Speed–Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites

Eukaryotic transcription factors can track and control their target genes using DNA antennas

(2020) Milagros Castellanos et al.   Nature Communications

Independent evolution of transcript abundance and gene regulatory dynamics

(2020) Gat Krieger et al.   GENOME RESEARCH

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

(2020) Jonathan Lerner et al.   MOLECULAR CELL

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

(2020) Sagie Brodsky et al.   MOLECULAR CELL

Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution

(2020) Pakavarin Louphrasitthiphol et al.   MOLECULAR CELL

Index and biological spectrum of human DNase I hypersensitive sites

(2020) Wouter Meuleman et al.   NATURE

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

DNA surface exploration and operator bypassing during target search

(2020) Emil Marklund et al.   NATURE

Transcription Factors and DNA Play Hide and Seek

(2020) David M. Suter   TRENDS IN CELL BIOLOGY

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

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes

(2019) Judith F. Kribelbauer et al.   Annual Review of Cell and Developmental Biology

Visualizing transcription: key to understanding gene expression dynamics

(2019) Ineke Brouwer et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation

(2019) Razvan V Chereji et al.   GENOME RESEARCH

Resolving noise–control conflict by gene duplication

(2019) Michal Chapal et al.   PLOS BIOLOGY

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

(2018) Jie Wang et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Visualizing transcription factor dynamics in living cells

(2018) Zhe Liu et al.   JOURNAL OF CELL BIOLOGY

Systematic Study of Nucleosome-Displacing Factors in Budding Yeast

(2018) Chao Yan et al.   MOLECULAR CELL

Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding

(2018) Daniel D. Le et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding

(2018) Ning Shen et al.   Cell Systems

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Intrinsic cooperativity potentiates parallel cis-regulatory evolution

(2018) Trevor R Sorrells et al.   eLife

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

(2018) Ann Boija et al.   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

Quantifying transcription factor binding dynamics at the single-molecule level in live cells

(2017) Diego M. Presman et al.   METHODS

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

(2017) Hideharu Hashimoto et al.   MOLECULAR CELL

PRODORIC2: the bacterial gene regulation database in 2018

(2017) Denitsa Eckweiler et al.   NUCLEIC ACIDS RESEARCH

20 years of the SMART protein domain annotation resource

(2017) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

How motif environment influences transcription factor search dynamics: Finding a needle in a haystack

(2016) Iris Dror et al.   BIOESSAYS

Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions

(2016) Erin E. Swinstead et al.   CELL

Proteomic and bioinformatic analysis of a nuclear intrinsically disordered proteome

(2016) Bozena Skupien-Rabian et al.   Journal of Proteomics

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

Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea

(2016) Chen Wang et al.   PROTEOMICS

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Intrinsically disordered proteins: emerging interaction specialists

(2015) Peter Tompa et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Zelda overcomes the high intrinsic nucleosome barrier at enhancers duringDrosophilazygotic genome activation

(2015) Yujia Sun et al.   GENOME RESEARCH

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

Diversification of Transcription Factor Paralogs via Noncanonical Modularity in C2H2 Zinc Finger DNA Binding

(2014) Trevor Siggers et al.   MOLECULAR CELL

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Protein−DNA binding in the absence of specific base-pair recognition

(2014) Ariel Afek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

(2013) M. A. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-scale prediction of proteins with long intrinsically disordered regions

(2013) Zhenling Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

(2013) Raluca Gordân et al.   Cell Reports

DNA binding specificities of the long zinc-finger recombination protein PRDM9

(2013) Timothy Billings et al.   GENOME BIOLOGY

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

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

Nucleosome-Driven Transcription Factor Binding and Gene Regulation

(2012) Cecilia Ballaré et al.   MOLECULAR CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

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

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

(2011) D. R. Larson et al.   SCIENCE

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

(2011) Xiao-Yong Li et al.   GENOME BIOLOGY

Nuclear proteins: finding and binding target sites in chromatin

(2010) Martin E. van Royen et al.   CHROMOSOME RESEARCH

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

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

Optimized localization analysis for single-molecule tracking and super-resolution microscopy

(2010) Kim I Mortensen et al.   NATURE METHODS

Genomic repertoires of DNA-binding transcription factors across the tree of life

(2010) Varodom Charoensawan et al.   NUCLEIC ACIDS RESEARCH

Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA

(2010) C. M. Etson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome-mediated cooperativity between transcription factors

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

Lineage-specific expansion of DNA-binding transcription factor families

(2010) Varodom Charoensawan et al.   TRENDS IN GENETICS

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

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

An end to 40 years of mistakes in DNA–protein association kinetics?

(2009) Stephen E. Halford   BIOCHEMICAL SOCIETY TRANSACTIONS

Tracking of Single Quantum Dot Labeled EcoRV Sliding along DNA Manipulated by Double Optical Tweezers

(2009) Andreas Biebricher et al.   BIOPHYSICAL JOURNAL

Using the Bias from Flow to Elucidate Single DNA Repair Protein Sliding and Interactions with DNA

(2009) Yihan Lin et al.   BIOPHYSICAL JOURNAL

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

(2009) Leonid Mirny et al.   Journal of Physics A-Mathematical and Theoretical

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability

(2008) Anahita Tafvizi et al.   BIOPHYSICAL JOURNAL

Combinatorial Regulation of Endothelial Gene Expression by Ets and Forkhead Transcription Factors

(2008) Sarah De Val et al.   CELL

The words of the regulatory code are arranged in a variable manner in highly conserved enhancers

(2008) Sepand Rastegar et al.   DEVELOPMENTAL BIOLOGY

Visualizing one-dimensional diffusion of proteins along DNA

(2008) Jason Gorman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Spatial effects on the speed and reliability of protein–DNA search

(2008) Zeba Wunderlich et al.   NUCLEIC ACIDS RESEARCH

Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA

(2008) Isabelle Bonnet et al.   NUCLEIC ACIDS RESEARCH

Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion

(2008) G. Komazin-Meredith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils

(2008) R. H. Porecha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics