Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
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Xiaowei Zhuang | X. Zhuang | B. Bintu | Jun-Han Su | Seon Kinrot | Pu Zheng | Jun-Han Su | Pu Zheng | Seon S. Kinrot | Bogdan Bintu
[1] S. Mango,et al. Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos. , 2020, Molecular cell.
[2] Daniel S. Day,et al. Coactivator condensation at super-enhancers links phase separation and gene control , 2018, Science.
[3] X. Xie,et al. Three-dimensional genome structures of single diploid human cells , 2018, Science.
[4] Daniel Capurso,et al. Multiplex chromatin interactions with single-molecule precision , 2019, Nature.
[5] Xiaoshu Xu,et al. A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology. , 2019, Journal of molecular biology.
[6] T. Cremer,et al. Chromosome territories. , 2010, Cold Spring Harbor perspectives in biology.
[7] Manolis Kellis,et al. Joint profiling of DNA methylation and chromatin architecture in single cells , 2019, Nature Methods.
[8] Nicholas A. Sinnott-Armstrong,et al. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells , 2018, Science.
[9] Robert H. Singer,et al. Fluorescence in situ hybridization: past, present and future , 2003, Journal of Cell Science.
[10] J. Dekker,et al. A chromosome folding intermediate at the condensin-to-cohesin transition during telophase , 2019, Nature Cell Biology.
[11] L. Mirny,et al. The 3D Genome as Moderator of Chromosomal Communication , 2016, Cell.
[12] X. Zhuang,et al. Spatially resolved, highly multiplexed RNA profiling in single cells , 2015, Science.
[13] Howard Y. Chang,et al. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing , 2016, Nature Methods.
[14] G. Papadopoulos,et al. Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms. , 2019, Molecular cell.
[15] Robert Tjian,et al. CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells , 2015, Proceedings of the National Academy of Sciences.
[16] Shaojie Zhang,et al. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow , 2016, Nature Biotechnology.
[17] Alma L. Burlingame,et al. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin , 2017, Nature.
[18] S. McKinney,et al. Nonblinking and long-lasting single-molecule fluorescence imaging , 2006, Nature Methods.
[19] Antonina Hafner,et al. Visualizing DNA folding and RNA in embryos at single-cell resolution , 2019, Nature.
[20] A. Tanay,et al. Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome , 2012, Cell.
[21] Jian Ma,et al. Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler , 2018, The Journal of cell biology.
[22] Erik L. G. Wernersson,et al. GPSeq reveals the radial organization of chromatin in the cell nucleus , 2020, Nature Biotechnology.
[23] Graham T Dempsey,et al. A user's guide to localization-based super-resolution fluorescence imaging. , 2013, Methods in cell biology.
[24] E. Heard,et al. Advances in epigenetics link genetics to the environment and disease , 2019, Nature.
[25] M. Cosma,et al. Visualizing the genome in high resolution challenges our textbook understanding , 2020, Nature Methods.
[26] Galt P. Barber,et al. BigWig and BigBed: enabling browsing of large distributed datasets , 2010, Bioinform..
[27] Neva C. Durand,et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.
[28] Lei S. Qi,et al. Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH , 2017, Biophysical journal.
[29] R. Young,et al. A Phase Separation Model for Transcriptional Control , 2017, Cell.
[30] Charles H. Li,et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates , 2018, Science.
[31] Howard Y. Chang,et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.
[32] Bo Huang,et al. Imaging Specific Genomic DNA in Living Cells. , 2016, Annual review of biophysics.
[33] E. Liu,et al. An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.
[34] Bas van Steensel,et al. Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression , 2017, Cell.
[35] William Stafford Noble,et al. Massively multiplex single-cell Hi-C , 2016, Nature Methods.
[36] Irina Solovei,et al. How to rule the nucleus: divide et impera. , 2016, Current opinion in cell biology.
