Visualizing transcription factor dynamics in living cells

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency

(2017) Liangqi Xie et al.   GENES & DEVELOPMENT

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

(2017) Diego M. Presman et al.   METHODS

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

FISH-ing for captured contacts: towards reconciling FISH and 3C

(2017) Geoffrey Fudenberg et al.   NATURE METHODS

Adaptive optical fluorescence microscopy

(2017) Na Ji   NATURE METHODS

Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling

(2017) Hui Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

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

(2017) Ville Paakinaho et al.   Nature Communications

Transcription factor clusters regulate genes in eukaryotic cells

(2017) Adam JM Wollman et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Phase Behavior of DNA in the Presence of DNA-Binding Proteins

(2016) Guillaume Le Treut et al.   BIOPHYSICAL JOURNAL

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

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

(2016) Cédric Deluz et al.   GENES & DEVELOPMENT

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

(2016) Yarui Diao et al.   GENOME RESEARCH

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

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

Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes

(2016) Francisco Balzarotti et al.   SCIENCE

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Cajal bodies are linked to genome conformation

(2016) Qiuyan Wang et al.   Nature Communications

Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

(2016) Chao Dai et al.   Nature Communications

Real-time imaging of Huntingtin aggregates diverting target search and gene transcription

(2016) Li Li et al.   eLife

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

A dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

(2015) Sigal Shachar et al.   CELL

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

Imaging Live-Cell Dynamics and Structure at the Single-Molecule Level

(2015) Zhe Liu 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

Simultaneous live imaging of the transcription and nuclear position of specific genes

(2015) Hiroshi Ochiai et al.   NUCLEIC ACIDS RESEARCH

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 super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

(2014) F. Song et al.   SCIENCE

Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution

(2014) Bi-Chang Chen et al.   SCIENCE

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

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

Single-Molecule Fluorescence Imaging in Living Cells

(2013) Tie Xia et al.   Annual Review of Physical Chemistry

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

(2013) Ilmin Kwon et al.   CELL

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Large-scale chromatin organization: the good, the surprising, and the still perplexing

(2013) Andrew S Belmont   CURRENT OPINION IN CELL BIOLOGY

Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP

(2013) Reagan W. Ching et al.   JOURNAL OF CELL BIOLOGY

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

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

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy

(2013) Z. W. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) I. I. Cisse et al.   SCIENCE

A biophysical model for transcription factories

(2013) Ana Z Canals-Hamann et al.   BMC Biophysics

Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming

(2012) M. Percharde et al.   GENES & DEVELOPMENT

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

(2011) O. Hakim et al.   GENOME RESEARCH

Biogenesis and function of nuclear bodies

(2011) Yuntao S. Mao et al.   TRENDS IN GENETICS

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

Cross-Validating FRAP and FCS to Quantify the Impact of Photobleaching on In Vivo Binding Estimates

(2010) Timothy J. Stasevich et al.   BIOPHYSICAL JOURNAL

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

Tomio Tada 1934–2010

(2010) Masaru Taniguchi   NATURE IMMUNOLOGY

Chromatin Higher-order Structure and Dynamics

(2010) C. L. Woodcock et al.   Cold Spring Harbor Perspectives in Biology

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

(2009) Stephen E. Halford   BIOCHEMICAL SOCIETY TRANSACTIONS

Finding distal regulatory elements in the human genome

(2009) Nathaniel D Heintzman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

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

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Association between active genes occurs at nuclear speckles and is modulated by chromatin environment

(2008) Jill M. Brown et al.   JOURNAL OF CELL BIOLOGY

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

(2008) Arnauld Sergé 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

Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy

(2008) L. Schermelleh et al.   SCIENCE