标题
Transcription Factor Dynamics: One Molecule at a Time
作者
关键词
-
出版物
Annual Review of Cell and Developmental Biology
Volume 39, Issue 1, Pages 277-305
出版商
Annual Reviews
发表日期
2023-08-05
DOI
10.1146/annurev-cellbio-022823-013847
参考文献
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注意：仅列出部分参考文献，下载原文获取全部文献信息。- MINFLUX dissects the unimpeded walking of kinesin-1
- (2023) Jan O. Wolff et al. SCIENCE
- Direct observation of motor protein stepping in living cells using MINFLUX
- (2023) Takahiro Deguchi et al. SCIENCE
- Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes
- (2023) Christopher H Bohrer et al. eLife
- Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states
- (2023) Kaustubh Wagh et al. Science Advances
- MYC amplifies gene expression through global changes in transcription factor dynamics
- (2022) Simona Patange et al. Cell Reports
- Kinetic Proofreading
- (2022) Hinrich Boeger Annual Review of Biochemistry
- Following the tracks: How transcription factor binding dynamics control transcription
- (2022) Wim J. de Jonge et al. BIOPHYSICAL JOURNAL
- Transcription activation is enhanced by multivalent interactions independent of phase separation
- (2022) Jorge Trojanowski et al. MOLECULAR CELL
- Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription
- (2022) Shasha Chong et al. MOLECULAR CELL
- Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging
- (2022) Michele Gabriele et al. SCIENCE
- Evolution of binding preferences among whole-genome duplicated transcription factors
- (2022) Tamar Gera et al. eLife
- The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation
- (2022) Lorenzo Rinaldi et al. Science Advances
- Kinetic principles underlying pioneer function of GAGA transcription factor in live cells
- (2022) Xiaona Tang et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model
- (2022) Timo Kuhn et al. Nature Communications
- Mechanisms governing target search and binding dynamics of hypoxia-inducible factors
- (2022) Yu Chen et al. eLife
- Imaging the unimaginable: leveraging signal generation of CRISPR-Cas for sensitive genome imaging
- (2022) Charlotte Van Tricht et al. TRENDS IN BIOTECHNOLOGY
- Speed–Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites
- (2021) Tamar Jana et al. TRENDS IN GENETICS
- What do Transcription Factors Interact With?
- (2021) Haining Chen et al. JOURNAL OF MOLECULAR BIOLOGY
- An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors
- (2021) David A. Garcia et al. MOLECULAR CELL
- Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model
- (2021) David A Garcia et al. NUCLEIC ACIDS RESEARCH
- Mechanical Regulation of Transcription: Recent Advances
- (2021) Kaustubh Wagh et al. TRENDS IN CELL BIOLOGY
- MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope
- (2021) Roman Schmidt et al. Nature Communications
- The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes
- (2021) Matteo Mazzocca et al. BIOCHEMICAL SOCIETY TRANSACTIONS
- Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection
- (2021) Yihan Wan et al. CELL
- Genome folding through loop extrusion by SMC complexes
- (2021) Iain F. Davidson et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Single molecule tracking and analysis framework including theory-predicted parameter settings
- (2021) Timo Kuhn et al. Scientific Reports
- Spatiotemporal coordination of transcription preinitiation complex assembly in live cells
- (2021) Vu Q. Nguyen et al. MOLECULAR CELL
- Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene
- (2021) Achim P Popp et al. NUCLEIC ACIDS RESEARCH
- Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin
- (2021) Jee Min Kim et al. eLife
- Phase separation in transcription factor dynamics and chromatin organization
- (2021) Kaustubh Wagh et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity
- (2021) Sagie Brodsky et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Caveat fluorophore: an insiders’ guide to small-molecule fluorescent labels
- (2021) Jonathan B. Grimm et al. NATURE METHODS
- MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells
- (2020) Klaus C. Gwosch et al. NATURE METHODS
- Nucleosomal proofreading of activator–promoter interactions
- (2020) Robert Shelansky et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Transcription in Living Cells: Molecular Mechanisms of Bursting
- (2020) Joseph Rodriguez et al. Annual Review of Biochemistry
- Gene Regulation in and out of Equilibrium
- (2020) Felix Wong et al. Annual Review of Biophysics
- Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity
- (2020) Sagie Brodsky et al. MOLECULAR CELL
- Transcription Factors and DNA Play Hide and Seek
- (2020) David M. Suter TRENDS IN CELL BIOLOGY
