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

Mouse Heterochromatin Adopts Digital Compaction States without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation

(2020) Fabian Erdel et al.   MOLECULAR CELL

Deep learning in single-molecule microscopy: fundamentals, caveats, and recent developments [Invited]

(2020) Leonhard Möckl et al.   Biomedical Optics Express

Transcription in Living Cells: Molecular Mechanisms of Bursting

(2020) Joseph Rodriguez et al.   Annual Review of Biochemistry

Unblending of Transcriptional Condensates in Human Repeat Expansion Disease

(2020) Shaon Basu et al.   CELL

Just Took a DNA Test, Turns Out 100% Not That Phase

(2020) Aaron D. Gitler et al.   MOLECULAR CELL

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

(2020) Anand Ranjan et al.   eLife

Nuclear actin regulates inducible transcription by enhancing RNA polymerase II clustering

(2020) Mian Wei et al.   Science Advances

CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies

(2020) Woonyung Hur et al.   DEVELOPMENTAL CELL

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

(2020) Jonathan Lerner et al.   MOLECULAR CELL

RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting

(2020) Porfirio Quintero-Cadena et al.   MOLECULAR CELL

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

(2020) Sagie Brodsky et al.   MOLECULAR CELL

DNA surface exploration and operator bypassing during target search

(2020) Emil Marklund et al.   NATURE

Long-term association of a transcription factor with its chromatin binding site can stabilize gene expression and cell fate commitment

(2020) J. B. Gurdon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Factors and DNA Play Hide and Seek

(2020) David M. Suter   TRENDS IN CELL BIOLOGY

Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

(2020) Ezequiel Miron et al.   Science Advances

Transcription factor activity and nucleosome organization in mitosis

(2019) Nicola Festuccia et al.   GENOME RESEARCH

CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning

(2019) Marlies E. Oomen et al.   GENOME RESEARCH

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

The C-Terminal Domain of RNA Polymerase II Is a Multivalent Targeting Sequence that Supports Drosophila Development with Only Consensus Heptads

(2019) Feiyue Lu et al.   MOLECULAR CELL

Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II

(2019) Ryosuke Nagashima et al.   JOURNAL OF CELL BIOLOGY

Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy

(2019) Fadi M. Jradi et al.   ACS Chemical Biology

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

(2019) Benjamin T Donovan et al.   EMBO JOURNAL

Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA

(2019) John W Biddle et al.   eLife

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation

(2019) David Trombley McSwiggen et al.   eLife

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Single-Particle Diffusion Characterization by Deep Learning

(2019) Naor Granik et al.   BIOPHYSICAL JOURNAL

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

(2019) Jieru Li et al.   CELL

Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics

(2019) O. Shukron et al.   TRENDS IN GENETICS

Determining cellular CTCF and cohesin abundances to constrain 3D genome models

(2019) Claudia Cattoglio et al.   eLife

Multi-enhancer transcriptional hubs confer phenotypic robustness

(2019) Albert Tsai et al.   eLife

Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis

(2019) Yuko Sato et al.   DEVELOPMENT

Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility

(2019) Diana A. Stavreva et al.   MOLECULAR CELL

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes

(2019) Alicia V. Zamudio et al.   MOLECULAR CELL

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

(2019) Yang Eric Guo et al.   NATURE

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences

(2019) David T. McSwiggen et al.   GENES & DEVELOPMENT

Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor

(2019) Maxime Mivelaz et al.   MOLECULAR CELL

Dynamic lineage priming is driven via direct enhancer regulation by ERK

(2019) William B. Hamilton et al.   NATURE

Guided nuclear exploration increases CTCF target search efficiency

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

Live-cell imaging reveals the dynamics of PRC2 and recruitment to chromatin by SUZ12-associated subunits

(2018) Daniel T. Youmans et al.   GENES & DEVELOPMENT

Visualizing transcription factor dynamics in living cells

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

Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription

(2018) Haitham A Shaban et al.   NUCLEIC ACIDS RESEARCH

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

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

(2018) Benjamin R. Sabari et al.   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

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells

(2018) J. O. Andrews et al.   Scientific Reports

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

(2018) Anders S Hansen et al.   eLife

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

RNA polymerase II clustering through carboxy-terminal domain phase separation

(2018) Marc Boehning et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-Molecule Kinetics in Living Cells

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

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

(2018) Ann Boija et al.   CELL

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity

(2018) Joseph Rodriguez et al.   CELL

Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation

(2018) Roubina Tatavosian 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

Single-molecule imaging correlates decreasing nuclear volume with increasing TF-chromatin associations during zebrafish development

(2018) Matthias Reisser et al.   Nature Communications

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

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

DNA residence time is a regulatory factor of transcription repression

(2017) Karen Clauß et al.   NUCLEIC ACIDS RESEARCH

Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions

(2017) Louise C. Bryan et al.   NUCLEIC ACIDS RESEARCH

Single-molecule analysis of steroid receptor and cofactor action in living cells

(2017) Ville Paakinaho et al.   Nature Communications

Nuclear microenvironments modulate transcription from low-affinity enhancers

(2017) Albert Tsai et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

(2015) Davide Normanno et al.   Nature Communications

Light-induced cell damage in live-cell super-resolution microscopy

(2015) Sina Wäldchen et al.   Scientific Reports

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Regulation of RNA polymerase II activation by histone acetylation in single living cells

(2014) Timothy J. Stasevich et al.   NATURE

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

(2014) Ignacio Izeddin et al.   eLife

Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres

(2014) Jan Wisniewski et al.   eLife

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

Extracting intracellular diffusive states and transition rates from single-molecule tracking data

(2013) Fredrik Persson et al.   NATURE METHODS

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

Transcription initiation by human RNA polymerase II visualized at single-molecule resolution

(2012) A. Revyakin et al.   GENES & DEVELOPMENT

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Segregation of molecules at cell division reveals native protein localization

(2012) Dirk Landgraf et al.   NATURE METHODS

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

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

(2008) Stefan Wieser et al.   METHODS