Molecular mechanisms driving transcriptional stress responses

Enhancer transcription: what, where, when, and why?

(2018) Nathaniel D. Tippens et al.   GENES & DEVELOPMENT

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

ATF4 regulates CCL2 expression to promote endometrial cancer growth by controlling macrophage infiltration

(2017) Bin Liu et al.   EXPERIMENTAL CELL RESEARCH

Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction

(2017) Britta Mueller et al.   GENES & DEVELOPMENT

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

(2017) Noah Dukler et al.   GENOME RESEARCH

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

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

(2017) Lydia Herzel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Regulation of heat shock transcription factors and their roles in physiology and disease

(2017) Rocio Gomez-Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

(2017) Anna Vilborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PAF1 regulation of promoter-proximal pause release via enhancer activation

(2017) Fei Xavier Chen et al.   SCIENCE

Olfactory experience primes the heat shock transcription factor HSF-1 to enhance the expression of molecular chaperones inC. elegans

(2017) Felicia K. Ooi et al.   Science Signaling

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

(2017) Anniina Vihervaara et al.   Nature Communications

The HSF1–PARP13–PARP1 complex facilitates DNA repair and promotes mammary tumorigenesis

(2017) Mitsuaki Fujimoto et al.   Nature Communications

Abnormal degradation of the neuronal stress-protective transcription factor HSF1 in Huntington’s disease

(2017) Rocio Gomez-Pastor et al.   Nature Communications

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

SUMO modification system facilitates the exchange of histone variant H2A.Z-2 at DNA damage sites

(2017) Atsuhiko Fukuto et al.   Nucleus

Olfactory experience primes the heat shock transcription factor HSF-1 to enhance the expression of molecular chaperones inC. elegans

(2017) Felicia K. Ooi et al.   Science Signaling

SUMO modification system facilitates the exchange of histone variant H2A.Z-2 at DNA damage sites

(2017) Atsuhiko Fukuto et al.   Nucleus

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

The Transcription Factor ATF5 Mediates a Mammalian Mitochondrial UPR

(2016) Christopher J. Fiorese et al.   CURRENT BIOLOGY

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation

(2016) Fabiana M. Duarte et al.   GENES & DEVELOPMENT

Genome-wide uniformity of human ‘open’ pre-initiation complexes

(2016) William K.M. Lai et al.   GENOME RESEARCH

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

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

Defining the Essential Function of Yeast Hsf1 Reveals a Compact Transcriptional Program for Maintaining Eukaryotic Proteostasis

(2016) Eric J. Solís et al.   MOLECULAR CELL

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Interplay between Ubiquitin, SUMO, and Poly(ADP-Ribose) in the Cellular Response to Genotoxic Stress

(2016) Stefania Pellegrino et al.   Frontiers in Genetics

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

(2015) Fei Chen et al.   GENES & DEVELOPMENT

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

Biology of Poly(ADP-Ribose) Polymerases: The Factotums of Cell Maintenance

(2015) Peter Bai   MOLECULAR CELL

Widespread Inducible Transcription Downstream of Human Genes

(2015) Anna Vilborg et al.   MOLECULAR CELL

Human Gene Promoters Are Intrinsically Bidirectional

(2015) Robin Andersson et al.   MOLECULAR CELL

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

New roles for mitochondrial proteases in health, ageing and disease

(2015) Pedro M. Quirós et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Getting up to speed with transcription elongation by RNA polymerase II

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

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Long-Range Chromatin Interactions

(2015) Job Dekker et al.   Cold Spring Harbor Perspectives in Biology

Widespread disruption of host transcription termination in HSV-1 infection

(2015) Andrzej J. Rutkowski et al.   Nature Communications

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters

(2015) Nicholas J. Fuda et al.   PLoS Genetics

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

(2015) Ana R Grosso et al.   eLife

Nucleosome Dancing at the Tempo of Histone Tail Acetylation

(2015) Angélique Galvani et al.   Genes

Wrestling with stress: Roles of protein SUMOylation and deSUMOylation in cell stress response

(2014) Chun Guo et al.   IUBMB LIFE

Expression of HSF2 decreases in mitosis to enable stress-inducible transcription and cell survival

(2014) Alexandra N. Elsing et al.   JOURNAL OF CELL BIOLOGY

HSF1 at a glance

(2014) A. Vihervaara et al.   JOURNAL OF CELL SCIENCE

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

(2014) Reut Shalgi et al.   Cell Reports

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

(2014) Iris Jonkers et al.   eLife

Regulation of Organismal Proteostasis by Transcellular Chaperone Signaling

(2013) Patricija van Oosten-Hawle et al.   CELL

Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing

(2013) Jian Li et al.   MOLECULAR CELL

Transcriptional response to stress in the dynamic chromatin environment of cycling and mitotic cells

(2013) Anniina Vihervaara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

HSF1 Drives a Transcriptional Program Distinct from Heat Shock to Support Highly Malignant Human Cancers

(2012) Marc L. Mendillo et al.   CELL

RPA Assists HSF1 Access to Nucleosomal DNA by Recruiting Histone Chaperone FACT

(2012) Mitsuaki Fujimoto et al.   MOLECULAR CELL

PARP1 Represses PAP and Inhibits Polyadenylation during Heat Shock

(2012) Dafne Campigli Di Giammartino et al.   MOLECULAR CELL

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

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

CTCF/cohesin-mediated DNA looping is required for protocadherin   promoter choice

(2012) Y. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancers as information integration hubs in development: lessons from genomics

(2012) Christa Buecker et al.   TRENDS IN GENETICS

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide

(2011) S. S. Teves et al.   GENES & DEVELOPMENT

Activator-Induced Spread of Poly(ADP-Ribose) Polymerase Promotes Nucleosome Loss at Hsp70

(2011) Steven J. Petesch et al.   MOLECULAR CELL

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

The Unfolded Protein Response: From Stress Pathway to Homeostatic Regulation

(2011) P. Walter et al.   SCIENCE

The Stress of Protein Misfolding: From Single Cells to Multicellular Organisms

(2011) T. Gidalevitz et al.   Cold Spring Harbor Perspectives in Biology

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Heat Shock Transcription Factor 1 Localizes to Sex Chromatin during Meiotic Repression

(2010) Malin Åkerfelt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Recruitment Timing and Dynamics of Transcription Factors at the Hsp70 Loci in Living Cells

(2010) Katie L. Zobeck et al.   MOLECULAR CELL

The Heat Shock Response: Life on the Verge of Death

(2010) Klaus Richter et al.   MOLECULAR CELL

Hypoxia-Inducible Factors and the Response to Hypoxic Stress

(2010) Amar J. Majmundar et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Intermediate filaments take the heat as stress proteins

(2010) D.M. Toivola et al.   TRENDS IN CELL BIOLOGY

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

(2010) Michael J. Guertin et al.   PLoS Genetics

PARP-1 transcriptional activity is regulated by sumoylation upon heat shock

(2009) Nadine Martin et al.   EMBO JOURNAL

Novel Proteomics Strategy Brings Insight into the Prevalence of SUMO-2 Target Sites

(2009) Henri A. Blomster et al.   MOLECULAR & CELLULAR PROTEOMICS

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Imaging transcription dynamics at endogenous genes in living Drosophila tissues

(2008) Jie Yao et al.   METHODS

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

Regulation of the Cellular Heat Shock Response in Caenorhabditis elegans by Thermosensory Neurons

(2008) V. Prahlad et al.   SCIENCE

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

(2008) Leighton J. Core et al.   SCIENCE