publication . Article . Other literature type . 2013

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

Jiang, Wenyan; Bikard, David; Cox, David; Zhang, Feng; Marraffini, Luciano A;
Open Access English
  • Published: 29 Jan 2013
  • Publisher: Nature Publishing Group
  • Country: United States
Abstract
Here we use the clustered, regularly interspaced, short palindromic repeats (CRISPR)–associated Cas9 endonuclease complexed with dual-RNAs to introduce precise mutations in the genomes of Streptococcus pneumoniae and Escherichia coli. The approach relies on dual-RNA:Cas9-directed cleavage at the targeted genomic site to kill unmutated cells and circumvents the need for selectable markers or counter-selection systems. We reprogram dual-RNA:Cas9 specificity by changing the sequence of short CRISPR RNA (crRNA) to make single- and multinucleotide changes carried on editing templates. Simultaneous use of two crRNAs enables multiplex mutagenesis. In S. pneumoniae, nea...
Subjects
free text keywords: Article, Biotechnology, Molecular Medicine, Applied Microbiology and Biotechnology, Bioengineering, Biomedical Engineering, Trans-activating crRNA, Genetics, Protospacer adjacent motif, CRISPR/Cpf1, Bacterial genome size, RNA, CRISPR, CRISPR interference, Molecular biology, Selectable marker, Biology
Funded by
NIH| Using CRISPR immunity to prevent the spread of virulence traits among pathogens
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1DP2AI104556-01
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Probing Neuropsychiatric Diseases Using Targeted Epigenome and Genome Engineering
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5DP1MH100706-02
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
45 references, page 1 of 3

Urnov, FD, Rebar, EJ, Holmes, MC, Zhang, HS, Gregory, PD. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 2010; 11: 636-646 [OpenAIRE] [PubMed]

Bogdanove, AJ, Voytas, DF. TAL effectors: customizable proteins for DNA targeting. Science. 2011; 333: 1843-1846 [OpenAIRE] [PubMed]

Stoddard, BL. Homing endonuclease structure and function. Q. Rev. Biophys. 2005; 38: 49-95 [PubMed]

Bae, T, Schneewind, O. Allelic replacement in Staphylococcus aureus with inducible counter-selection. Plasmid. 2006; 55: 58-63 [OpenAIRE] [PubMed]

Sung, CK, Li, H, Claverys, JP, Morrison, DA. An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae. Appl. Environ. Microbiol. 2001; 67: 5190-5196 [OpenAIRE] [PubMed]

Sharan, SK, Thomason, LC, Kuznetsov, SG, Court, DL. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 2009; 4: 206-223 [OpenAIRE] [PubMed]

Jinek, M. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012; 337: 816-821 [OpenAIRE] [PubMed]

Deveau, H, Garneau, JE, Moineau, S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu. Rev. Microbiol. 2010; 64: 475-493 [OpenAIRE] [PubMed]

Horvath, P, Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010; 327: 167-170 [OpenAIRE] [PubMed]

Terns, MP, Terns, RM. CRISPR-based adaptive immune systems. Curr. Opin. Microbiol. 2011; 14: 321-327 [OpenAIRE] [PubMed]

van der Oost, J, Jore, MM, Westra, ER, Lundgren, M, Brouns, SJ. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends. Biochem. Sci. 2009; 34: 401-407 [OpenAIRE] [PubMed]

Brouns, SJ. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008; 321: 960-964 [OpenAIRE] [PubMed]

Carte, J, Wang, R, Li, H, Terns, RM, Terns, MP. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 2008; 22: 3489-3496 [OpenAIRE] [PubMed]

Deltcheva, E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011; 471: 602-607 [OpenAIRE] [PubMed]

Hatoum-Aslan, A, Maniv, I, Marraffini, LA. Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site. Proc. Natl. Acad. Sci. U.S.A. 2011; 108: 21218-21222 [OpenAIRE] [PubMed]

