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We are analyzing https://www.nature.com/articles/s41467-019-09987-0.

Title:
High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases | Nature Communications
Description:
The development of site-specific recombinases (SSRs) as genome editing agents is limited by the difficulty of altering their native DNA specificities. Here we describe Rec-seq, a method for revealing the DNA specificity determinants and potential off-target substrates of SSRs in a comprehensive and unbiased manner. We applied Rec-seq to characterize the DNA specificity determinants of several natural and evolved SSRs including Cre, evolved variants of Cre, and other SSR family members. Rec-seq profiling of these enzymes and mutants thereof revealed previously uncharacterized SSR interactions, including specificity determinants not evident from SSR:DNA structures. Finally, we used Rec-seq specificity profiles to predict off-target substrates of Tre and Brec1 recombinases, including endogenous human genomic sequences, and confirmed their ability to recombine these off-target sequences in human cells. These findings establish Rec-seq as a high-resolution method for rapidly characterizing the DNA specificity of recombinases with single-nucleotide resolution, and for informing their further development. The development of site-specific recombinases as genome editing tools is limited by the difficulty of altering their DNA sequence specificity. Here the authors present Rec-seq, a method for identifying specificity determinants and off-target substrates of recombinases in an unbiased manner.
Website Age:
30 years and 10 months (reg. 1994-08-11).

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Keywords {🔍}

recseq, cre, dna, specificity, article, fig, google, scholar, cas, loxp, recombinase, positions, brec, tre, recombinases, substrate, supplementary, substrates, interactions, position, enrichment, halfsite, recombination, ssrs, cells, activity, sequence, data, wildtype, nature, sequences, base, residues, preference, offtarget, showed, genome, proteindna, bxb, target, library, acids, relative, site, evolved, variants, ssr, halfsites, values, res,

Topics {✒️}

search parameters a14c13nt11nnt8a7t6t5nnnnnnnnt5′a6′t7′nnc10′a11′a12′ c11ng9nt7t6a5nnnnnnnnt5′a6′a7′nnc10′nt12′g13′ nature portfolio privacy policy slide-a-lyzer dialysis cassette 1 mm isopropyl-β-d-1-thiogalactopyranoside advertising nature communications poly-d-lysine-coated plates pcalnl-egfp-bsai acceptor vector pbt100-neomycin-terminator donor vector tyrosine-based site-specific recombinases high-throughput sequencing-based method reprints author information authors site-specific recombination synapse zymo research corporation modified pcalnl-egfp-esp3i vector half-site libraries based ptet-mrfp cassette flanked endotoxin-removal plasmid-purification system half-site log-enrichment values nature 389 nature cationic lipid-mediated delivery site-specific recombination systems pcalnl-gfp subcloning vector full log-enrichment profile phage-encoded serine integrases yeast endonuclease i-scei bac/pac recombineering techniques post-recombination library versus t-sne visualization relates long-range specificity-determining role source data file efficient site-specific integration donor pbt100-neomycin-terminator single-stranded bridging oligonucleotides model-guided engineering site-specific genomic integration pcalnl-egfp-esp3i vector19 high-throughput dna sequencing multi-dimensional similarity analysis n-terminal tev-cleavable pcalnl-egfp-esp3i vector full rec-seq profile high-resolution conditional mutagenesis post-recombinase-treated dataset r1–r4 half-sites flanking site-specific dna recombinases

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      headline:High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases
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            address:
               name:Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, USA
               type:PostalAddress
            type:Organization
      name:David R. Liu
      url:http://orcid.org/0000-0002-9943-7557
      affiliation:
            name:Broad Institute of Harvard and MIT
            address:
               name:Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, USA
               type:PostalAddress
            type:Organization
            name:Harvard University
            address:
               name:Department of Chemistry and Chemical Biology, Harvard University, Cambridge, USA
               type:PostalAddress
            type:Organization
            name:Harvard University
            address:
               name:Howard Hughes Medical Institute, Harvard University, Cambridge, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, USA
      name:Department of Chemistry and Chemical Biology, Harvard University, Cambridge, USA
      name:Howard Hughes Medical Institute, Harvard University, Cambridge, USA
      name:Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, USA
      name:Department of Chemistry and Chemical Biology, Harvard University, Cambridge, USA
      name:Howard Hughes Medical Institute, Harvard University, Cambridge, USA
      name:Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, USA
      name:Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, USA
      name:Department of Chemistry and Chemical Biology, Harvard University, Cambridge, USA
      name:Howard Hughes Medical Institute, Harvard University, Cambridge, USA
      name:Department of Chemistry and Chemical Biology, Harvard University, Cambridge, USA
      name:Howard Hughes Medical Institute, Harvard University, Cambridge, USA
      name:Google Inc., Mountain View, USA
      name:Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, USA
      name:Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, USA
      name:Department of Chemistry and Chemical Biology, Harvard University, Cambridge, USA
      name:Howard Hughes Medical Institute, Harvard University, Cambridge, USA

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