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.

Fig 3: ARID1B contributes to the upregulation of HERVH in the absence of ARID1A.a–c Heatmaps of the expression levels of different repetitive sequences in WT or ARID1A KO HCT116 cells treated with control or ARID1B (KD) shRNA generated with the GSE101966 dataset. d qPCR results showing the expression levels of ARID1B and HERVH in ARID1A WT or KO cells treated with shRNA targeting GFP or ARID1B. Two different shRNA sequences targeting ARID1B are used to exclude potential off-target effects. Data are presented as mean values ± SD from three independent experiments, two-tailed unpaired t test, **p < 0.01, ***p < 0.001. e qPCR analysis of ARID1B and HERVH expression levels in ARID1A KO cells treated with the indicated shRNAs and overexpression plasmids. Data are presented as mean values ± SD from three independent experiments, two-tailed unpaired t test, *p < 0.05, **p < 0.01, ***p < 0.001. f Heatmap showing the expression levels of the derepressed HERVH loci (27) in ARID1A KO cells 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 | > 0.585). The majority of them (25) display reduced expression when ARID1B is knocked down (KO-KD). g Genomic snapshot of RNA-seq signals at a representative HERVH locus (HERVH_3). Two primer sets targeting this locus for ChIP-qPCR analysis are shown. h–j ChIP-qPCR results with two different primer sets showing decreased ARID1A and increased ARID1B at the HERVH_3 locus in ARID1A KO cells, whereas the amount of another BAF component SMARCA4 remains unchanged. Data are presented as mean values ± SD from three independent experiments, two-tailed unpaired t test, ns: not significant, *p < 0.05, **p < 0.01, ****p < 0.0001. Source data including exact p values are provided as a Source data file.