- Nucleated transcriptional condensates amplify gene expression
- (2020) Ming-Tzo Wei et al. NATURE CELL BIOLOGY
- Phase-Separated Transcriptional Condensates Accelerate Target-Search Process Revealed by Live-Cell Single-Molecule Imaging
- (2020) Samantha Kent et al. Cell Reports
- A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting
- (2020) Nicholas C. Lammers et al. CURRENT OPINION IN CELL BIOLOGY
- Advances in visualizing transcription factor – DNA interactions
- (2020) Rachel M. Price et al. GENOME
- Chromatin accessibility and the regulatory epigenome
- (2019) Sandy L. Klemm et al. NATURE REVIEWS GENETICS
- Single-molecule imaging of the transcription factor SRF reveals prolonged chromatin-binding kinetics upon cell stimulation
- (2019) Lisa Hipp et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
- (2019) Andrea Callegari et al. PLoS Genetics
- Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II
- (2019) Ryosuke Nagashima et al. JOURNAL OF CELL BIOLOGY
- Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting
- (2019) Benjamin T Donovan et al. EMBO JOURNAL
- Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation
- (2019) Leighton Core et al. GENES & DEVELOPMENT
- 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
- Gene expression across mammalian organ development
- (2019) Margarida Cardoso-Moreira et al. NATURE
- Dynamics of Notch-Dependent Transcriptional Bursting in Its Native Context
- (2019) ChangHwan Lee et al. DEVELOPMENTAL CELL
- Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility
- (2019) Diana A. Stavreva et al. MOLECULAR CELL
- Mechanisms of Interplay between Transcription Factors and the 3D Genome
- (2019) Seungsoo Kim et al. MOLECULAR CELL
- Organization of fast and slow chromatin revealed by single-nucleosome dynamics
- (2019) S. S. Ashwin 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
- Structure and Function of the 26S Proteasome
- (2018) Jared A.M. Bard et al. Annual Review of Biochemistry
- The Human Transcription Factors
- (2018) Samuel A. Lambert et al. CELL
- Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes
- (2018) Michele Di Pierro et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II
- (2018) Barbara Steurer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Accurate and sensitive quantification of protein-DNA binding affinity
- (2018) Chaitanya Rastogi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution
- (2018) Yvan Eilers et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mediator and RNA polymerase II clusters associate in transcription-dependent condensates
- (2018) Won-Ki Cho et al. SCIENCE
- Theoretical principles of transcription factor traffic on folded chromatin
- (2018) Ruggero Cortini et al. Nature Communications
- Robust model-based analysis of single-particle tracking experiments with Spot-On
- (2018) Anders S Hansen et al. eLife
- Interphase human chromosome exhibits out of equilibrium glassy dynamics
- (2018) Guang Shi et al. Nature Communications
- Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity
- (2018) Joseph Rodriguez et al. CELL
- Hsp90 and Hsp70 chaperones: Collaborators in protein remodeling
- (2018) Olivier Genest et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- 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
- Organizational principles of 3D genome architecture
- (2018) M. Jordan Rowley et al. NATURE REVIEWS GENETICS
- Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos
- (2018) Mustafa Mir et al. eLife
- Dense Bicoid hubs accentuate binding along the morphogen gradient
- (2017) Mustafa Mir et al. GENES & DEVELOPMENT
- Quantifying transcription factor binding dynamics at the single-molecule level in live cells
- (2017) Diego M. Presman et al. METHODS
- Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging
- (2017) Tadasu Nozaki et al. MOLECULAR CELL
- DNA residence time is a regulatory factor of transcription repression
- (2017) Karen Clauß et al. NUCLEIC ACIDS RESEARCH
- Live-cell p53 single-molecule binding is modulated by C-terminal acetylation and correlates with transcriptional activity
- (2017) Alessia Loffreda et al. Nature Communications
- Single-molecule analysis of steroid receptor and cofactor action in living cells
- (2017) Ville Paakinaho et al. Nature Communications
- Mapping the Dynamics of the Glucocorticoid Receptor within the Nuclear Landscape
- (2017) Martin Stortz et al. Scientific Reports
- CTCF and cohesin regulate chromatin loop stability with distinct dynamics
- (2017) Anders S Hansen et al. eLife
- 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
- Long-Lived Binding of Sox2 to DNA Predicts Cell Fate in the Four-Cell Mouse Embryo
- (2016) Melanie D. White et al. CELL
- Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response
