Discovery and characterization of novel Cre-type tyrosine site-specific recombinases for advanced genome engineering

Research output: Contribution to journalResearch articleContributedpeer-review



Tyrosine-type site-specific recombinases (Y-SSRs) are versatile tools for genome engineering due to their ability to mediate excision, integration, inversion and exchange of genomic DNA with single nucleotide precision. The ever-increasing need for sophisticated genome engineering is driving efforts to identify novel SSR systems with intrinsic properties more suitable for particular applications. In this work, we develop a systematic computational workflow for annotation of putative Y-SSR systems and apply this pipeline to identify and characterize eight new naturally occurring Cre-type SSR systems. We test their activity in bacterial and mammalian cells and establish selectivity profiles for the new and already established Cre-type SSRs with regard to their ability to mutually recombine their target sites. These data form the basis for sophisticated genome engineering experiments using combinations of Y-SSRs in research fields including advanced genomics and synthetic biology. Finally, we identify putative pseudo-sites and potential off-targets for Y-SSRs in the human and mouse genome. Together with established methods for altering the DNA-binding specificity of this class of enzymes, this work should facilitate the use of Y-SSRs for future genome surgery applications.


Original languageEnglish
Article numbergkad366
Pages (from-to)5285-5297
Number of pages13
JournalNucleic acids research
Issue number10
Early online date9 May 2023
Publication statusPublished - 9 May 2023

External IDs

WOS 000983029800001
Scopus 85162256837



  • Base, Chromosome, Circuits, Directed evolution, Dna, Expression, Integration, Mammalian-cells, Phi, Vectors