HPV16-cellular DNA junctions validated by junction-PCR.

1)The viral-cellular DNA junctions (DJ) are sorted by chromosomal map position of the cellular sequences (fifth column).2)u/r: u = unique cellular sequence; r = repetitive cellular sequence; the names of repeat sequences are given in parentheses.3)t/d: t = gene directly targeted by HPV16 integration; d = the first gene located within 500 kb downstream of the DNA junction.4)Orientation of the cellular gene with regard to the early region of integrated HPV16 DNA.a)DNA junctions 2319_DJ1, DJ2 and DJ3 were discovered in the TEN16 sequence library by searching for DNA junctions located upstream of the identified RNA junction 2319_RJ (Table 2 and Figure 3). DJ2 contains a 65-bp sequence of chromosome 15 between HPV16 and chromosome 1 sequences. DJ1 and DJ3 were below the cutoff of 15 read pairs. DJ1 has also been identified by DIPS-PCR [44].b)DNA junction 0892_DJ2 contains repetitive cellular sequence (AluSx), but could be assigned to chromosome 2 by taking into account the other DNA junction (0892_DJ1) and the RNA junction (0892_RJ; Table 2 and Figure 3).c)DNA junctions 4426_DJ1 and 4024_DJ2 with Table 2).d)DNA junction 3966_DJ1 was identified in the TEN16 sequence library after the second-round sequence-sorting.e)DNA junction 2231_DJ1 was first mapped to two chromosome regions 4p16.3 and 4q35.2 with long identical sequences downstream of the junction. The mapping was then refined by long-range PCR to be on 4q35.2.f)DNA junction CS_DJ1 with [54].g)DNA junction 4793_DJ3 with h)Chromosome mapping of 4793_DJ1 and DJ2 was impossible because the flanking cellular sequences are composed mainly of the simple repeat sequence GGAAT.