[37] A. Tanay,et al. Cell-cycle dynamics of chromosomal organisation at single-cell resolution , 2016, Nature.
[38] Mustafa Mir,et al. Phase separation drives heterochromatin domain formation , 2017, Nature.
[39] Bo Huang,et al. Tracking multiple genomic elements using correlative CRISPR imaging and sequential DNA FISH , 2017, bioRxiv.
[40] A. Belmont,et al. Genome organization around nuclear speckles. , 2019, Current opinion in genetics & development.
[41] Peter H. L. Krijger,et al. Regulation of disease-associated gene expression in the 3D genome , 2016, Nature Reviews Molecular Cell Biology.
[42] Ilya M. Flyamer,et al. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition , 2017, Nature.
[43] S. P. Lloyd,et al. Least squares quantization in PCM , 1982, IEEE Trans. Inf. Theory.
[44] Wendy A Bickmore,et al. The spatial organization of the human genome. , 2013, Annual review of genomics and human genetics.
[45] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[46] R. Tjian,et al. Genomes in Focus: Development and Applications of CRISPR-Cas9 Imaging Technologies. , 2018, Angewandte Chemie.
[47] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[48] Siddharth S. Dey,et al. scDam&T‐seq combines DNA adenine methyltransferase-based labeling of protein-DNA contact sites with transcriptome sequencing to analyze regulatory programs in single cells , 2019, Nature biotechnology.
[49] Hazen P Babcock,et al. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization , 2016, Proceedings of the National Academy of Sciences.
[50] Conor Fitzpatrick,et al. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells , 2019, Nature Methods.
[51] X. Darzacq,et al. Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II , 2018, Nature.
[52] S. Q. Xie,et al. Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM) , 2017, Nature.
[53] Robert Tjian,et al. Looping Back to Leap Forward: Transcription Enters a New Era , 2014, Cell.
[54] Jan Vogelsang,et al. On the mechanism of Trolox as antiblinking and antibleaching reagent. , 2009, Journal of the American Chemical Society.
[55] D. Gerlich,et al. Organization of Chromatin by Intrinsic and Regulated Phase Separation , 2019, Cell.
[56] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[57] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[58] R. Tjian,et al. Imaging dynamic and selective low-complexity domain interactions that control gene transcription , 2018, Science.
[59] Miao Yu,et al. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq , 2016, Cell Research.
[60] A. Tanay,et al. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture , 2011, Nature Genetics.
[61] B. Tabak,et al. Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus , 2018, Cell.
[62] J. Dekker,et al. Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation , 2015, Nature.
[63] Andre J. Faure,et al. 3D structure of individual mammalian genomes studied by single cell Hi-C , 2017, Nature.
[64] L. Mirny,et al. Heterochromatin drives compartmentalization of inverted and conventional nuclei , 2019, Nature.
[65] Bing Ren,et al. The Three-Dimensional Organization of Mammalian Genomes. , 2017, Annual review of cell and developmental biology.
[66] T. Misteli,et al. Causes and consequences of nuclear gene positioning , 2017, Journal of Cell Science.
[67] R. Eils,et al. Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes , 2005, PLoS biology.
[68] J. Sedat,et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.
[69] W. de Laat,et al. Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription , 2008, PloS one.
[70] Multiplexed imaging of nucleome architectures in single cells of mammalian tissue , 2020, Nature Communications.
[71] James T. Robinson,et al. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. , 2016, Cell systems.
[72] Victor O. Leshyk,et al. The 4D nucleome project , 2017, Nature.
[73] A. Pombo,et al. Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations , 2006, PLoS biology.
[74] S. Dokudovskaya,et al. Nucleolus: A Central Hub for Nuclear Functions. , 2019, Trends in cell biology.
[75] Steven P. Callahan,et al. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling , 2018, bioRxiv.
[76] Brian J. Beliveau,et al. Spatial organization of chromatin domains and compartments in single chromosomes , 2016, Science.