Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation.

[1]  L. Lai,et al.  Highly efficient RNA-guided base editing in rabbit , 2018, Nature Communications.

[2]  Max J. Kellner,et al.  RNA editing with CRISPR-Cas13 , 2017, Science.

[3]  Aviv Regev,et al.  RNA targeting with CRISPR–Cas13 , 2017, Nature.

[4]  Jun Ma,et al.  The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a , 2017, Cell.

[5]  D. Burstein,et al.  RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes. , 2017, Molecular cell.

[6]  Jiehua Zhou,et al.  Aptamers as targeted therapeutics: current potential and challenges , 2017, Nature Reviews Drug Discovery.

[7]  Aviv Regev,et al.  Nucleic acid detection with CRISPR-Cas13a/C2c2 , 2017, Science.

[8]  Akihiko Kondo,et al.  Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion , 2017, Nature Biotechnology.

[9]  Rui Zhang,et al.  Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion , 2017, Nature Biotechnology.

[10]  Daesik Kim,et al.  Highly efficient RNA-guided base editing in mouse embryos , 2017, Nature Biotechnology.

[11]  F. Slack,et al.  MicroRNA therapeutics: towards a new era for the management of cancer and other diseases , 2017, Nature Reviews Drug Discovery.

[12]  Kevin T. Zhao,et al.  Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions , 2017, Nature Biotechnology.

[13]  Kira S. Makarova,et al.  Diversity and evolution of class 2 CRISPR–Cas systems , 2017, Nature Reviews Microbiology.

[14]  Yanli Wang,et al.  Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities , 2017, Cell.

[15]  Jennifer A. Doudna,et al.  New CRISPR-Cas systems from uncultivated microbes , 2016, Nature.

[16]  Sergey A. Shmakov,et al.  Cas13b is a Type VI-B CRISPR-associated RNA-Guided RNase differentially regulated by accessory proteins Csx27 and Csx28 , 2016, bioRxiv.

[17]  M. Mahfouz,et al.  Engineering Plant Immunity: Using CRISPR/Cas9 to Generate Virus Resistance , 2016, Front. Plant Sci..

[18]  M. Mahfouz,et al.  Genome editing: the road of CRISPR/Cas9 from bench to clinic , 2016, Experimental & Molecular Medicine.

[19]  Jennifer A. Doudna,et al.  Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection , 2016, Nature.

[20]  A. Kondo,et al.  Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems , 2016, Science.

[21]  A. Sherman,et al.  Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. , 2016, Molecular plant pathology.

[22]  H. Puchta.  Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. , 2016, The Plant journal : for cell and molecular biology.

[23]  A. Molnár,et al.  Engineering of CRISPR/Cas9‐mediated potyvirus resistance in transgene‐free Arabidopsis plants , 2016, Molecular plant pathology.

[24]  M. Mahfouz,et al.  CRISPR/Cas9-Mediated Immunity to Geminiviruses: Differential Interference and Evasion , 2016, Scientific Reports.

[25]  Eric S. Lander,et al.  C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector , 2016, Science.

[26]  David R. Liu,et al.  Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage , 2016, Nature.

[27]  Jennifer A. Doudna,et al.  Programmable RNA Tracking in Live Cells with CRISPR/Cas9 , 2016, Cell.

[28]  A. Grakoui,et al.  Harnessing the Prokaryotic Adaptive Immune System as a Eukaryotic Antiviral Defense. , 2016, Trends in microbiology.

[29]  Luciano A. Marraffini,et al.  Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity , 2016, Cell.

[30]  Takanori Nakane,et al.  Structure and Engineering of Francisella novicida Cas9 , 2016, Cell.

[31]  Jennifer A. Doudna,et al.  Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering , 2016, Cell.

[32]  Antonia A. Dominguez,et al.  Transcriptional regulation of hepatic lipogenesis , 2015, Nature Reviews Molecular Cell Biology.

[33]  M. Swanson,et al.  RNA mis-splicing in disease , 2015, Nature Reviews Genetics.

[34]  M. Mahfouz,et al.  CRISPR/Cas9-mediated viral interference in plants , 2015, Genome Biology.

[35]  R. Barrangou.  Diversity of CRISPR-Cas immune systems and molecular machines , 2015, Genome Biology.

[36]  Zefeng Wang,et al.  Engineering RNA‐binding proteins with diverse activities , 2015, Wiley interdisciplinary reviews. RNA.

[37]  Eugene V Koonin,et al.  Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. , 2015, Molecular cell.

[38]  Sita J. Saunders,et al.  An updated evolutionary classification of CRISPR–Cas systems , 2015, Nature Reviews Microbiology.

