Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

Cell - Tập 159 - Trang 647-661 - 2014
Luke A. Gilbert1,2,3,4, Max A. Horlbeck1,2,3,4, Britt Adamson1,2,3,4, Jacqueline E. Villalta1,2,3,4, Yuwen Chen1,2,3,4, Evan H. Whitehead1,3,5, Carla Guimaraes6, Barbara Panning7, Hidde L. Ploegh6, Michael C. Bassik1,2,3,4, Lei S. Qi1,3,5, Martin Kampmann1,2,3,4, Jonathan S. Weissman1,2,3,4
1Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
2Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
3California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA
4Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
5Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
6Department of Biology, Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
7Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA

Tài liệu tham khảo

Adamson, 2012, A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response, Nat. Cell Biol., 14, 318, 10.1038/ncb2426 Alberich-Jordà, 2012, C/EBPγ deregulation results in differentiation arrest in acute myeloid leukemia, J. Clin. Invest., 122, 4490, 10.1172/JCI65102 Bassett, 2014, Considerations when investigating lncRNA function in vivo, eLife, 3, e03058, 10.7554/eLife.03058 Bassik, 2009, Rapid creation and quantitative monitoring of high coverage shRNA libraries, Nat. Methods, 6, 443, 10.1038/nmeth.1330 Bassik, 2013, A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility, Cell, 152, 909, 10.1016/j.cell.2013.01.030 Beerli, 1998, Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks, Proc. Natl. Acad. Sci. USA, 95, 14628, 10.1073/pnas.95.25.14628 Beerli, 2000, Positive and negative regulation of endogenous genes by designed transcription factors, Proc. Natl. Acad. Sci. USA, 97, 1495, 10.1073/pnas.040552697 Bonifacino, 2006, Retrograde transport from endosomes to the trans-Golgi network, Nat. Rev. Mol. Cell Biol., 7, 568, 10.1038/nrm1985 Boone, 2007, Exploring genetic interactions and networks with yeast, Nat. Rev. Genet., 8, 437, 10.1038/nrg2085 Carette, 2009, Haploid genetic screens in human cells identify host factors used by pathogens, Science, 326, 1231, 10.1126/science.1178955 Cech, 2014, The noncoding RNA revolution-trashing old rules to forge new ones, Cell, 157, 77, 10.1016/j.cell.2014.03.008 Chang, 2006, Lessons from Nature: microRNA-based shRNA libraries, Nat. Methods, 3, 707, 10.1038/nmeth923 Costanzo, 2010, The genetic landscape of a cell, Science, 327, 425, 10.1126/science.1180823 Davis, 1987, Expression of a single transfected cDNA converts fibroblasts to myoblasts, Cell, 51, 987, 10.1016/0092-8674(87)90585-X Derrien, 2012, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res., 22, 1775, 10.1101/gr.132159.111 Djebali, 2012, Landscape of transcription in human cells, Nature, 489, 101, 10.1038/nature11233 Duan, 2014, Genome-wide identification of CRISPR/Cas9 off-targets in human genome, Cell Res., 24, 1009, 10.1038/cr.2014.87 Gaj, 2013, ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering, Trends Biotechnol., 31, 397, 10.1016/j.tibtech.2013.04.004 Geisler, 2013, RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts, Nat. Rev. Mol. Cell Biol., 14, 699, 10.1038/nrm3679 Gilbert, 2013, CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes, Cell, 154, 442, 10.1016/j.cell.2013.06.044 Guimaraes, 2011, Identification of host cell factors required for intoxication through use of modified cholera toxin, J. Cell Biol., 195, 751, 10.1083/jcb.201108103 Habedanck, 2005, The Polo kinase Plk4 functions in centriole duplication, Nat. Cell Biol., 7, 1140, 10.1038/ncb1320 Huang, 1996, Sensitivity and selectivity of the DNA damage sensor responsible for activating p53-dependent G1 arrest, Proc. Natl. Acad. Sci. USA, 93, 4827, 10.1073/pnas.93.10.4827 Huang, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211 Huang, 2009, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Res., 37, 1, 10.1093/nar/gkn923 Jackson, 2002, Sensing and repairing DNA double-strand breaks, Carcinogenesis, 23, 687, 10.1093/carcin/23.5.687 Jackson, 2003, Expression profiling reveals off-target gene regulation by RNAi, Nat. Biotechnol., 21, 635, 10.1038/nbt831 Kampmann, 