Coupling 1D modifications and 3D nuclear organization: data, models and function.
暂无分享,去创建一个
[1] Neva C. Durand,et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.
[2] Wolfgang Huber,et al. Enhancer loops appear stable during development and are associated with paused polymerase , 2014, Nature.
[3] W. D. Laat,et al. A Decade of 3c Technologies: Insights into Nuclear Organization References , 2022 .
[4] Jill M Dowen,et al. Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes , 2014, Cell.
[5] J. Haber,et al. Effect of Chromosome Tethering on Nuclear Organization in Yeast , 2014, PloS one.
[6] D. Duboule,et al. Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci , 2014, Science.
[7] G. I. Menon,et al. Chromosome positioning from activity-based segregation , 2014, Nucleic acids research.
[8] D. Heermann,et al. Expression-Dependent Folding of Interphase Chromatin , 2012, PloS one.
[9] Romain Koszul,et al. Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms , 2014, eLife.
[10] William Stafford Noble,et al. Comparative analysis of metazoan chromatin , 2014 .
[11] Neva C. Durand,et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes , 2015, Proceedings of the National Academy of Sciences.
[12] Leonid A. Mirny,et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states , 2015, Nature.
[13] Roel van Driel,et al. Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling , 2014, PLoS Comput. Biol..
[14] Jing Liang,et al. Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.
[15] J. Vilar,et al. Systems biophysics of gene expression. , 2013, Biophysical journal.
[16] Patrick Schorderet,et al. Chromatin topology is coupled to Polycomb group protein subnuclear organization , 2016, Nature Communications.
[17] Daniel Jost,et al. Bifurcation in epigenetics: implications in development, proliferation, and diseases. , 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.
[18] P. Meister,et al. From single genes to entire genomes: the search for a function of nuclear organization , 2016, Development.
[19] B. Müller-Hill,et al. Quality and position of the three lac operators of E. coli define efficiency of repression. , 1994, The EMBO journal.
[20] Bertrand R. Caré,et al. Chromatin epigenomic domain folding: size matters , 2015 .
[21] Shlomo Havlin,et al. Crumpled globule model of the three-dimensional structure of DNA , 1993 .
[22] Guillaume J. Filion,et al. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation , 2014, Genes & development.
[23] S. Nechaev,et al. A statistical model of intra-chromosome contact maps. , 2013, Soft matter.
[24] C. Dean,et al. A Polycomb-based switch underlying quantitative epigenetic memory , 2011, Nature.
[25] D. Schwarzer,et al. Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin , 2016, Nature Communications.
[26] J. Sedat,et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.
[27] Davide Marenduzzo,et al. Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models , 2016, Genome Biology.
[28] Robert E. Kingston,et al. Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. , 2013, Molecular cell.
[29] D. Jost,et al. The folding landscape of the epigenome , 2016, Physical biology.
[30] J. Dekker,et al. Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription , 2014, Cell.
[31] Benjamin Leblanc,et al. Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila , 2011, Cell.
[32] D. Odom,et al. Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture , 2015, Cell reports.
[33] Davide Marenduzzo,et al. Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains , 2016, Nucleic acids research.
[34] J. Dekker,et al. Capturing Chromosome Conformation , 2002, Science.
[35] Dieter W. Heermann,et al. Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization , 2010, PloS one.
[36] B. Bernstein,et al. SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. , 2013, Developmental cell.
[37] Renato Paro,et al. Silencing chromatin: comparing modes and mechanisms , 2011, Nature Reviews Genetics.
[38] V. Orlando,et al. The function of the epigenome in cell reprogramming , 2007, Cellular and Molecular Life Sciences.
[39] Moritz Herrmann,et al. Comparative analysis of metazoan chromatin organization , 2014, Nature.
[40] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[41] Ilya M. Flyamer,et al. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains , 2016, Genome research.
[42] Diana B. Marina,et al. A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly , 2013, Nature.
[43] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[44] J. Dekker,et al. Structural and functional diversity of Topologically Associating Domains , 2015, FEBS letters.
[45] L. Mirny,et al. Chromosome Compaction by Active Loop Extrusion , 2016, Biophysical journal.
