Fig. 2: ARID1A loss leads to upregulation of HERVH.

a–c Heatmaps of the expression of different repetitive sequences in wild-type (WT) and ARID1A knockout (KO) HCT116 cells. The differential expression is tested based on a model using the negative binomial distribution by DESeq2 (version v1.22.2, with two-tailed likelihood ratio test). The adjusted p values are labeled as *p < 0.05, **p < 0.01. The schematic of a typical full-length HERVH element is shown in c. d Scatter plot of the expression of all 580 ERVs in WT and KO HCT116 cells. The up (red) and down (green) regulated ERVs are determined by DESeq2 (version v1.22.2, with two-tailed likelihood ratio test) using cut-off values of adjusted p value <0.05 and |Log₂ FC | > 1. e Venn diagram showing that HERVH is repetitively upregulated in three independent sequencing experiments with HCT116 ARID1A WT and KO cells. f Western blots of different ARID1A WT and KO cell lines. Results are representative of three independent experiments. g, h qPCR analyses of HERVH expression in ARID1A WT and KO cell lines using two different primer sets. Data are presented as mean values ± SD from at least three independent experiments, two-tailed unpaired t test, **p < 0.01, ***p < 0.001, ****p < 0.0001. i Western blots showing ARID1A protein levels in WT, KO, and ARID1A rescued KO HCT116 cells. Results are representative of three independent experiments. Arrow indicates the full-length ARID1A band. j qPCR analysis of ARID1A and HERVH expression in the indicated cells. Data are presented as mean values ± SD from three independent experiments, two-tailed unpaired t test, *p < 0.05. k qPCR analysis of ARID1B and HERVH expression. Data are presented as mean values ± SD from three independent experiments, two-tailed unpaired t test, ns: not significant, **p < 0.01. Source data including exact p-values are provided as a Source data file.