2013, Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells, Proc. Natl. Acad. Sci. USA, 110, E2317, 10.1073/pnas.1307002110 Kampmann, 2014, Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps, Nat. Protoc., 9, 1825, 10.1038/nprot.2014.103 Koike-Yusa, 2014, Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library, Nat. Biotechnol., 32, 267, 10.1038/nbt.2800 Kuscu, 2014, Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease, Nat. Biotechnol., 32, 677, 10.1038/nbt.2916 Mittler, 2003, A novel docking site on Mediator is critical for activation by VP16 in mammalian cells, EMBO J., 22, 6494, 10.1093/emboj/cdg619 Qi, 2013, Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression, Cell, 152, 1173, 10.1016/j.cell.2013.02.022 Rine, 1983, Targeted selection of recombinant clones through gene dosage effects, Proc. Natl. Acad. Sci. USA, 80, 6750, 10.1073/pnas.80.22.6750 Sander, 2014, CRISPR-Cas systems for editing, regulating and targeting genomes, Nat. Biotechnol., 32, 347, 10.1038/nbt.2842 Shalem, 2014, Genome-scale CRISPR-Cas9 knockout screening in human cells, Science, 343, 84, 10.1126/science.1247005 Sigoillot, 2012, A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens, Nat. Methods, 9, 363, 10.1038/nmeth.1898 Smith, 2009, The COG complex, Rab6 and COPI define a novel Golgi retrograde trafficking pathway that is exploited by SubAB toxin, Traffic, 10, 1502, 10.1111/j.1600-0854.2009.00965.x Spitz, 2012, Transcription factors: from enhancer binding to developmental control, Nat. Rev. Genet., 13, 613, 10.1038/nrg3207 Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024 Tanenbaum, 2011, A complex of Kif18b and MCAK promotes microtubule depolymerization and is negatively regulated by Aurora kinases, Curr. Biol., 21, 1356, 10.1016/j.cub.2011.07.017 Tanenbaum, 2014, A versatile protein tagging system for signal amplification in single molecule imaging and gene regulation, Cell, 159, 635, 10.1016/j.cell.2014.09.039 Van Ness, 1980, ADP-ribosylation of elongation factor 2 by diphtheria toxin. Isolation and properties of the novel ribosyl-amino acid and its hydrolysis products, J. Biol. Chem., 255, 10717, 10.1016/S0021-9258(19)70366-4 Vogelstein, 2013, Cancer genome landscapes, Science, 339, 1546, 10.1126/science.1235122 Wang, 2014, Genetic screens in human cells using the CRISPR-Cas9 system, Science, 343, 80, 10.1126/science.1246981 Wernick, 2010, Cholera toxin: an intracellular journey into the cytosol by way of the endoplasmic reticulum, Toxins (Basel), 2, 310, 10.3390/toxins2030310 Wu, 2014, Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells, Nat. Biotechnol., 32, 670, 10.1038/nbt.2889 Zhang, 2000, PU.1 inhibits GATA-1 function and erythroid differentiation by blocking GATA-1 DNA binding, Blood, 96, 2641, 10.1182/blood.V96.8.2641 Zhang, 2011, Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription, Nat. Biotechnol., 29, 149, 10.1038/nbt.1775 Zhao, 2013, TSGene: a web resource for tumor suppressor genes, Nucleic Acids Res., 41, D970, 10.1093/nar/gks937 Bernardi, 2008, Derlin-1 facilitates the retro-translocation of cholera toxin, Mol. Biol. Cell, 19, 877, 10.1091/mbc.E07-08-0755 Chen, 2013, Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system, Cell, 155, 1479, 10.1016/j.cell.2013.12.001 Davoli, 2013, Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome, Cell, 155, 948, 10.1016/j.cell.2013.10.011 Fu, 2013, High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells, Nat. Biotechnol., 31, 822, 10.1038/nbt.2623 Hsu, 2013, DNA targeting specificity of RNA-guided Cas9 nucleases, Nat. Biotechnol., 31, 827, 10.1038/nbt.2647 Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25 Mootha, 2003, PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes, Nat. Genet., 34, 267, 10.1038/ng1180 Panning, 2004, X inactivation in mouse ES cells: histone modifications and FISH, Methods Enzymol., 376, 419, 10.1016/S0076-6879(03)76028-5 Rodriguez, 2013, APPRIS: annotation of principal and alternative splice isoforms, Nucleic Acids Res., 41, D110, 10.1093/nar/gks1058 Solimini, 2012, Recurrent hemizygous deletions in cancers may optimize proliferative potential, Science, 337, 104, 10.1126/science.1219580