Genetic and epigenetic control of gene expression by CRISPR–Cas systems

The discovery and adaption of bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems has revolutionized the way researchers edit genomes. Engineering of catalytically inactivated Cas variants (nuclease-deficient or nuclease-deactivated [dCas]) combined with transcriptional repressors, activators, or epigenetic modifiers enable sequence-specific regulation of gene expression and chromatin state. These CRISPR–Cas-based technologies have contributed to the rapid development of disease models and functional genomics screening approaches, which can facilitate genetic target identification and drug discovery. In this short review, we will cover recent advances of CRISPR–dCas9 systems and their use for transcriptional repression and activation, epigenome editing, and engineered synthetic circuits for complex control of the mammalian genome.

[1]  T. Sera Zinc-finger-based artificial transcription factors and their applications. , 2009, Advanced drug delivery reviews.

[2]  Travis Ostbye,et al.  New vectors for simple and streamlined CRISPR–Cas9 genome editing in Saccharomyces cerevisiae , 2015, Yeast.

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

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

[5]  Feng Zhang,et al.  Selection-Free Zinc-Finger Nuclease Engineering by Context-Dependent Assembly (CoDA) , 2010, Nature Methods.

[6]  Prashant Mali,et al.  Orthogonal Cas9 Proteins for RNA-Guided Gene Regulation and Editing , 2013, Nature Methods.

[7]  H. Stefánsson,et al.  Genetics of gene expression and its effect on disease , 2008, Nature.

[8]  B. Bernstein,et al.  Charting histone modifications and the functional organization of mammalian genomes , 2011, Nature Reviews Genetics.

[9]  Yusuke Miyanari,et al.  Live visualization of chromatin dynamics with fluorescent TALEs , 2013, Nature Structural &Molecular Biology.

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

[11]  Randall J. Platt,et al.  Optical Control of Mammalian Endogenous Transcription and Epigenetic States , 2013, Nature.

[12]  Pamela A. Silver,et al.  Engineering synthetic TAL effectors with orthogonal target sites , 2012, Nucleic acids research.

[13]  Yuta Nihongaki,et al.  Photoactivatable CRISPR-Cas9 for optogenetic genome editing , 2015, Nature Biotechnology.

[14]  G. Vergnaud,et al.  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. , 2005, Microbiology.

[15]  E. Lander,et al.  Genetic Screens in Human Cells Using the CRISPR-Cas9 System , 2013, Science.

[16]  L. Lai,et al.  Efficient Generation of Myostatin Gene Mutated Rabbit by CRISPR/Cas9 , 2016, Scientific Reports.

[17]  John G Doench,et al.  CRISPR/Cas9 Screens Reveal Requirements for Host Cell Sulfation and Fucosylation in Bacterial Type III Secretion System-Mediated Cytotoxicity. , 2016, Cell host & microbe.

[18]  A. Regev,et al.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System , 2015, Cell.

[19]  Piyush K Jain,et al.  Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors. , 2016, Angewandte Chemie.

[20]  Moritoshi Sato,et al.  CRISPR-Cas9-based photoactivatable transcription system. , 2015, Chemistry & biology.

[21]  Yang Liang,et al.  Sequence-specific inhibition of microRNA via CRISPR/CRISPRi system , 2014, Scientific Reports.

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

[23]  H. Cedar,et al.  Linking DNA methylation and histone modification: patterns and paradigms , 2009, Nature Reviews Genetics.

[24]  Victoria C. Corey,et al.  UDP-galactose and Acetyl-CoA transporters as Plasmodium multidrug resistance genes , 2016, Nature Microbiology.

[25]  Yi Zhang,et al.  Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA , 2016, Nature Communications.

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

[27]  Ron Weiss,et al.  Highly-efficient Cas9-mediated transcriptional programming , 2014, Nature Methods.

