Constraints and limitations on decoding positional information: the Bicoid case-study
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[1] L. Mirny,et al. Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. , 2004, Biophysical journal.
[2] Hernan G. Garcia,et al. Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos , 2014, Proceedings of the National Academy of Sciences.
[3] Aleksandra M. Walczak,et al. Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos , 2013, Current Biology.
[4] Lars Hufnagel,et al. Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis , 2018, bioRxiv.
[5] W. Bialek,et al. Stability and Nuclear Dynamics of the Bicoid Morphogen Gradient , 2007, Cell.
[6] Maxime Dahan,et al. Intra-nuclear mobility and target search mechanisms of transcription factors: a single-molecule perspective on gene expression. , 2012, Biochimica et biophysica acta.
[7] Heng Xu,et al. COMBINING PROTEIN AND mRNA QUANTIFICATION TO DECIPHER TRANSCRIPTIONAL REGULATION , 2015, Nature Methods.
[8] C. Desplan,et al. Down-regulation of the Drosophila morphogen bicoid by the torso receptor-mediated signal transduction cascade , 1993, Cell.
[9] Michael W. Perry,et al. Precision of Hunchback Expression in the Drosophila Embryo , 2012, Current Biology.
[10] Winship Herr,et al. Basal promoter elements as a selective determinant of transcriptional activator function , 1995, Nature.
[11] Nathalie Dostatni,et al. High mobility of bicoid captured by fluorescence correlation spectroscopy: implication for the rapid establishment of its gradient. , 2010, Biophysical journal.
[12] Ann M. Powers,et al. Bioluminescent Imaging and Histopathologic Characterization of WEEV Neuroinvasion in Outbred CD-1 Mice , 2013, PloS one.
[13] L. Mirny,et al. Nucleosome-mediated cooperativity between transcription factors , 2009, Proceedings of the National Academy of Sciences.
[14] Danyang Yu,et al. Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila , 2014, Genes & development.
[15] J. Stamatoyannopoulos,et al. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding , 2011, Genome Biology.
[16] T. Duke,et al. Conformational spread: the propagation of allosteric states in large multiprotein complexes. , 2004, Annual review of biophysics and biomolecular structure.
[17] C. Fradin,et al. The time to measure positional information: maternal Hunchback is required for the synchrony of the Bicoid transcriptional response at the onset of zygotic transcription , 2010, Development.
[18] 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.
[19] Lior Pachter,et al. Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species , 2010, PLoS biology.
[20] Pierre Gönczy,et al. A single amino acid can determine the DNA binding specificity of homeodomain proteins , 1989, Cell.
[21] J. Elf,et al. Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell , 2007, Science.
[22] Thomas Gregor,et al. Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network , 2013, Proceedings of the National Academy of Sciences.
[23] R. MacKinnon,et al. Quantitative analysis of mammalian GIRK2 channel regulation by G proteins, the signaling lipid PIP2 and Na+ in a reconstituted system , 2014, eLife.
[24] Roger Brent,et al. DNA specificity of the bicoid activator protein is determined by homeodomain recognition helix residue 9 , 1989, Cell.
[25] Wolfgang Driever,et al. Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen , 1989, Nature.
[26] Julia Zeitlinger,et al. Paused RNA polymerase II inhibits new transcriptional initiation , 2017, Nature Genetics.
[27] Nikolaus Rajewsky,et al. The Drosophila embryo at single-cell transcriptome resolution , 2017, Science.
[28] Andrej Kosmrlj,et al. How a protein searches for its site on DNA: the mechanism of facilitated diffusion , 2009 .
[29] Luciano da Fontoura Costa,et al. Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation , 2011, PLoS Comput. Biol..
[30] Michael B. Eisen,et al. Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene , 2018, bioRxiv.
[31] Mustafa Mir,et al. Dense Bicoid hubs accentuate binding along the morphogen gradient , 2017, bioRxiv.
[32] Aleksandra M. Walczak,et al. hunchback Promoters Can Readout Morphogenetic Positional Information in Less Than a Minute , 2019, bioRxiv.
[33] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[34] David W Tank,et al. Measurement and perturbation of morphogen lifetime: effects on gradient shape. , 2011, Biophysical journal.
