Fig. 3: t-neopeptide encoding transcripts are mostly LTR12-derived.
a The number of DAC + SB939-induced transcripts giving rise to peptides identified in more than one biological replicate of DAC + SB939 treated samples and absent in DMSO treated samples. b Locus plot of a selected treatment-induced novel polyA+ transcript (TINPAT) giving rise to t-neopeptides outside repeat sequence, showing (from top to bottom) LTRs, the de novo transcriptome assembly, normalized RNA-seq coverage of DMSO, SB939, DAC, and DAC + SB939 treated NCI-H1299 cells, predicted ORF, and corresponding t-neopeptide LLLSYRYIY. The region containing the t-neopeptide is zoomed in and reversed for improved visualization. c Classification of transcripts giving rise to t-neopeptides in known, chimeric, and non-chimeric novel transcripts. d The number of transcriptional start sites of transcripts that give rise to t-neopeptides and overlap with transposable element families. e Locus overlap and enrichment analysis of transcripts that give rise to t-neopeptides with transposable element families, subfamilies, and classes. The most significant enrichment result for transposable element families and subfamilies, as well as all LTR12-derived classes, are visualized. Transcriptional start sites of all DAC + SB939 treatment-induced transcripts were used as a background for enrichment analysis. p-values were calculated using Fisher’s exact test. f Transcript expression fold changes of transcripts that give rise to t-neopeptides (red) and all transcripts (gray) in the DAC + SB939 vs DMSO, DAC vs DMSO, and SB939 vs DMSO comparison. Box plots indicate the largest value within the 1.5 times interquartile range above 75th percentile, 75th percentile, median, 25th percentile, and smallest value within the 1.5 times interquartile range below 25th percentile (n = 3 biological replicates).
