Table 1.

Integration sites of the lesion shuttle vector in human chromosomes

	Chromosome	Location	ϕC31-int mediated?*	Known hotspot?†	No. independent events	Genomic context	Gene
1	1	q41	√	No	1	Intron	USH2A
2	2	p11.1	√	No	1	intergenic
3	2	q23.2	√	Yes	1	intergenic
4	3	p23	√	No	1	Intergenic
5	4	p13	x	No	1	Intergenic
6	4	q35.1	√	No	2	Intergenic
7	5	q14.3	√	No	1	Intron	MGC33214
8	6	p21.1	√	No	1	intergenic
9	7	p14.1	√	Yes	1	Intergenic
10	8	p22	√	No	3	Intron	DLC1
11	9	p13.2	√	No	1	Intron	PAX5
12	9	p21.2	√	No	1	Intergenic
13	10	q22.1	√	Yes	1	Intergenic
14	12	q22	x	No	1	Intergenic
15	13	q13.3	√	No	1	Intron	DCLK1
16	19	q13.31	√	Yes	11	Intron	ZNF223
17	20	p13	√	No	1	Intron	CDC25B
18	X	q22.3	x	No	1	Intergenic
Total sites:					31

Human XPA cells were stably transfected with a lesion shuttle vector containing two BP-G lesions in a staggered configuration, after which the integrated plasmids were rescued along with the chromosomal junction sequences. The chromosomal DNA sequences at the junction sites were determined by PCR followed by DNA sequence analysis. The detailed protocol is described in Materials and Methods, and the sequences in the insertion junctions are in Table S8. The genes in which integration was observed were: USH2A, usher syndrome 2A; MGC33214, transmembrane protein 161B; DLC1, Rho GTPase-activating protein 7; PAX5, paired box protein Pax-5; DCLK1, doublecortin-like kinase 1; ZNF223, zinc finger protein 223; CDC25B, cell division cycle 25 homolog B.

^*Integrase-mediated insertion events were identified on the basis of the DNA sequence at the insertion site (which are shown in Table S8). √, ϕC31 integrase-mediated insertion; x, random insertion.

^†Previously identified ϕC31 integrase-mediated integration hotspots are described in ref. 27.