45 references, page 1 of 3
Abstract
Here we use the clustered, regularly interspaced, short palindromic repeats (CRISPR)–associated Cas9 endonuclease complexed with dual-RNAs to introduce precise mutations in the genomes of Streptococcus pneumoniae and Escherichia coli. The approach relies on dual-RNA:Cas9-directed cleavage at the targeted genomic site to kill unmutated cells and circumvents the need for selectable markers or counter-selection systems. We reprogram dual-RNA:Cas9 specificity by changing the sequence of short CRISPR RNA (crRNA) to make single- and multinucleotide changes carried on editing templates. Simultaneous use of two crRNAs enables multiplex mutagenesis. In S. pneumoniae, nea...
Subjects
free text keywords: Article, Biotechnology, Molecular Medicine, Applied Microbiology and Biotechnology, Bioengineering, Biomedical Engineering, Trans-activating crRNA, Genetics, Protospacer adjacent motif, CRISPR/Cpf1, Bacterial genome size, RNA, CRISPR, CRISPR interference, Molecular biology, Selectable marker, Biology
Funded by
NIH| Using CRISPR immunity to prevent the spread of virulence traits among pathogens
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1DP2AI104556-01
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
,
NIH| Probing Neuropsychiatric Diseases Using Targeted Epigenome and Genome Engineering
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5DP1MH100706-02
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
45 references, page 1 of 3

Urnov, FD, Rebar, EJ, Holmes, MC, Zhang, HS, Gregory, PD. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 2010; 11: 636-646 [OpenAIRE] [PubMed]

Bogdanove, AJ, Voytas, DF. TAL effectors: customizable proteins for DNA targeting. Science. 2011; 333: 1843-1846 [OpenAIRE] [PubMed]

Stoddard, BL. Homing endonuclease structure and function. Q. Rev. Biophys. 2005; 38: 49-95 [PubMed]

Bae, T, Schneewind, O. Allelic replacement in Staphylococcus aureus with inducible counter-selection. Plasmid. 2006; 55: 58-63 [OpenAIRE] [PubMed]

Sung, CK, Li, H, Claverys, JP, Morrison, DA. An rpsL cassette, janus, for gene replacement through negative selection in Streptococcus pneumoniae. Appl. Environ. Microbiol. 2001; 67: 5190-5196 [OpenAIRE] [PubMed]

Sharan, SK, Thomason, LC, Kuznetsov, SG, Court, DL. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 2009; 4: 206-223 [OpenAIRE] [PubMed]

Jinek, M. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012; 337: 816-821 [OpenAIRE] [PubMed]

Deveau, H, Garneau, JE, Moineau, S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu. Rev. Microbiol. 2010; 64: 475-493 [OpenAIRE] [PubMed]

Horvath, P, Barrangou, R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010; 327: 167-170 [OpenAIRE] [PubMed]

Terns, MP, Terns, RM. CRISPR-based adaptive immune systems. Curr. Opin. Microbiol. 2011; 14: 321-327 [OpenAIRE] [PubMed]

van der Oost, J, Jore, MM, Westra, ER, Lundgren, M, Brouns, SJ. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends. Biochem. Sci. 2009; 34: 401-407 [OpenAIRE] [PubMed]

Brouns, SJ. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008; 321: 960-964 [OpenAIRE] [PubMed]

Carte, J, Wang, R, Li, H, Terns, RM, Terns, MP. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes. Genes Dev. 2008; 22: 3489-3496 [OpenAIRE] [PubMed]

Deltcheva, E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011; 471: 602-607 [OpenAIRE] [PubMed]

Hatoum-Aslan, A, Maniv, I, Marraffini, LA. Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site. Proc. Natl. Acad. Sci. U.S.A. 2011; 108: 21218-21222 [OpenAIRE] [PubMed]

45 references, page 1 of 3
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publication . Article . Other literature type . 2013

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

Jiang, Wenyan; Bikard, David; Cox, David; Zhang, Feng; Marraffini, Luciano A;