[28]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[29]  Lei S. Qi,et al.  CRISPR/Cas9 in Genome Editing and Beyond. , 2016, Annual review of biochemistry.

[30]  Yarden Katz,et al.  Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system , 2013, Cell Research.

[31]  G. Church,et al.  CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering , 2013, Nature Biotechnology.

[32]  C. Gersbach,et al.  A light-inducible CRISPR/Cas9 system for control of endogenous gene activation , 2015, Nature chemical biology.

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

[34]  F. Crick Central Dogma of Molecular Biology , 1970, Nature.

[35]  R. Cobb,et al.  High-Efficiency Genome Editing of Streptomyces Species by an Engineered CRISPR/Cas System. , 2016, Methods in enzymology.

[36]  Elo Leung,et al.  Targeted Genome Editing Across Species Using ZFNs and TALENs , 2011, Science.

[37]  Christopher M. Vockley,et al.  Epigenome editing by a CRISPR/Cas9-based acetyltransferase activates genes from promoters and enhancers , 2015, Nature Biotechnology.

[38]  Seung Woo Cho,et al.  Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease , 2013, Nature Biotechnology.

[39]  Yonatan Stelzer,et al.  Editing DNA Methylation in the Mammalian Genome , 2016, Cell.

[40]  Xiaoqiang Guo,et al.  Directing cellular information flow via CRISPR signal conductors , 2016, Nature Methods.

[41]  Timothy E. Reddy,et al.  Highly Specific Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements , 2015, Nature Methods.

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

[43]  Lei S. Qi Faculty of 1000 evaluation for Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering. , 2017 .

[44]  M. Isalan,et al.  Advances in zinc finger engineering. , 2000, Current opinion in structural biology.

[45]  Xiaolong Wang,et al.  Generation of gene-modified goats targeting MSTN and FGF5 via zygote injection of CRISPR/Cas9 system , 2015, Scientific Reports.

[46]  Yanpeng Wang,et al.  Genome editing in rice and wheat using the CRISPR/Cas system , 2014, Nature Protocols.

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

[48]  Alexander Deiters,et al.  Optical Control of CRISPR/Cas9 Gene Editing. , 2015, Journal of the American Chemical Society.

[49]  David R. Liu,et al.  CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes , 2017, Cell.

[50]  Botao Zhang,et al.  Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis , 2014, Proceedings of the National Academy of Sciences.

[51]  Daesik Kim,et al.  Method Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas 9 ribonucleoproteins , 2014 .

[52]  Detlef Weigel,et al.  Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease , 2013, Nature Biotechnology.

[53]  Stephen Wilcox,et al.  An inducible lentiviral guide RNA platform enables the identification of tumor-essential genes and tumor-promoting mutations in vivo. , 2015, Cell reports.

[54]  Andrew Martens,et al.  Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation , 2016, Biology Open.

[55]  Samuel H Sternberg,et al.  Rational design of a split-Cas9 enzyme complex , 2015, Proceedings of the National Academy of Sciences.

[56]  Hicham Mansour,et al.  Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein , 2011, Plant Molecular Biology.

[57]  Lei S. Qi,et al.  The New State of the Art: Cas9 for Gene Activation and Repression , 2015, Molecular and Cellular Biology.

[58]  J. Vogel,et al.  CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III , 2011, Nature.

[59]  G. Prelich Gene Overexpression: Uses, Mechanisms, and Interpretation , 2012, Genetics.

[60]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[61]  Jennifer Doudna,et al.  RNA-programmed genome editing in human cells , 2013, eLife.

[62]  V. Kim,et al.  Regulation of microRNA biogenesis , 2014, Nature Reviews Molecular Cell Biology.

[63]  Donghai Wu,et al.  Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers , 2014, Nucleic acids research.

[64]  Christopher M. Vockley,et al.  Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators , 2015, Genome research.

[65]  Jay D. Keasling,et al.  A Cas9-based toolkit to program gene expression in Saccharomyces cerevisiae , 2016, Nucleic acids research.