- (2016) Ido Goldstein et al. GENOME RESEARCH
- Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes
- (2016) Francisco Balzarotti et al. SCIENCE
- Single molecule study of non-specific binding kinetics of LacI in mammalian cells
- (2015) Laura Caccianini et al. FARADAY DISCUSSIONS
- A general method to improve fluorophores for live-cell and single-molecule microscopy
- (2015) Jonathan B Grimm et al. NATURE METHODS
- Getting up to speed with transcription elongation by RNA polymerase II
- (2015) Iris Jonkers et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- A review of progress in single particle tracking: from methods to biophysical insights
- (2015) Carlo Manzo et al. REPORTS ON PROGRESS IN PHYSICS
- Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher
- (2015) Davide Normanno et al. Nature Communications
- Single molecule study of non-specific binding kinetics of LacI in mammalian cells
- (2015) Laura Caccianini et al. FARADAY DISCUSSIONS
- Dynamic regulation of transcription factors by nucleosome remodeling
- (2015) Ming Li et al. eLife
- Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
- (2014) Jiji Chen et al. CELL
- Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution
- (2014) Bi-Chang Chen et al. SCIENCE
- Single-molecule analysis of transcription factor binding at transcription sites in live cells
- (2014) Tatsuya Morisaki et al. Nature Communications
- Transcription Factors Modulate c-Fos Transcriptional Bursts
- (2014) Adrien Senecal et al. Cell Reports
- Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus
- (2014) Ignacio Izeddin et al. eLife
- 3D imaging of Sox2 enhancer clusters in embryonic stem cells
- (2014) Zhe Liu et al. eLife
- Reprogramming the Chromatin Landscape: Interplay of the Estrogen and Glucocorticoid Receptors at the Genomic Level
- (2013) T. B. Miranda et al. CANCER RESEARCH
- C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements
- (2013) Lars Grøntved et al. EMBO JOURNAL
- Single-molecule imaging of transcription factor binding to DNA in live mammalian cells
- (2013) J Christof M Gebhardt et al. NATURE METHODS
- Dynamic regulation of transcriptional states by chromatin and transcription factors
- (2013) Ty C. Voss et al. NATURE REVIEWS GENETICS
- Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells
- (2013) I. I. Cisse et al. SCIENCE
- Transcription factors: from enhancer binding to developmental control
- (2012) François Spitz et al. NATURE REVIEWS GENETICS
- A benchmark for chromatin binding measurements in live cells
- (2012) Davide Mazza et al. NUCLEIC ACIDS RESEARCH
- The lac Repressor Displays Facilitated Diffusion in Living Cells
- (2012) P. Hammar et al. SCIENCE
- Lessons in Fluctuation Correlation Spectroscopy
- (2011) Michelle A. Digman et al. Annual Review of Physical Chemistry
- Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism
- (2011) Ty C. Voss et al. CELL
- Regulation of chromatin by histone modifications
- (2011) Andrew J Bannister et al. CELL RESEARCH
- Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding
- (2011) Simon C. Biddie et al. MOLECULAR CELL
- Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics
- (2011) D. M. Suter et al. SCIENCE
- Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene
- (2011) D. R. Larson et al. SCIENCE
- FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?
- (2010) Florian Mueller et al. CURRENT OPINION IN CELL BIOLOGY
- Optimized localization analysis for single-molecule tracking and super-resolution microscopy
- (2010) Kim I Mortensen et al. NATURE METHODS
- Transcription Dynamics
- (2009) Gordon L. Hager et al. MOLECULAR CELL
- Transient Anomalous Diffusion of Telomeres in the Nucleus of Mammalian Cells
- (2009) I. Bronstein et al. PHYSICAL REVIEW LETTERS
- HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis
- (2008) Georgyi V. Los et al. ACS Chemical Biology
- Kinetic proofreading of gene activation by chromatin remodeling
- (2008) R. Blossey et al. HFSP Journal
- Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes
- (2008) Arnauld Sergé et al. NATURE METHODS
- Highly inclined thin illumination enables clear single-molecule imaging in cells
- (2008) Makio Tokunaga et al. NATURE METHODS
- Robust single-particle tracking in live-cell time-lapse sequences
- (2008) Khuloud Jaqaman et al. NATURE METHODS
- High-density mapping of single-molecule trajectories with photoactivated localization microscopy
- (2008) Suliana Manley et al. NATURE METHODS
- Regulation of TATA-binding protein dynamics in living yeast cells
- (2008) R. O. Sprouse et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter
- (2008) T. S. Karpova et al. SCIENCE
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