Fig. 4: Cryptic splice acceptor in cHS4 causes transcription termination and aberrant fusion transcripts when inserted in same orientation of almost all target genes confirmed in iPS clones.

No fusion transcript is observed for proviral integration with reverse orientation as the gene. Four iPSC clones were analyzed by RNAseq. Gene labels with the same color denote LV-insertion in the same iPSC clone. a Almost all LV insertions that are in the same orientation as the insert gene generated fusion transcripts of the upstream exons or even upstream introns into cHS4 in the LV, except for CTSS (not expressed in iPSCs, and therefore not possible to detect transcripts). Red arrows denote LV-insertion site in the gene in the same orientation. Fusion transcript sequences were identified by RNAseq and labeled above the junction. Black text indicates the sequences from upstream exons/introns and red text indicates the sequences derived from cHS4. b LV insertions in the reverse orientation of target gene or outside the gene do not produce fusion transcripts. Blue arrows indicate LV integration site and orientation relative to the gene. Insertion in TALDO1 is the only exonic insertion.