yeast heat shock response

(2018) Joanna Krakowiak et al.   eLife

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

Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome

(2018) David Pincus et al.   MOLECULAR BIOLOGY OF THE CELL

Heat Shock Protein Genes Undergo Dynamic Alteration in Their Three-Dimensional Structure and Genome Organization in Response to Thermal Stress

(2017) Surabhi Chowdhary et al.   MOLECULAR AND CELLULAR BIOLOGY

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

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

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Evidence for Multiple Mediator Complexes in Yeast Independently Recruited by Activated Heat Shock Factor

(2016) Jayamani Anandhakumar et al.   MOLECULAR AND CELLULAR BIOLOGY

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

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

mRNA quality control is bypassed for immediate export of stress-responsive transcripts

(2016) Gesa Zander et al.   NATURE

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Dynamic control of Hsf1 during heat shock by a chaperone switch and phosphorylation

(2016) Xu Zheng et al.   eLife

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

(2015) Avinash Patel et al.   CELL

ClearVolume: open-source live 3D visualization for light-sheet microscopy

(2015) Loic A Royer et al.   NATURE METHODS

Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules

(2015) Sonja Kroschwald et al.   eLife

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

The novel proteins Rng8 and Rng9 regulate the myosin-V Myo51 during fission yeast cytokinesis

(2014) Ning Wang et al.   JOURNAL OF CELL BIOLOGY

Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast

(2014) Brian M. Zid et al.   NATURE

FindFoci: A Focus Detection Algorithm with Automated Parameter Training That Closely Matches Human Assignments, Reduces Human Inconsistencies and Increases Speed of Analysis

(2014) Alex D. Herbert et al.   PLoS One

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

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Mediator Recruitment to Heat Shock Genes Requires Dual Hsf1 Activation Domains and Mediator Tail Subunits Med15 and Med16

(2013) Sunyoung Kim et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Single-molecule analysis of gene expression using two-color RNA labeling in live yeast

(2012) Sami Hocine et al.   NATURE METHODS

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

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY