Visualizing transcription factor dynamics in living cells

Liu and Tjian review how superresolution and live-cell imaging are providing new insights into transcription factor dynamics and genome organization.

[1]  C. Brangwynne,et al.  Liquid phase condensation in cell physiology and disease , 2017, Science.

[2]  Sharon E. Torigoe,et al.  A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency , 2017, Genes & development.

[3]  Maxime Woringer,et al.  Spot-On : robust model-based analysis of single-particle tracking experiments 1 2 , 2017 .

[4]  Sébastien Phan,et al.  ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells , 2017, Science.

[5]  Jonathan B Grimm,et al.  Quantifying transcription factor binding dynamics at the single-molecule level in live cells. , 2017, Methods.

[6]  G. Hager,et al.  Single-molecule analysis of steroid receptor and cofactor action in living cells , 2017, Nature Communications.

[7]  Minoru Koyama,et al.  Visualizing long-term single-molecule dynamics in vivo by stochastic protein labeling , 2017, Proceedings of the National Academy of Sciences.

[8]  Nicholas A Moringo,et al.  Single Particle Tracking: From Theory to Biophysical Applications. , 2017, Chemical reviews.

[9]  Matthias Reisser,et al.  Direct Observation of Cell-Cycle-Dependent Interactions between CTCF and Chromatin , 2017, Biophysical journal.

[10]  Mustafa Mir,et al.  Dense Bicoid hubs accentuate binding along the morphogen gradient , 2017, bioRxiv.

[11]  S. Hohmann,et al.  Transcription factor clusters regulate genes in eukaryotic cells , 2017, bioRxiv.

[12]  Na Ji Adaptive optical fluorescence microscopy , 2017, Nature Methods.

[13]  S. Q. Xie,et al.  Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM) , 2017, Nature.

[14]  R. Young,et al.  A Phase Separation Model for Transcriptional Control , 2017, Cell.

[15]  Ilya M. Flyamer,et al.  Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition , 2017, Nature.

[16]  J. Elf,et al.  Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes , 2016, Science.

[17]  Maxim Imakaev,et al.  FISH-ing for captured contacts: towards reconciling FISH and 3C , 2016, Nature Methods.

[18]  R. Tjian,et al.  CTCF and cohesin regulate chromatin loop stability with distinct dynamics , 2016, bioRxiv.

[19]  S. Manley,et al.  A role for mitotic bookmarking of SOX2 in pluripotency and differentiation , 2016, Genes & development.

[20]  J. McNally,et al.  Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin , 2016, Nucleic acids research.

[21]  Brian J. Beliveau,et al.  Spatial organization of chromatin domains and compartments in single chromosomes , 2016, Science.

[22]  Wesley R. Legant,et al.  Real-time imaging of Huntingtin aggregates diverting target search and gene transcription , 2016, eLife.

[23]  R. Tjian,et al.  A dynamic mode of mitotic bookmarking by transcription factors , 2016, bioRxiv.

[24]  Michael Levine,et al.  Enhancer Control of Transcriptional Bursting , 2016, Cell.

[25]  Frank Alber,et al.  Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities , 2016, Nature Communications.

[26]  I. Goldstein,et al.  Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions , 2016, Cell.

[27]  J. Grimm,et al.  RNA Polymerase II cluster dynamics predict mRNA output in living cells , 2016, eLife.

[28]  Valeria Levi,et al.  Long-Lived Binding of Sox2 to DNA Predicts Cell Fate in the Four-Cell Mouse Embryo , 2016, Cell.

[29]  D. Sturgill,et al.  Cajal bodies are linked to genome conformation , 2016, Nature Communications.

[30]  L. Mirny,et al.  The 3D Genome as Moderator of Chromosomal Communication , 2016, Cell.

[31]  Bin Li,et al.  A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening , 2016, Genome research.

[32]  Leonid A. Mirny,et al.  Super-resolution imaging reveals distinct chromatin folding for different epigenetic states , 2015, Nature.

[33]  H. Orland,et al.  Phase Behavior of DNA in the Presence of DNA-Binding Proteins. , 2015, Biophysical journal.

[34]  M. Garcia-Parajo,et al.  A review of progress in single particle tracking: from methods to biophysical insights , 2015, Reports on progress in physics. Physical Society.

[35]  Marco Y. Hein,et al.  A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation , 2015, Cell.

[36]  Sigal Shachar,et al.  Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping , 2015, Cell.

