Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function

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

(2019) Benjamin T Donovan et al.   EMBO JOURNAL

Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

(2019) Benjamin T Donovan et al.   eLife

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Promoter-specific dynamics of TATA-binding protein association with the human genome

(2019) Yuko Hasegawa et al.   GENOME RESEARCH

Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor

(2019) Maxime Mivelaz et al.   MOLECULAR CELL

Epigenome Regulation by Dynamic Nucleosome Unwrapping

(2019) Sandipan Brahma et al.   TRENDS IN BIOCHEMICAL SCIENCES

High‐resolution transcription maps reveal the widespread impact of roadblock termination in yeast

(2018) Tito Candelli et al.   EMBO JOURNAL

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors

(2018) Matthew J. Rossi et al.   GENOME RESEARCH

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

(2018) Slawomir Kubik et al.   MOLECULAR CELL

Simplified ChIP-exo assays

(2018) Matthew J. Rossi et al.   Nature Communications

Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome

(2018) Brandon Ho et al.   Cell Systems

Single-Molecule Kinetics in Living Cells

(2018) Johan Elf et al.   Annual Review of Biochemistry

Second-generation method for analysis of chromatin binding with formaldehyde–cross-linking kinetics

(2017) Hussain Zaidi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays

(2017) Michal Levo et al.   MOLECULAR CELL

Understanding nucleosome dynamics and their links to gene expression and DNA replication

(2017) William K. M. Lai 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

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

(2016) Wim J de Jonge et al.   EMBO JOURNAL

Common genomic elements promote transcriptional and DNA replication roadblocks

(2016) Kevin Roy et al.   GENOME RESEARCH

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

Epigenomics and the structure of the living genome

(2015) Nir Friedman et al.   GENOME RESEARCH

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

(2015) Slawomir Kubik et al.   MOLECULAR CELL

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

(2015) Gabriel E. Zentner et al.   Nature Communications

Chromatin Mediation of a Transcriptional Memory Effect in Yeast

(2015) Emily Paul et al.   G3-Genes Genomes Genetics

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

Roadblock Termination by Reb1p Restricts Cryptic and Readthrough Transcription

(2014) Jessie Colin et al.   MOLECULAR CELL

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation

(2014) Petter Hammar et al.   NATURE GENETICS

Genome-Wide Mapping of Yeast RNA Polymerase II Termination

(2014) Paul Schaughency et al.   PLoS Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

Quantifying transcription factor kinetics: At work or at play?

(2013) Florian Mueller et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

(2013) Y. Grimaldi et al.   GENOME RESEARCH

High-resolution mapping of transcription factor binding sites on native chromatin

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosomes accelerate transcription factor dissociation

(2013) Y. Luo et al.   NUCLEIC ACIDS RESEARCH

Widespread Misinterpretable ChIP-seq Bias in Yeast

(2013) Daechan Park et al.   PLoS One

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring Chromatin Interaction Dynamics on the Second Time Scale at Single-Copy Genes

(2013) K. Poorey et al.   SCIENCE

A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription

(2013) Harm van Bakel et al.   PLoS Genetics

Cellular Response to Heat Shock Studied by Multiconfocal Fluorescence Correlation Spectroscopy

(2012) Meike Kloster-Landsberg et al.   BIOPHYSICAL JOURNAL

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

3C-based technologies to study the shape of the genome

(2012) Wouter de Laat et al.   METHODS

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

What do expression dynamics tell us about the mechanism of transcription?

(2011) Daniel R Larson   CURRENT OPINION IN GENETICS & DEVELOPMENT

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

(2011) Steven Hahn et al.   GENETICS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Current State of Chromatin Immunoprecipitation

(2010) Philippe Collas   MOLECULAR BIOTECHNOLOGY

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast

(2010) Mythily Ganapathi et al.   NUCLEIC ACIDS RESEARCH

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

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

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

Quantification of Nuclear Protein Transport using Induced Heterodimerization

(2009) Albert Busch et al.   TRAFFIC

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

(2008) Hirohito Haruki et al.   MOLECULAR CELL

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA

Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter

(2008) T. S. Karpova et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY