Fig. 4.

Transposable element (TE) reactivation and increased mutations predominate in heterochromatin of TET-deficient NKT-cell lymphoma. (A) Genome-wide distribution (Top), and percentage of SNVs (Bottom) located within euchromatin and heterochromatin compartments in Tet2/3 DKO expanded NKT cells. (B) Coding mutations resulting in change in the amino acid sequence in 5 independent WGS samples from Tet2/3 DKO expanded NKT cells. Mutant allele frequencies are shown in parentheses. (C) Distribution of the changes in expression (log₂ fold change) of TEs belonging to the LTR, LINE, and SINE families in Tet2/3 DKO young NKT cells compared with WT, obtained from analysis of total RNA-seq data. Fold change differences for all genes in the genome are shown for reference. (D) Volcano plots of expression of TEs belonging to the LTR, LINE, and SINE families, in Tet2/3 DKO young NKT cells compared with WT. Differentially expressed (DE) TEs (adjusted P value < 0.1) are highlighted. (E) Percentage of SNVs in Tet2/3 DKO expanded NKT cells that overlap with LINEs, LTRs, and SINEs, compared with the mm10 genome distribution of each TE families. P values were calculated by 1-sample t test.