Retargeted serine integrases for one-step, precise integration of large DNA sequences in human cells

Abstract

Serine integrases can precisely integrate large DNA constructs into desired chromosomal sites but only if their natural target site is first installed into the recipient genome. Here, to retarget serine integrases to a desired genomic site, we develop a modular integrase (MINT) system for genome editing. Through a combination of structural modeling, single-round directed evolution and screening in human cells, we retargeted the specificity of the serine integrase Bxb1. We demonstrate the therapeutic potential of the MINT system by retargeting Bxb1 to the human AAVS1 and TRAC loci, where wild-type Bxb1 has no detectable activity. By combining MINT constructs with both known activity-increasing Bxb1 mutants and zinc-finger DNA-binding domains, we achieve efficiencies of 29% at the AAVS1 locus and 35% at the TRAC locus in K562 cells. To further demonstrate clinical potential, we achieved 29% GFP integration efficiencies at the TRAC locus in human T cells.