[66]  R. Maehr,et al.  Functional annotation of native enhancers with a Cas9 -histone demethylase fusion , 2015, Nature Methods.

[67]  R. Barrangou,et al.  Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria , 2012, Proceedings of the National Academy of Sciences.

[68]  Feng Zhang,et al.  Multidimensional chemical control of CRISPR-Cas9. , 2016, Nature chemical biology.

[69]  Andrew P. Feinberg,et al.  Epigenetic modulators, modifiers and mediators in cancer aetiology and progression , 2016, Nature Reviews Genetics.

[70]  Magnus Lundgren,et al.  The CRISPR-Cas immune system: biology, mechanisms and applications. , 2015, Biochimie.

[71]  Jeffry D Sander,et al.  FLAsH assembly of TALeNs for high-throughput genome editing , 2022 .

[72]  R. Weiss,et al.  CRISPR transcriptional repression devices and layered circuits in mammalian cells , 2014, Nature Methods.

[73]  Yi Cui,et al.  CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter , 2016, Oncotarget.

[74]  Huimin Zhao,et al.  Orthogonal Genetic Regulation in Human Cells Using Chemically Induced CRISPR/Cas9 Activators. , 2017, ACS synthetic biology.

[75]  Feng Zhang,et al.  Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system , 2013, Nucleic acids research.

[76]  Vanja Tadić,et al.  Repurposing the CRISPR-Cas9 system for targeted DNA methylation , 2016, Nucleic acids research.

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

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

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

[80]  Wolfgang Wurst,et al.  Development of an intein-mediated split–Cas9 system for gene therapy , 2015, Nucleic acids research.

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

[82]  Shane J. Neph,et al.  Systematic Localization of Common Disease-Associated Variation in Regulatory DNA , 2012, Science.

[83]  J. Keith Joung,et al.  Efficient Delivery of Genome-Editing Proteins In Vitro and In Vivo , 2014, Nature Biotechnology.

[84]  George M. Church,et al.  Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems , 2013, Nucleic acids research.

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

[86]  Ruhong Zhou,et al.  Comprehensive Interrogation of Natural TALE DNA Binding Modules and Transcriptional Repressor Domains , 2012, Nature Communications.

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

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

[89]  Erin L. Doyle,et al.  Targeting DNA Double-Strand Breaks with TAL Effector Nucleases , 2010, Genetics.

[90]  Kabin Xie,et al.  RNA-guided genome editing in plants using a CRISPR-Cas system. , 2013, Molecular plant.

[91]  Philippe Horvath,et al.  The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli , 2011, Nucleic acids research.

[92]  John R. Haliburton,et al.  Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation , 2014, ACS synthetic biology.

[93]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[94]  Andrew J. Bannister,et al.  Regulation of chromatin by histone modifications , 2011, Cell Research.

[95]  Qi Zhou,et al.  Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems , 2013, Nature Biotechnology.

[96]  Suresh Ramakrishna,et al.  Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA , 2014, Genome research.

[97]  John S. Hawkins,et al.  A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria , 2016, Cell.

[98]  Soon Il Kwon,et al.  DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins , 2015, Nature Biotechnology.

[99]  David Baltimore,et al.  Chimeric Nucleases Stimulate Gene Targeting in Human Cells , 2003, Science.

[100]  M. Spalding,et al.  Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice , 2014, Nucleic acids research.

[101]  Ronald D. Vale,et al.  A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging , 2014, Cell.

[102]  J. Doudna,et al.  CRISPR-Cas9 Structures and Mechanisms. , 2017, Annual review of biophysics.

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

[104]  Luke A. Gilbert,et al.  CRISPR interference (CRISPRi) for sequence-specific control of gene expression , 2013, Nature Protocols.

[105]  Joshua K Young,et al.  Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes , 2016, Nature Communications.

