Journal ArticleDOI
Live visualization of chromatin dynamics with fluorescent TALEs
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TLDR
This work established TALE-mediated genome visualization (TGV) to label genomic sequences and follow nuclear positioning and chromatin dynamics in cultured mouse cells and in the living organism, and provides a framework to address the function of genome architecture through visualization of nuclear dynamics in vivo.Abstract:
The spatiotemporal organization of genomes in the nucleus is an emerging key player to regulate genome function Live imaging of nuclear organization dynamics would be a breakthrough toward uncovering the functional relevance and mechanisms regulating genome architecture Here, we used transcription activator-like effector (TALE) technology to visualize endogenous repetitive genomic sequences We established TALE-mediated genome visualization (TGV) to label genomic sequences and follow nuclear positioning and chromatin dynamics in cultured mouse cells and in the living organism TGV is highly specific, thus allowing differential labeling of parental chromosomes by distinguishing between single-nucleotide polymorphisms (SNPs) Our findings provide a framework to address the function of genome architecture through visualization of nuclear dynamics in vivoread more
Citations
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Journal ArticleDOI
Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System
Baohui Chen,Luke A. Gilbert,Beth A. Cimini,Joerg Schnitzbauer,Wei Zhang,Gene-Wei Li,Jason Park,Elizabeth H. Blackburn,Jonathan S. Weissman,Lei S. Qi,Bo Huang +10 more
TL;DR: Using an EGFP-tagged endonuclease-deficient Cas9 protein and a structurally optimized small guide (sg) RNA, robust imaging of repetitive elements in telomeres and coding genes in living cells is demonstrated by repurposing the bacterial CRISPR/Cas system.
Journal ArticleDOI
The CRISPR tool kit for genome editing and beyond.
TL;DR: A brief history of gene-editing tools is presented and the wide range of CRISPR-based genome-targeting tools are described, to conclude with future directions and the broader impact ofCRISPR technologies.
Journal ArticleDOI
A guide to genome engineering with programmable nucleases
Hyongbum Kim,Jin-Soo Kim +1 more
TL;DR: Known nuclease-specific features are essential for researchers to choose the most appropriate tool for a range of applications, including their composition, targetable sites, specificities and mutation signatures, among other characteristics.
Journal ArticleDOI
CRISPR/Cas9 in Genome Editing and Beyond
TL;DR: The Cas9 protein, derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms.
Journal ArticleDOI
Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo
Maria Aurelia Ricci,Carlo Manzo,Maria F. Garcia-Parajo,Melike Lakadamyali,Maria Pia Cosma,Maria Pia Cosma +5 more
TL;DR: This work combined quantitative super-resolution nanoscopy with computer simulations to visualize and count nucleosomes along the chromatin fiber in single nuclei and reveal how the Chromatin fiber is formed at nanoscale level and link chromatin Fiber architecture to stem cell state.
References
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Mark A. Larkin,Gordon Blackshields,Nigel P. Brown,R. Chenna,Paul A. McGettigan,Hamish McWilliam,Franck Valentin,Iain M. Wallace,Andreas Wilm,Rodrigo Lopez,J.D. Thompson,Toby J. Gibson,Desmond G. Higgins +12 more
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Tandem repeats finder: a program to analyze DNA sequences
TL;DR: A new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size is presented and its ability to detect tandem repeats that have undergone extensive mutational change is demonstrated.
Journal ArticleDOI
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon,Siddarth Selvaraj,Siddarth Selvaraj,Feng Yue,Audrey Kim,Yan-Yan Li,Yin-Zhong Shen,Ming Hu,Jun Liu,Bing Ren,Bing Ren +10 more
TL;DR: It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
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Laurie A. Boyer,Tong Ihn Lee,Megan F. Cole,Sarah E. Johnstone,Stuart S. Levine,Jacob P. Zucker,Matthew G. Guenther,Roshan M. Kumar,Heather L. Murray,Richard G. Jenner,David K. Gifford,David K. Gifford,David K. Gifford,Douglas A. Melton,Douglas A. Melton,Rudolf Jaenisch,Richard A. Young,Richard A. Young +17 more
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Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors
Jens Boch,Heidi Scholze,Sebastian Schornack,Angelika Landgraf,Simone Hahn,Sabine Kay,Thomas Lahaye,Anja Nickstadt,Ulla Bonas +8 more
TL;DR: The functionality of a distinct type of DNA binding domain is described and allows the design ofDNA binding domains for biotechnology.