[37]  M. Dahan,et al.  Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher , 2015, Nature Communications.

[38]  Hiroshi Ochiai,et al.  Simultaneous live imaging of the transcription and nuclear position of specific genes , 2015, Nucleic acids research.

[39]  E. Betzig,et al.  Imaging live-cell dynamics and structure at the single-molecule level. , 2015, Molecular cell.

[40]  Peng Yin,et al.  Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes , 2015, Nature Communications.

[41]  R. Mann,et al.  Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness , 2015, Cell.

[42]  J. J. Macklin,et al.  A general method to improve fluorophores for live-cell and single-molecule microscopy , 2014, Nature Methods.

[43]  Wesley R. Legant,et al.  3D imaging of Sox2 enhancer clusters in embryonic stem cells , 2014, eLife.

[44]  Robert S Illingworth,et al.  Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization , 2014, Genes & development.

[45]  J. Doudna,et al.  The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.

[46]  Wesley R. Legant,et al.  Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution , 2014, Science.

[47]  M. Dahan,et al.  Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus , 2014, eLife.

[48]  Mingzhu Wang,et al.  Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units , 2014, Science.

[49]  Robert Tjian,et al.  Looping Back to Leap Forward: Transcription Enters a New Era , 2014, Cell.

[50]  Wesley R. Legant,et al.  Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells , 2014, Cell.

[51]  Andrew S. Belmont,et al.  Large-scale chromatin organization: the good, the surprising, and the still perplexing. , 2014, Current opinion in cell biology.

[52]  Wei Zhang,et al.  Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System , 2014, Cell.

[53]  Rahul Roy,et al.  Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy , 2013, Proceedings of the National Academy of Sciences.

[54]  Luke A. Gilbert,et al.  Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System , 2013, Cell.

[55]  S. McKnight,et al.  Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains , 2013, Cell.

[56]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[57]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[58]  Ignacio Izeddin,et al.  Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells , 2013, Science.

[59]  L. Mirny,et al.  Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data , 2013, Nature Reviews Genetics.

[60]  P. Boutros,et al.  Identifying gene locus associations with promyelocytic leukemia nuclear bodies using immuno-TRAP , 2013, The Journal of cell biology.

[61]  X. Fang,et al.  Single-molecule fluorescence imaging in living cells. , 2013, Annual review of physical chemistry.

[62]  X. Xie,et al.  Single Molecule Imaging of Transcription Factor Binding to DNA in Live Mammalian Cells , 2013, Nature Methods.

[63]  Shamit Soneji,et al.  A biophysical model for transcription factories , 2013, BMC biophysics.

[64]  H. Ng,et al.  Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming. , 2012, Genes & development.

[65]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[66]  J. McNally,et al.  A benchmark for chromatin binding measurements in live cells , 2012, Nucleic acids research.

[67]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[68]  W. D. Laat,et al.  A Decade of 3c Technologies: Insights into Nuclear Organization References , 2022 .

[69]  Michael B. Eisen,et al.  Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition , 2011, PLoS genetics.

[70]  Ty C. Voss,et al.  Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism , 2011, Cell.

[71]  Bin Zhang,et al.  Biogenesis and function of nuclear bodies. , 2011, Trends in genetics : TIG.

[72]  J. Stamatoyannopoulos,et al.  Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. , 2011, Genome research.

[73]  J. McNally,et al.  Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates. , 2010, Biophysical journal.

[74]  R. Tjian,et al.  Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation , 2010, Nature Reviews Genetics.

[75]  Masaru Taniguchi Tomio Tada 1934–2010 , 2010, Nature Immunology.

[76]  Davide Mazza,et al.  FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know? , 2010, Current opinion in cell biology.

[77]  R. Ghosh,et al.  Chromatin higher-order structure and dynamics. , 2010, Cold Spring Harbor perspectives in biology.

[78]  J. T. Kadonaga,et al.  Regulation of gene expression via the core promoter and the basal transcriptional machinery. , 2010, Developmental biology.

[79]  Nathaniel D Heintzman,et al.  Finding distal regulatory elements in the human genome. , 2009, Current opinion in genetics & development.

[80]  Andrej Kosmrlj,et al.  How a protein searches for its site on DNA: the mechanism of facilitated diffusion , 2009 .

[81]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[82]  S. Halford,et al.  An end to 40 years of mistakes in DNA-protein association kinetics? , 2009, Biochemical Society transactions.

[83]  F. Iborra,et al.  Association between active genes occurs at nuclear speckles and is modulated by chromatin environment , 2008, The Journal of cell biology.