[39]  X. Ji,et al.  Establishing a CRISPR–Cas-like immune system conferring DNA virus resistance in plants , 2015, Nature Plants.

[40]  D. Voytas,et al.  Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system , 2015, Nature Plants.

[41]  Luciano A. Marraffini,et al.  Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity , 2015, Cell.

[42]  M. Mahfouz,et al.  RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. , 2015, Plant biotechnology journal.

[43]  David S. Weiss,et al.  Cas9-mediated targeting of viral RNA in eukaryotic cells , 2015, Proceedings of the National Academy of Sciences.

[44]  David A. Scott,et al.  In vivo genome editing using Staphylococcus aureus Cas9 , 2015, Nature.

[45]  Luke A. Gilbert,et al.  Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds , 2015, Cell.

[46]  S. Thore,et al.  An artificial PPR scaffold for programmable RNA recognition , 2014, Nature Communications.

[47]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[48]  Albert J R Heck,et al.  RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus. , 2014, Molecular cell.

[49]  J. P. Ferreira,et al.  Evaluation of sgRNA Target Sites for CRISPR-Mediated Repression of TP53 , 2014, PloS one.

[50]  Max A. Horlbeck,et al.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation , 2014, Cell.

[51]  C. N. Stewart,et al.  Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. , 2014, Plant biotechnology journal.

[52]  Norbert Perrimon,et al.  RNAi screening comes of age: improved techniques and complementary approaches , 2014, Nature Reviews Molecular Cell Biology.

[53]  Benjamin L. Oakes,et al.  Programmable RNA recognition and cleavage by CRISPR/Cas9 , 2014, Nature.

[54]  H. Endtz,et al.  A CRISPR-Cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion , 2014, Proceedings of the National Academy of Sciences.

[55]  J. Oost,et al.  Unravelling the structural and mechanistic basis of CRISPR–Cas systems , 2014, Nature Reviews Microbiology.

[56]  E. Lander,et al.  Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.

[57]  D. Schaffer,et al.  Bidirectional regulation of mRNA translation in mammalian cells by using PUF domains. , 2014, Angewandte Chemie.

[58]  Rodolphe Barrangou,et al.  CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. , 2014, Molecular cell.

[59]  H. Kim,et al.  A guide to genome engineering with programmable nucleases , 2014, Nature Reviews Genetics.

[60]  Kwong Wai Choy,et al.  Therapeutic potentials of gene silencing by RNA interference: principles, challenges, and new strategies. , 2014, Gene.

[61]  Christopher A. Voigt,et al.  Principles of genetic circuit design , 2014, Nature Methods.

[62]  G. Poon,et al.  Structural complementation of the catalytic domain of pseudomonas exotoxin A. , 2014, Journal of molecular biology.

[63]  Zefeng Wang,et al.  Treatment of Type 1 Myotonic Dystrophy by Engineering Site-specific RNA Endonucleases that Target (CUG)n Repeats. , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

[64]  Jennifer A. Doudna,et al.  DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 , 2014, Nature.

[65]  G. Poon,et al.  Structural Complementation of the Catalytic Domain of Pseudomonas Exotoxin A , 2014 .

[66]  S. Leppla,et al.  Cytolethal distending toxin B as a cell-killing component of tumor-targeted anthrax toxin fusion proteins , 2014, Cell Death and Disease.

[67]  O. Voinnet,et al.  RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence , 2013, Nature Reviews Microbiology.

[68]  Albert J R Heck,et al.  Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. , 2013, Molecular cell.

[69]  Joshua J C Rosenthal,et al.  Correction of mutations within the cystic fibrosis transmembrane conductance regulator by site-directed RNA editing , 2013, Proceedings of the National Academy of Sciences.

[70]  Gabriele Varani,et al.  Engineering RNA‐binding proteins for biology , 2013, The FEBS journal.

[71]  Christopher M. Vockley,et al.  RNA-guided gene activation by CRISPR-Cas9-based transcription factors , 2013, Nature Methods.

[72]  Morgan L. Maeder,et al.  CRISPR RNA-guided activation of endogenous human genes , 2013, Nature Methods.

[73]  Luke A. Gilbert,et al.  CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes , 2013, Cell.

[74]  E. Koonin,et al.  Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing , 2013, Biology Direct.

[75]  Rotem Sorek,et al.  CRISPR-mediated adaptive immune systems in bacteria and archaea. , 2013, Annual review of biochemistry.

[76]  David S. Weiss,et al.  A CRISPR-CAS System Mediates Bacterial Innate Immune Evasion and Virulence , 2013, Nature.