[35] Stephen Butcher,et al. Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo , 2011, PLoS genetics.
[36] Aleksandra M. Walczak,et al. Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern , 2018, bioRxiv.
[37] Jeremy Gunawardena,et al. Information Integration and Energy Expenditure in Gene Regulation , 2016, Cell.
[38] Eugene W. Myers,et al. Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans , 2009, Cell.
[39] Aleksandra M. Walczak,et al. Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos , 2016, PLoS Comput. Biol..
[40] Claude C. Warzecha,et al. Ldb1 complexes: the new master regulators of erythroid gene transcription. , 2014, Trends in genetics : TIG.
[41] C. Desplan,et al. Bicoid functions without its TATA-binding protein-associated factor interaction domains. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[42] S. Leibler,et al. Establishment of developmental precision and proportions in the early Drosophila embryo , 2002, Nature.
[43] Claude Desplan,et al. Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila , 1994, Cell.
[44] A. Riggs,et al. The lac represser-operator interaction , 1970 .
[45] G. Raposo,et al. BLOC-1 Brings Together the Actin and Microtubule Cytoskeletons to Generate Recycling Endosomes , 2016, Current Biology.
[46] Michael Levine,et al. Rapid Rates of Pol II Elongation in the Drosophila Embryo , 2017, Current Biology.
[47] Tetsuya Nakamura,et al. Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation , 2011, Nature Cell Biology.
[48] Johan Elf,et al. The lac Repressor Displays Facilitated Diffusion in Living Cells , 2012, Science.
[49] Shawn C. Little,et al. Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting , 2018, Cell.
[50] W. Bialek,et al. Probing the Limits to Positional Information , 2007, Cell.
[51] H. Berg,et al. Physics of chemoreception. , 1977, Biophysical journal.
[52] Adam M. Corrigan,et al. Author response: A continuum model of transcriptional bursting , 2016 .
[53] Gasper Tkacik,et al. Positional information, in bits , 2010, Proceedings of the National Academy of Sciences.
[54] Aleksandra M Walczak,et al. 3 minutes to precisely measure morphogen concentration , 2018, bioRxiv.
[55] Hernan G. Garcia,et al. Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning , 2013, Current Biology.
[56] Shawn C. Little,et al. Precise Developmental Gene Expression Arises from Globally Stochastic Transcriptional Activity , 2013, Cell.
[57] A. Durbin,et al. A Dengue Vaccine , 2016, Cell.
[58] David S. Lorberbaum,et al. Genetic evidence that Nkx2.2 acts primarily downstream of Neurog3 in pancreatic endocrine lineage development , 2017, eLife.
[59] R. Tjian,et al. DNA Template and Activator-Coactivator Requirements for Transcriptional Synergism by Drosophila Bicoid , 1995, Science.
[60] W. Bialek,et al. Diffusion and scaling during early embryonic pattern formation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[61] A. Riggs,et al. The lac repressor-operator interaction. 3. Kinetic studies. , 1970, Journal of molecular biology.
[62] Mustafa Mir,et al. Author response: Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos , 2018 .
[63] C. Nüsslein-Volhard,et al. The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner , 1988, Cell.
[64] Mathieu Coppey,et al. Modelling the Bicoid gradient , 2010, Development.
[65] Aleksandra M. Walczak,et al. New methods to image transcription in living fly embryos: the insights so far, and the prospects , 2016, Wiley interdisciplinary reviews. Developmental biology.
[66] R. Singer,et al. Localization of ASH1 mRNA particles in living yeast. , 1998, Molecular cell.
[67] N. Dostatni,et al. Bicoid Determines Sharp and Precise Target Gene Expression in the Drosophila Embryo , 2005, Current Biology.
[68] H. Jäckle,et al. Cooperative DNA‐binding by Bicoid provides a mechanism for threshold‐dependent gene activation in the Drosophila embryo , 1998, The EMBO journal.
[69] Tyler J. Gibson,et al. Continued Activity of the Pioneer Factor Zelda Is Required to Drive Zygotic Genome Activation. , 2019, Molecular cell.
[70] Mariela D. Petkova,et al. Optimal Decoding of Cellular Identities in a Genetic Network , 2016, Cell.