[84]  A. Sergé,et al.  Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes , 2008, Nature Methods.

[85]  K. Jaqaman,et al.  Robust single particle tracking in live cell time-lapse sequences , 2008, Nature Methods.

[86]  M. Gustafsson,et al.  Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy , 2008, Science.

[87]  J. Lippincott-Schwartz,et al.  High-density mapping of single-molecule trajectories with photoactivated localization microscopy , 2008, Nature Methods.

[88]  Huimin Chen,et al.  Chapter 1: In vivo applications of fluorescence correlation spectroscopy. , 2008, Methods in cell biology.

[89]  X. Darzacq,et al.  In vivo dynamics of RNA polymerase II transcription , 2007, Nature Structural &Molecular Biology.

[90]  J. Elf,et al.  Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell , 2007, Science.

[91]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[92]  R. Hochstrasser,et al.  Wide-field subdiffraction imaging by accumulated binding of diffusing probes , 2006, Proceedings of the National Academy of Sciences.

[93]  Michael J Rust,et al.  Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) , 2006, Nature Methods.

[94]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[95]  D. Tranchina,et al.  Stochastic mRNA Synthesis in Mammalian Cells , 2006, PLoS biology.

[96]  V. Verkhusha,et al.  Photoactivatable fluorescent proteins , 2005, Nature Reviews Molecular Cell Biology.

[97]  T. Richmond,et al.  X-ray structure of a tetranucleosome and its implications for the chromatin fibre , 2005, Nature.

[98]  V. Verkhusha,et al.  Innovation: Photoactivatable fluorescent proteins. , 2005, Nature reviews. Molecular cell biology.

[99]  Holm Zaehres,et al.  LIF/STAT3 Signaling Fails to Maintain Self‐Renewal of Human Embryonic Stem Cells , 2004, Stem cells.

[100]  R. Pego,et al.  Analysis of binding reactions by fluorescence recovery after photobleaching. , 2004, Biophysical journal.

[101]  J. Lawrence,et al.  Repositioning of muscle-specific genes relative to the periphery of SC-35 domains during skeletal myogenesis. , 2003, Molecular biology of the cell.

[102]  Tom Misteli,et al.  Maintenance of Stable Heterochromatin Domains by Dynamic HP1 Binding , 2003, Science.

[103]  George H. Patterson,et al.  A Photoactivatable GFP for Selective Photolabeling of Proteins and Cells , 2002, Science.

[104]  Roy Riblet,et al.  Subnuclear Compartmentalization of Immunoglobulin Loci During Lymphocyte Development , 2002, Science.

[105]  Frank R. Lin,et al.  Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. , 2002, Molecular cell.

[106]  J. Monypenny,et al.  Fluorescence localization after photobleaching (FLAP): a new method for studying protein dynamics in living cells. , 2002, Journal of microscopy.

[107]  Hiroshi Kimura,et al.  Kinetics of Core Histones in Living Human Cells , 2001, The Journal of cell biology.

[108]  B. O’Malley,et al.  FRAP reveals that mobility of oestrogen receptor-alpha is ligand- and proteasome-dependent. , 2001, Nature cell biology.

[109]  J. McNally,et al.  The glucocorticoid receptor: rapid exchange with regulatory sites in living cells. , 2000, Science.

[110]  K. Zaret,et al.  An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA. , 1999, Molecular cell.

[111]  P. Cook The organization of replication and transcription. , 1999, Science.

[112]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[113]  M. Ptashne,et al.  Transcriptional activation by recruitment , 1997, Nature.

[114]  M. Chalfie GREEN FLUORESCENT PROTEIN , 1995, Photochemistry and photobiology.

[115]  W. Webb,et al.  Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules. , 1994, Biophysical journal.

[116]  R. Tjian,et al.  DNA looping between sites for transcriptional activation: self-association of DNA-bound Sp1. , 1991, Genes & development.

[117]  R. Tjian,et al.  Analysis of Sp1 in vivo reveals mutiple transcriptional domains, including a novel glutamine-rich activation motif , 1988, Cell.

[118]  W. Webb,et al.  Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. , 1976, Biophysical journal.

[119]  W. Webb,et al.  Thermodynamic Fluctuations in a Reacting System-Measurement by Fluorescence Correlation Spectroscopy , 1972 .

[120]  R. Brown XXVII. A brief account of microscopical observations made in the months of June, July and August 1827, on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies , 1828 .