Fig. 5: Establishment and characterization of JET cell clones infected with HTLV-1-wt and mut_3.

a Experimental workflow to establish clones infected with HTLV-1-wt or mut_3 by limiting dilution. b, c Local transcriptome and splice junction near the viral integration site in a JET clone infected with b HTLV-1-wt (wt_#1) and c mut_3 (mut_3_#1) are visualized by IGV. The splice junctions are shown in red for sense transcripts and blue for antisense transcripts. The line thickness indicates the frequency of specific splice patterns detected. Host genes near the IS and direction of HTLV-1 provirus are shown in the lower panel. SRF/ELK-1 ChIP-seq results are also shown for each clone in the bottom row. d Differential expression analysis in cell lines (ED and TBX-4B), parent cells (JET), wild type, and mutated clones (see Supplementary Table 2) visualized by principal component analysis (PCA) plot. Gene expression levels of each cell were quantified using mRNA-seq data performed in duplicates. The percentage variance for each PC were shown on the respective PC axis. e The fraction of upregulated genes in JET clones infected with HTLV-1-wt (left pie) and mut_3 (right pie). The analysis was performed with genes within 100 kb from viral IS. The presence or absence of CTCF ChIP-seq signals in the upregulated group (bottom left) or “no change” group (bottom right) of JET clones infected with HTLV-1-wt. P value was calculated by a two-sided Chi-square test.