Fig 1: ARID1A loss promotes intermixing of small chromosomes.(A) Mean interchromosomal interaction changes across chromosomes. Number of chromosome pairs that showed significant [false discovery rate (FDR) < 5%] increase of interaction for each chromosome are indicated on the top of bars. Red bars highlight chromosomes with >50% significantly increased interchromosomal interactions. (B) Correlation between ARID1A ChIP-seq signal reads within significant peaks per megabase of chromosome length and changes in interchromosomal interaction. (C) NCAPH2 redistribution (relative change in number of NCAPH2 peaks in ARID1A knockout versus control RMG1 cells) across chromosomes. (D) Correlation between NCAPH2 redistribution and interchromosomal interactions. (E) Representative images of 3D chromosomal painting showing chr18 (green), chr19 (purple), and chr22 (white) in parental control and ARID1A knockout RMG1 cells. (F) Volumes of chr18, chr19, and chr22 (calculated on the basis of 3D chromosome painting from at least 790 nuclei) in parental control and two independent ARID1A knockout RMG1 clones. Error bars = mean with SD. (G and H) Distribution of 3D chromosome overlap area (G) or contact frequency (H) (from at least 747 nuclei) between chr19 and chr22 in parental control and ARID1A knockout RMG1 cells. Error bars = mean with SEM. P value was calculated by Mann-Whitney U test. Note that chr18 was excluded from the analysis in (B) to (D). Correlation was calculated by Pearson analysis. ***P < 0.001.
Fig 2: The SWI/SNF complex interacts with the condensin II complex.(A) Validation of the interaction between the SWI/SNF and condensin II complexes by co-IP in RMG1 cells with endogenously FLAG-tagged ARID1A. Nuclear fractions were subjected to IP using an anti-FLAG antibody and immunoblotting using the indicated antibodies. (B) Expression of the indicated SWI/SNF and condensin II subunits in ARID1A wild-type OVCAR429 and RMG1 cells with or without ARID1A knockout determined by immunoblotting. (C) Co-IP analysis between NCAPH2 and BAF155 using an anti-NCAPH2 antibody from nuclear extracts prepared from RMG1 cells treated with or without DNase I. (D) Venn diagram showing the overlap of ChIP-seq peaks among NCAPH2, ARID1A, H3K27ac, and H3K4me3 in RMG1 cells. (E) Heatmap clustering of ChIP-seq profiles of NCAPH2, ARID1A, SNF5, H3K27ac, and H3K4me3 in RMG1 cells. The number of binding sites in each of the four clusters is indicated. (F) Average profiles of the ChIP-seq signal for the indicated antibodies within four distinct clusters found by k-means clustering. Immunoglobulin G, IgG.
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.
Fig 4: Survival patterns of ARID1A, CSMD1, and SENP3 expression in HCC tissues. (A) Survival pattern of ARID1A expression. P > 0.05. (B) Survival pattern of CSMD1 gene. P > 0.05.
Fig 5: ARID1A inactivation causes DNA damage at telomeres. a, b Schematic of synchronization and release (a) and immunoblot of DNA damage marker ?H2AX (b) in parental and ARID1A knockout RMG1 cells. Phosphorylated Histone H3 at serine 10 (pH3S10) was used as a marker of mitosis. Relative intensities of immunoblot bands were quantified underneath. c, d Co-staining of telomere by FISH and ?H2AX (c) and quantification of telomeric DNA damage (d) in mitotic parental and ARID1A knockout RMG1 cells after cytospin. e, f Co-staining of telomere by FISH and ?H2AX in ARID1A-mutated TOV21G mitotic cells (e) and quantification of mitotic telomeric DNA damage in a panel of clear cell ovarian cancer cell lines or primary cultures highlighted in red (f). g, h Representative images (g) and quantification (h) of telomere DNA damage in parental, P53-/-/Pten-/- and P53-/-/Pten-/-/Arid1a-/- mouse bladder organoid cultures. n = 3 independent experiments unless otherwise stated. Data represent mean ± s.e.m. Scale bar = 10 µm. P values were calculated using a two-tailed t test except in 2f and 2h by multilevel mixed-effects models
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