Fig. 5: IDH mutation disrupts chromatin structure around DSB through DNA hypermethylation.

a ChIP-seq assay shows alteration of CTCF coverage around AsiSI DSB sites in IDH1^WT and IDH1^R132H DIvA cells. Two biological replicates were performed. b Top, genomic tracks show differential 4C-seq signal (log2[+DSB/−DSB]) in IDH1^WT and IDH1^R132H DIvA cells treated with 4-OHT (300 nM) for 4 h. Bottom, CTCF enrichment at the same genomics loci. Two biological replicates were performed. c Bisulfite PCR shows the DNA methylation status of the CpG islands around AsiSI sites shown in (b). d ChIP-qPCR assay shows the CTCF, BRCA2, RAD51 binding, and γH2A.X modification around the DSB sites. DD-Sce-I-GR DRGFP U2OS cells were treated with 0.5 μM Shield1 and 0.2 mM TA for 0.5, 1, 2, 4, 6, 12, or 24 h before collection for ChIP-qPCR. Two genomic regions (−180 bp and +150 bp) adjacent of DSB sites were monitored. Cells were transfected with TET1 CD/dCD. The recruitments were quantified relative to the IgG control. e MeDIP/hMeDIP assay shows epigenetic status around the Sce-I site. DD-Sce-I-GR DRGFP U2OS cells were treated with D-2-HG (0.5 mM), αKG (10 mM), or overexpression of TET CD/dCD, or TET2. DSB was induced with 0.5 μM Shield1 and 0.2 mM TA. Data are presented as mean ± SEM from three independent experiments. Source Data are provided as a Source Data file.