High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms
Fig 5
Complex integration pattern of UM-MCC-52.
(A)+(B): MCPyV-host fusion reads from capture sequencing of sample UM-MCC-52 were mapped to the human genome. Shown is the coverage at the breakpoints in the host genome on Chr4 (A) and Chr5 (B). Red arrows indicate the direction of the viral sequences in the virus-host fusion reads. (RC) = Reverse complement orientation of MCPyV genome compared to the other junctions. Deduced integration patterns are shown below with a Z-pattern containing amplification of 17kbp host DNA in Chr4. The integration into Chr5 in addition to a Z-pattern must contain further inversions based on the read directions. As there is no indication for an inversion in the MCPyV genome, parts of host DNA at the right junction (R) must be inverted. (C)+(D): Reads from nanopore sequencing of UM-MCC-52 are mapped to both integration sites (Chr4, (C) and Chr5, (D)). In Chr4 0.52 MCPyV copies with three specific SNPs (bp 1,708; 1,792; 1,816; not present at the Chr5 integration) are integrated as a Z-pattern with duplication of 17kbp host DNA. In Chr5, MCPyV is integrated as a concatemer of at least 3.9 copies. MinION reads proof a Z-pattern integration with an insertion of 5.7kbp inverted duplicated host sequence at the right side that originates from 38kbp upstream of the 135kbp host sequence that is duplicated afterwards. Dashed coloured arrows indicate the complex structure of the integration locus. Duplicated host transcripts are shown in grey. L and R indicate the left and right virus-host junction while (L) and (R) mark the position of the left and right junction sites in the host reference genome according to Table 1.