Fig. 6: Establishment and characterization of HTLV-1-mut_3 clones by CRISPR/Cas9.
From: Identification and characterization of a novel enhancer in the HTLV-1 proviral genome
a, b mRNA-seq and SRF/ELK-1 ChIP-seq results of a HTLV-1-wt (wt_#5) and b CRISPR-mutated HTLV-1-mut_3 (C-mut) clone. Representative results from two independent experiments are visualized by IGV. The range in square brackets indicates the range of read count. c Level of proviral expression of J HTLV-1-wt (wt_#5) or CRISPR-mutated (C-mut) clones. Data were shown as transcripts per million reads (TPM) from two independent mRNA-seq analyses. d MNase assay of JET clones infected with HTLV-1-wt (wt_#5) or C-mut. The degree of nucleosome freeness was evaluated by MNase treatment and ddPCR. Values of indicated proviral regions are shown after normalization to values from non-MNase digestion samples. n = 2 biologically independent samples. e, f mRNA-seq and SRF/ELK-1 ChIP-seq results of JET cells infected with e HTLV-1-wt (wt_#1) and CRISPR-mutated f HTLV-1 (C-mut). Representative results from two independent experiments are visualized by IGV. The range in square brackets indicates the range of read counts. g Level of proviral expression of JET cells infected with HTLV-1-wt (wt_#1) or C-mut clones. Data were shown as transcripts per million reads (TPM) from two independent mRNA-seq analyses. h, i Local transcriptome and splice junction near the viral integration site are visualized in a JET cell clone infected with HTLV-1-wt (wt_#1) and C-mut by IGV in each integration site; h chr11 and i chrX. The splice junctions are shown in red for sense transcripts and blue for antisense transcripts. The line thickness of splice junctions 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.
