This review summarizes the overall downstream applications of currently available genome customization systems, based on cell-based assays ( in cellulo ) or animal models ( in vivo ). These include (i) functional genomics, (ii) drug discovery, (iii) bioproduction, (iv) cell transformation (i.e. immortalization, reprogrammation and differentiation), as well as (v) molecular biology and microbiology tools. The different enzymatic systems that exist to speci fi cally modify ( insertional or sitedirected mutagenesis ), modulate ( knock-down ) and disrupt ( constitutive or conditional knock-out ) cellular genes, or to integrate transgenic elements ( knock-in ) at speci fi c chromosomal loci will be discussed herein.