Correction to: Nature Methods https://doi.org/10.1038/s41592-025-02839-4, published online 2 October 2025.

In the version of this article initially published, there was a figure referencing error in the “Nucleosome occupancy direct DNA methylation maintenance following DNA replication” section due to changes during revisions. The text “These dynamics are also visible upon normalization of CpG methylation (Fig. 3d; z-scoring CpG methylation per chromatin mark)” has now been removed, while in the text now reading “In line with this observation, CpG methylation on DNA wrapped around nucleosomes was altered by a maximum of 12% compared to 4% in linker regions (Fig. 3d),” Fig. 3e was originally cited. In the third paragraph of the “Profiling of mouse intestinal cells reveals cell-type-specific differential DNA methylation within H3K27me3 regions” section, in the text now reading “Last, we found three subclusters in the coarse immune cluster … Syk (Extended Data Fig. 6j; T cells, not B cells or myeloid) and Il10ra (Extended Data Fig. 6i,” the citations of Extended Data Fig. 6j and 6i were originally reversed. In the caption to Extended Data Fig. 2i, due to changes following figure revisions, the text “and previously published single-cell sortChiC data (H3K9me3)” has now been removed. In the legend to Extended Data Fig. 5, captions d, e were originally interchanged and are now swapped, beginning, respectively, as “d, Fluorescent intensities of FUCCI markers” and “e, CpG Methylation values.” The changes are made in the HTML and PDF versions of the article.