[77]  Luke A. Gilbert,et al.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.

[78]  R. Barrangou,et al.  In vitro reconstitution of Cascade‐mediated CRISPR immunity in Streptococcus thermophilus , 2013, The EMBO journal.

[79]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[80]  J. Keith Joung,et al.  Robust, synergistic regulation of human gene expression using TALE activators , 2013, Nature Methods.

[81]  Farshid Guilak,et al.  Synergistic and tunable human gene activation by combinations of synthetic transcription factors , 2013, Nature Methods.

[82]  Yamile Marquez,et al.  Alternative splicing in plants – coming of age , 2012, Trends in plant science.

[83]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[84]  B. Napier,et al.  Subversion of Host Recognition and Defense Systems by Francisella spp , 2012, Microbiology and Molecular Reviews.

[85]  Randall W. King,et al.  A Bioinformatics Method Identifies Prominent Off-targeted Transcripts in RNAi Screens , 2012, Nature Methods.

[86]  J. Doudna,et al.  RNA-guided genetic silencing systems in bacteria and archaea , 2012, Nature.

[87]  Joshua R. Elmore,et al.  Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. , 2012, Molecular cell.

[88]  J. Burnett,et al.  RNA-based therapeutics: current progress and future prospects. , 2012, Chemistry & biology.

[89]  M. Piatek,et al.  Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification , 2012, Plant Molecular Biology.

[90]  A. Krainer,et al.  RNA therapeutics: beyond RNA interference and antisense oligonucleotides , 2012, Nature Reviews Drug Discovery.

[91]  Yang Wang,et al.  Engineering RNA Endonucleases with Customized Sequence Specificities , 2012, Nature Communications.

[92]  M. Esteller.  Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.

[93]  A. Bogdanove,et al.  TAL Effectors: Customizable Proteins for DNA Targeting , 2011, Science.

[94]  M. Wickens,et al.  Targeted translational regulation using the PUF protein family scaffold , 2011, Proceedings of the National Academy of Sciences.

[95]  Aleksandra Filipovska,et al.  A universal code for RNA recognition by PUF proteins. , 2011, Nature chemical biology.

[96]  Toshimichi Yamada,et al.  Visualization of nonengineered single mRNAs in living cells using genetically encoded fluorescent probes. , 2011, Analytical chemistry.

[97]  Yang Wang,et al.  Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains*♦ , 2011, The Journal of Biological Chemistry.

[98]  Stan J. J. Brouns,et al.  Evolution and classification of the CRISPR–Cas systems , 2011, Nature Reviews Microbiology.

[99]  T. Lithgow,et al.  PUF proteins: repression, activation and mRNA localization. , 2011, Trends in cell biology.

[100]  G. Church,et al.  Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. , 2011, Nature biotechnology.

[101]  Philippe Horvath,et al.  The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA , 2010, Nature.

[102]  Aaron Klug,et al.  The discovery of zinc fingers and their applications in gene regulation and genome manipulation. , 2010, Annual review of biochemistry.

[103]  Jens Boch,et al.  Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors , 2009, Science.

[104]  Matthew J. Moscou,et al.  A Simple Cipher Governs DNA Recognition by TAL Effectors , 2009, Science.

[105]  B. Graveley,et al.  RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex , 2009, Cell.

[106]  Yang Wang,et al.  Engineering splicing factors with designed specificities , 2009, Nature Methods.

[107]  K. Martin,et al.  mRNA Localization: Gene Expression in the Spatial Dimension , 2009, Cell.

[108]  K. Oparka,et al.  Live-cell imaging of viral RNA genomes using a Pumilio-based reporter. , 2009, The Plant journal : for cell and molecular biology.

[109]  Mihaela Zavolan,et al.  Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System , 2008, PloS one.

[110]  T. Glisovic,et al.  RNA‐binding proteins and post‐transcriptional gene regulation , 2008, FEBS letters.

[111]  N. Mukherjee,et al.  Ribonomic Analysis of Human Pum1 Reveals cis-trans Conservation across Species despite Evolution of Diverse mRNA Target Sets , 2008, Molecular and Cellular Biology.

[112]  Tycho Heimbach,et al.  Prodrugs: design and clinical applications , 2008, Nature Reviews Drug Discovery.

[113]  Gabriele Varani,et al.  RNA is rarely at a loss for companions; as soon as RNA , 2008 .

[114]  Yoshio Umezawa,et al.  Imaging dynamics of endogenous mitochondrial RNA in single living cells , 2007, Nature Methods.

[115]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[116]  John J. Rossi,et al.  Strategies for silencing human disease using RNA interference , 2007, Nature Reviews Genetics.

