Spatiotemporal coordination of transcription preinitiation complex assembly in live cells

Single-molecule tracking of transcription protein dynamics in living cells: seeing is believing, but what are we seeing?

(2021) Timothée Lionnet et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA

(2020) Rafal Donczew et al.   eLife

Kin28 depletion increases association of TFIID subunits Taf1 and Taf4 with promoters in Saccharomyces cerevisiae

(2020) Elisabeth R Knoll et al.   NUCLEIC ACIDS RESEARCH

Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

(2020) Anand Ranjan et al.   eLife

Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin

(2020) Jonathan Lerner et al.   MOLECULAR CELL

Phase-Separated Transcriptional Condensates Accelerate Target-Search Process Revealed by Live-Cell Single-Molecule Imaging

(2020) Samantha Kent et al.   Cell Reports

Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex

(2019) Avital Klein-Brill et al.   Cell Reports

Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting

(2019) Benjamin T Donovan et al.   EMBO JOURNAL

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

(2019) David Trombley McSwiggen et al.   eLife

Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells

(2019) Jieru Li et al.   CELL

The TAFs of TFIID Bind and Rearrange the Topology of the TATA-Less RPS5 Promoter

(2019) Sarah N. Le et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

TFIIE orchestrates the recruitment of the TFIIH kinase module at promoter before release during transcription

(2019) Emmanuel Compe et al.   Nature Communications

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

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging

(2019) Qinsi Zheng et al.   ACS Central Science

The capping enzyme facilitates promoter escape and assembly of a follow-on preinitiation complex for reinitiation

(2019) Rina Fujiwara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Guided nuclear exploration increases CTCF target search efficiency

(2019) Anders S. Hansen et al.   Nature Chemical Biology

Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription

(2018) Slawomir Kubik et al.   MOLECULAR CELL

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The essential and multifunctional TFIIH complex

(2018) Jenna K. Rimel et al.   PROTEIN SCIENCE

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

(2018) Won-Ki Cho et al.   SCIENCE

Live-cell single-molecule dynamics of PcG proteins imposed by the DIPG H3.3K27M mutation

(2018) Roubina Tatavosian et al.   Nature Communications

Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex

(2018) Lisa M. Tuttle et al.   Cell Reports

Robust model-based analysis of single-particle tracking experiments with Spot-On

(2018) Anders S Hansen et al.   eLife

Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome

(2018) Brandon Ho et al.   Cell Systems

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

(2018) Maxime Woringer et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

(2018) Ann Boija et al.   CELL

RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast

(2018) Sandipan Brahma et al.   MOLECULAR CELL

Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast

(2018) Gunjan D. Mehta et al.   MOLECULAR CELL

Structure of human TFIID and mechanism of TBP loading onto promoter DNA

(2018) Avinash B. Patel et al.   SCIENCE

Role of the pre-initiation complex in Mediator recruitment and dynamics

(2018) Elisabeth R Knoll et al.   eLife

Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation

(2017) Yoo Jin Joo et al.   GENES & DEVELOPMENT

Multi-scale tracking reveals scale-dependent chromatin dynamics after DNA damage

(2017) Judith Miné-Hattab et al.   MOLECULAR BIOLOGY OF THE CELL

Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals

(2017) Yong Xue et al.   MOLECULAR CELL

Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

(2017) Linda Warfield et al.   MOLECULAR CELL

Structures of transcription pre-initiation complex with TFIIH and Mediator

(2017) S. Schilbach et al.   NATURE

Histone chaperone networks shaping chromatin function

(2017) Colin M. Hammond et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Live-cell p53 single-molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity

(2017) Alessia Loffreda et al.   Nature Communications

Evidence that Mediator is essential for Pol II transcription, but is not a required component of the preinitiation complex in vivo

(2017) Natalia Petrenko et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex

(2016) Philip J. Robinson et al.   CELL

Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters

(2016) Sebastian Grünberg et al.   EMBO JOURNAL

Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis

(2016) Zhengjian Zhang et al.   GENES & DEVELOPMENT

Mediator Undergoes a Compositional Change during Transcriptional Activation

(2016) Natalia Petrenko et al.   MOLECULAR CELL

Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization

(2016) Juan B. Rodríguez-Molina et al.   MOLECULAR CELL

Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo

(2016) Célia Jeronimo et al.   MOLECULAR CELL

Single molecule tracking of Ace1p inSaccharomyces cerevisiaedefines a characteristic residence time for non-specific interactions of transcription factors with chromatin

(2016) David A. Ball et al.   NUCLEIC ACIDS RESEARCH

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

Uncoupling Promoter Opening from Start-Site Scanning

(2015) Kenji Murakami et al.   MOLECULAR CELL

Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast

(2015) Slawomir Kubik et al.   MOLECULAR CELL

A general method to improve fluorophores for live-cell and single-molecule microscopy

(2015) Jonathan B Grimm et al.   NATURE METHODS

Gene looping facilitates TFIIH kinase-mediated termination of transcription

(2015) Scott Medler et al.   Scientific Reports

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Geometry of the nucleus: a perspective on gene expression regulation

(2014) Maxime Woringer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Asymmetric nucleosomes flank promoters in the budding yeast genome

(2014) Srinivas Ramachandran et al.   GENOME RESEARCH

RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast

(2014) Dwaipayan Ganguli et al.   GENOME RESEARCH

TFIIH Phosphorylation of the Pol II CTD Stimulates Mediator Dissociation from the Preinitiation Complex and Promoter Escape

(2014) Koon Ho Wong et al.   MOLECULAR CELL

Kin28 regulates the transient association of Mediator with core promoters

(2014) Célia Jeronimo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by synergistic and independent mechanisms

(2014) V. Schweikhard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Ignacio Izeddin et al.   eLife

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

(2013) Shannon M. Lauberth et al.   CELL

Chromatin Movement in the Maintenance of Genome Stability

(2013) Vincent Dion et al.   CELL

Independent RNA polymerase II preinitiation complex dynamics and nucleosome turnover at promoter sites in vivo

(2013) Y. Grimaldi et al.   GENOME RESEARCH

Direct TFIIA-TFIID Protein Contacts Drive Budding Yeast Ribosomal Protein Gene Transcription

(2013) Justin H. Layer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Tri-track: Free Software for Large-Scale Particle Tracking

(2013) Pascal Vallotton et al.   MICROSCOPY AND MICROANALYSIS

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

(2013) J Christof M Gebhardt et al.   NATURE METHODS

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

(2013) I. I. Cisse et al.   SCIENCE

Intra-nuclear mobility and target search mechanisms of transcription factors: A single-molecule perspective on gene expression

(2012) Davide Normanno et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

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

(2012) Johannes Schindelin et al.   NATURE METHODS

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation

(2010) Gabor Papai et al.   NATURE

A Complete Set of Nascent Transcription Rates for Yeast Genes

(2010) Vicent Pelechano et al.   PLoS One

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome

(2009) Folkert J van Werven et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mediator complex association with constitutively transcribed genes in yeast

(2009) S. A. Ansari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis

(2008) Georgyi V. Los et al.   ACS Chemical Biology

A PCR-based strategy to generate yeast strains expressing endogenous levels of amino-terminal epitope-tagged proteins

(2008) Keith R. Booher et al.   Biotechnology Journal

Tracking single molecules in the live cell plasma membrane—Do’s and Don’t’s

(2008) Stefan Wieser et al.   METHODS

The Anchor-Away Technique: Rapid, Conditional Establishment of Yeast Mutant Phenotypes

(2008) Hirohito Haruki et al.   MOLECULAR CELL