[46] K. Sneppen,et al. Nucleation and spreading of a heterochromatic domain in fission yeast , 2016, Nature Communications.
[47] Scott B. Dewell,et al. Greater Than the Sum of Parts: Complexity of the Dynamic Epigenome. , 2016, Molecular cell.
[48] A. Tanay,et al. Single cell Hi-C reveals cell-to-cell variability in chromosome structure , 2013, Nature.
[49] Guido Tiana,et al. Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains. , 2016, Biophysical journal.
[50] S. Leibler,et al. DNA looping and physical constraints on transcription regulation. , 2003, Journal of molecular biology.
[51] Suliana Manley,et al. Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states , 2015, Proceedings of the National Academy of Sciences.
[52] A. Visel,et al. Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.
[53] Yan Li,et al. A high-resolution map of three-dimensional chromatin interactome in human cells , 2013, Nature.
[54] Mario Nicodemi,et al. Complexity of chromatin folding is captured by the strings and binders switch model , 2012, Proceedings of the National Academy of Sciences.
[55] Wei Wang,et al. Constructing 3D interaction maps from 1D epigenomes , 2016, Nature Communications.
[56] J. Dekker,et al. Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation , 2015, Nature.
[57] Leonor Saiz,et al. DNA looping: the consequences and its control. , 2006, Current opinion in structural biology.
[58] Leonid A. Mirny,et al. Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions , 2014, bioRxiv.
[59] S. Mundlos,et al. Formation of new chromatin domains determines pathogenicity of genomic duplications , 2016, Nature.
[60] Christophe Zimmer,et al. A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus , 2012, Current Biology.
[61] L. Mirny. The fractal globule as a model of chromatin architecture in the cell , 2011, Chromosome Research.
[62] F. Spitz. Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles. , 2016, Seminars in cell & developmental biology.
[63] K. Sneppen,et al. Theoretical Analysis of Epigenetic Cell Memory by Nucleosome Modification , 2007, Cell.
[64] Ralf Everaers,et al. Structure and Dynamics of Interphase Chromosomes , 2008, PLoS Comput. Biol..
[65] John F. Marko,et al. Self-organization of domain structures by DNA-loop-extruding enzymes , 2012, Nucleic acids research.
[66] L. Mirny,et al. Formation of Chromosomal Domains in Interphase by Loop Extrusion , 2015, bioRxiv.
[67] Anton Goloborodko,et al. Compaction and segregation of sister chromatids via active loop extrusion , 2016, bioRxiv.
[68] Michael Q. Zhang,et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function , 2015, Cell.
[69] Kurt Kremer,et al. From a melt of rings to chromosome territories: the role of topological constraints in genome folding , 2013, Reports on progress in physics. Physical Society.
[70] Daniel Jost,et al. Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains , 2014, Nucleic acids research.
[71] Benno Müller-Hill,et al. Induction of the lac promoter in the absence of DNA loops and the stoichiometry of induction , 2006, Nucleic acids research.
[72] K. Nasmyth. THE GENOME : Joining , Resolving , and Separating Sister Chromatids During Mitosis and Meiosis , 2006 .
[73] A. Mirsky,et al. REPRESSED AND ACTIVE CHROMATIN ISOLATED FROM INTERPHASE LYMPHOCYTES. , 1963, Proceedings of the National Academy of Sciences of the United States of America.
[74] Sharon Y. R. Dent,et al. Chromatin modifiers and remodellers: regulators of cellular differentiation , 2013, Nature Reviews Genetics.
[75] S. Sugiyama,et al. The genome folding mechanism in yeast. , 2013, Journal of biochemistry.
[76] Julien Dorier,et al. Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes , 2013, Nucleic acids research.
[77] Jie Liang,et al. Spatial confinement is a major determinant of the folding landscape of human chromosomes , 2014, Nucleic acids research.
[78] S. Q. Xie,et al. Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation , 2015, Molecular systems biology.
[79] Job Dekker,et al. Organization of the Mitotic Chromosome , 2013, Science.
[80] A. Tanay,et al. Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome , 2012, Cell.
[81] N. Brockdorff,et al. The interplay of histone modifications – writers that read , 2015, EMBO reports.