[117]  Frédéric H.-T. Allain,et al.  Sequence-specific binding of single-stranded RNA: is there a code for recognition? , 2006, Nucleic acids research.

[118]  C. Cheong,et al.  Engineering RNA sequence specificity of Pumilio repeats , 2006, Proceedings of the National Academy of Sciences.

[119]  L. Lim,et al.  Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. , 2006, RNA.

[120]  S. Dinesh-Kumar,et al.  Mechanisms of plant resistance to viruses , 2005, Nature Reviews Microbiology.

[121]  C. Dominguez,et al.  The RNA recognition motif, a plastic RNA‐binding platform to regulate post‐transcriptional gene expression , 2005, The FEBS journal.

[122]  Olivier Voinnet,et al.  Induction and suppression of RNA silencing: insights from viral infections , 2005, Nature Reviews Genetics.

[123]  T. Tuschl,et al.  Mechanisms of gene silencing by double-stranded RNA , 2004, Nature.

[124]  Thomas Tuschl,et al.  siRNAs: applications in functional genomics and potential as therapeutics , 2004, Nature Reviews Drug Discovery.

[125]  R. Bhatnagar,et al.  RNA Interference: Biology, Mechanism, and Applications , 2003, Microbiology and Molecular Biology Reviews.

[126]  John J Rossi,et al.  Approaches for the sequence-specific knockdown of mRNA , 2003, Nature Biotechnology.

[127]  A. Bogdanove,et al.  Understanding the functions of plant disease resistance proteins. , 2003, Annual review of plant biology.

[128]  B. Li,et al.  Expression profiling reveals off-target gene regulation by RNAi , 2003, Nature Biotechnology.

[129]  P. Opolon,et al.  Comparison of antisense oligonucleotides and siRNAs in cell culture and in vivo. , 2002, Biochemical and biophysical research communications.

[130]  Phillip D. Zamore,et al.  Modular Recognition of RNA by a Human Pumilio-Homology Domain , 2002, Cell.

[131]  G. Orphanides,et al.  A Unified Theory of Gene Expression , 2002, Cell.

[132]  R. Beerli,et al.  Engineering polydactyl zinc-finger transcription factors , 2002, Nature Biotechnology.

[133]  H. Scrable,et al.  The lac operator-repressor system is functional in the mouse. , 2001, Genes & development.

[134]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[135]  W. Hauswirth,et al.  Ribozyme gene therapy: applications for molecular medicine. , 2001, Trends in molecular medicine.

[136]  D J Segal,et al.  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. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[137]  R. Singer,et al.  Localization of ASH1 mRNA particles in living yeast. , 1998, Molecular cell.

[138]  L. Sperling,et al.  Homology-dependent gene silencing in Paramecium. , 1998, Molecular biology of the cell.

[139]  T. Maniatis,et al.  Arginine/serine-rich domains of SR proteins can function as activators of pre-mRNA splicing. , 1998, Molecular cell.

[140]  A. Fire,et al.  Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.

[141]  J. Birchler,et al.  Cosuppression in Drosophila: Gene Silencing of Alcohol dehydrogenase by white-Adh Transgenes Is Polycomb Dependent , 1997, Cell.

[142]  A. Spence,et al.  Post-transcriptional regulation of sex determination in Caenorhabditis elegans: widespread expression of the sex-determining gene fem-1 in both sexes. , 1996, Molecular biology of the cell.

[143]  G. Macino,et al.  Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences , 1992, Molecular microbiology.

[144]  M. Gossen,et al.  Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[145]  C. Napoli,et al.  Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. , 1990, The Plant cell.

[146]  J. Mol,et al.  Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. , 1990, The Plant cell.

[147]  R. Brent,et al.  A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor , 1985, Cell.

[148]  Claire E. J. Cheetham,et al.  Genetically Encoded Fluorescent Probes and Live Cell Imaging , 2016 .

[149]  Ceslovas Venclovas,et al.  Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus. , 2014, Molecular cell.

[150]  J. García-Martínez,et al.  Short motif sequences determine the targets of the prokaryotic CRISPR defence system. , 2009, Microbiology.

[151]  D. St Johnston.  Moving messages: the intracellular localization of mRNAs , 2005, Nature reviews. Molecular cell biology.

[152]  G. Hannon.  RNA interference : RNA , 2002 .

[153]  C. Pabo,et al.  DNA recognition by Cys2His2 zinc finger proteins. , 2000, Annual review of biophysics and biomolecular structure.

[154]  M. Stephenson,et al.  Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. , 1978, Proceedings of the National Academy of Sciences of the United States of America.