Fig 4. RNA-seq analysis of edited populations showing unique gene expression profile and hybrid transcripts in BACH2 LTR-MSD targeted T cells.
a) Volcano plot showing the 452 differentially expressed genes between BACH2 LTR-MSD and Solo-LTR edited CD4 T cell populations at 48 days of culture (309 genes upregulated in LTR-MSD and 143 down-regulated in LTR-MSD compared to Solo-LTR, respectively). Each dot represents a gene with: grey not reaching significance and less than an absolute log2 fold change of 1; green not reaching significance but an absolute log2 fold change > 1; blue having an adjusted p-value < 0.05 but less than an absolute log2 fold change of 1; and red having an adjusted p-value < 0.05 and an absolute log2 fold change > 1. Log2 fold change > 0 means higher expression in LTR-MSD, and vice versa. A select number of genes were annotated. b) Shown are the top 30 alphabetically sorted genesets, fold-enrichment scores, and false discovery rate (FDR) determined from a PANTER (Protein ANalysis Through Evolutionary Relationships) overrepresentation test of homo sapien gene-ontology biological processes. c) Coverage map of RNA-seq reads mapped to the hg38 chr6 BACH2 locus. Gene polarity is displayed right to left as on chromosome 6 for mock edited control cells, LTR-solo edited, and LTR-MSD edited cells. Accumulation of reads are shown as histograms scaled to read count (y-axis). Exons 1–9 are shown as orange rectangles with the LTR insertion into intron 5 indicated as a red bar.