Cells were treated with either UVA or TMP/UVA. a Sequential IP demonstrates association of early-replicating Alu sequences with DONSON and late-replicating Satellite 3 sequences with FANCM. LINE-1 elements replicate throughout the S phase and are found in all fractions. Representative blot (n = 3). b DONSON interaction with the H3K4me3 euchromatin mark is more frequent in early S phase cells than in late S phase, while there is little interaction with the H3K9me3 heterochromatin mark in either stage. Sorted early and late S phase cells were examined by PLA. Scored nuclei: PLA between GFP-D: H3K4me3 of early S phase = 67, late S phase = 64, PLA between GFP-D: H3K9me3 of early S phase = 70, late S phase = 85, from three biological replicates. Data are mean ± s.e.m. c FANCM interaction with H3K9me3 heterochromatin mark is biased toward late S phase, while there is low interaction frequency with H3K4me3 in either stage. Scored nuclei: PLA between FANCM: H3K4me3 of early S phase = 64, late S phase = 66, PLA between FANCM: H3K9me3 of early S phase = 67, late S phase = 77, from three biological replicates. Data are mean ± s.e.m. d Sequential IP demonstrates greater association of DONSON with H3K4me3 than H3K9me3 and greater association of FANCM with H3K9me3 than H3K4me3. Representative blot (n = 3). For PLA experiments in b, c, a two-sided Mann–Whitney rank-sum test was used to determine if differences were statistically significant. NS: not significant: P > 0.05. Source data are provided as a Source Data file.