[106]  Yinqing Li,et al.  Crystal Structure of Staphylococcus aureus Cas9 , 2015, Cell.

[107]  C. Mello,et al.  Revealing the world of RNA interference , 2004, Nature.

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

[109]  David R. Liu,et al.  Small Molecule-Triggered Cas9 Protein with Improved Genome-Editing Specificity , 2015, Nature chemical biology.

[110]  Feng Zhang,et al.  CRISPR-assisted editing of bacterial genomes , 2013, Nature Biotechnology.

[111]  Martin J. Simard,et al.  Argonaute proteins: key players in RNA silencing , 2008, Nature Reviews Molecular Cell Biology.

[112]  L. Marraffini,et al.  CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA , 2008, Science.

[113]  Lei Zhang,et al.  A CRISPR-based approach for targeted DNA demethylation , 2016, Cell Discovery.

[114]  James J. Collins,et al.  Comparative Analysis of Cas9 Activators Across Multiple Species , 2016, Nature Methods.

[115]  Feng Zhang,et al.  A split-Cas9 architecture for inducible genome editing and transcription modulation , 2015, Nature Biotechnology.

[116]  J. García-Martínez,et al.  Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements , 2005, Journal of Molecular Evolution.

[117]  Neville E Sanjana,et al.  A transcription activator-like effector toolbox for genome engineering , 2012, Nature Protocols.

[118]  H. Ouyang,et al.  Efficient Generation of Myostatin Mutations in Pigs Using the CRISPR/Cas9 System , 2015, Scientific Reports.

[119]  Jeffry D. Sander,et al.  Efficient In Vivo Genome Editing Using RNA-Guided Nucleases , 2013, Nature Biotechnology.

[120]  Lukas E Dow,et al.  Inducible in vivo genome editing with CRISPR/Cas9 , 2015, Nature Biotechnology.

[121]  Adam James Waite,et al.  An improved zinc-finger nuclease architecture for highly specific genome editing , 2007, Nature Biotechnology.

[122]  Kira S. Makarova,et al.  SnapShot: Class 2 CRISPR-Cas Systems , 2017, Cell.

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

[124]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[125]  Chase L. Beisel,et al.  Guide RNA functional modules direct Cas9 activity and orthogonality. , 2014, Molecular cell.

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

[127]  Zengrong Zhu,et al.  An iCRISPR platform for rapid, multiplexable, and inducible genome editing in human pluripotent stem cells. , 2014, Cell stem cell.

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

[129]  R. Barrangou,et al.  CRISPR-Cas Systems: RNA-mediated Adaptive Immunity in Bacteria and Archaea , 2013 .

[130]  Huimin Zhao,et al.  Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. , 2015, ACS synthetic biology.

[131]  Davide Cittaro,et al.  Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing , 2016, Cell.

[132]  M. Rots,et al.  Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner , 2016, Nature Communications.

[133]  Kira S. Makarova,et al.  Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems , 2013, Nucleic acids research.

[134]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[135]  Kenichiro Hata,et al.  Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions , 2016, Nature Biotechnology.

[136]  Alexander Bolotin,et al.  Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. , 2005, Microbiology.

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

[138]  J. Rinn,et al.  Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display , 2015, Nature Methods.

[139]  Rudolf Jaenisch,et al.  One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering , 2013, Cell.

[140]  D. Voytas,et al.  High-frequency, precise modification of the tomato genome , 2015, Genome Biology.

[141]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[142]  Benjamin L. Oakes,et al.  Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch , 2016, Nature Biotechnology.

[143]  Daesik Kim,et al.  Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins , 2014, Genome research.

[144]  Wendell A Lim,et al.  Complex transcriptional modulation with orthogonal and inducible dCas9 regulators , 2016, Nature Methods.

[145]  Botao Zhang,et al.  Efficient genome editing in plants using a CRISPR/Cas system , 2013, Cell Research.

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