Fig. 3: Chromatin conformation contributes to epigenetic bystander modifications.

a, ATAC-seq data of HEK293T cells²⁸ was used to estimate chromatin accessibility at epigenetic bystander modifications upon modification of PDE4C with either dCas9-DNMT3A or CRISPRoff. The higher ATAC-seq signals indicate that bystander modifications are enriched at open chromatin regions (two-tailed, unpaired t-test). b, In analogy, we tested whether CpGs with age-associated DNAm changes are also associated to chromatin accessibility in the ATAC-seq data HEK293T cells. The 4,389 age-hypomethylated CpGs revealed overall lower ATAC signal, whereas the 5,328 age-hypermethylated CpGs were enriched at open chromatin (two-tailed unpaired t-test). c, Intrinsic 4C-sequencing in HEK293T cells for three age-associated sites in PDE4C, FHL2 and MEIS1-AS3 (triplicates per viewpoint). The Manhattan plots depict the number of reads (rpm, reads per million) at the cis-interacting regions on the corresponding chromosomes. The highest signal was observed around the 4C viewpoints. d, Bystander effects of PDE4C become enriched with increasing coverage in 4C-sequencing of PDE4C-interacting sites. The association is best described by an exponential model (adjusted R²: 0.586, model P value < 1.801 × 10⁻⁷). Different symbols correspond to the three replicates. e–g, Overlap of 4,389 age-hypo and 5,328 age-hypermethylated CpGs at interacting genomic regions in 4C-sequencing data (chi-squared tests were performed for the threshold of 100 rpm: PDE4C: age-hypermethylated sites P = 0.0004 and age-hypomethylated sites P = 0.0019 (e); FHL2: age-hypermethylated sites P = 0.0008 and age-hypomethylated sites P = 0.0088 (f); and MEIS1-AS3: age-hypermethylated sites P = 0.0008 and age-hypomethylated sites P = 0.009 (g); all d.f = 1).