biostudies-literatureWiseman AKAmerican Cancer SocietyU.S. Department of Health & Human Services | NIH | National Cancer InstituteNCI NIH HHSAmerican Cancer Society, Michigan Cancer Research Fund528https://www.ebi.ac.uk/biostudies/studies/S-EPMC9163065biostudies-literatureUnknown5(1)The DNA methylation status of the X-chromosome in cancer cells is often overlooked because of computational difficulties. Most of the CpG islands on the X-chromosome are mono-allelically methylated in normal female cells and only present as a single copy in male cells. We treated two colorectal cancer cell lines from a male (HCT116) and a female (RKO) with increasing doses of a DNA methyltransferase 1 (DNMT1)-specific inhibitor (GSK3685032/GSK5032) over several months to remove as much non-essential CpG methylation as possible. Profiling of the remaining DNA methylome revealed an unexpected, enriched retention of DNA methylation on the X-chromosome. Strikingly, the identified retained X-chromosome DNA methylation patterns accurately predicted de novo DNA hypermethylation in colon cancer paCommunications biologyChromosome-specific retention of cancer-associated DNA hypermethylation following pharmacological inhibition of DNMT1.PMC9163065R35CA209859R35 CA209859PF-16-245-01-DMBFan HTiedemann RLMcCabe MTMadaj ZPappalardi MBWiseman AKJones PAShen HfalseChromosome-specific retention of cancer-associated DNA hypermethylation following pharmacological inhibition of DNMT1.The DNA methylation status of the X-chromosome in cancer cells is often overlooked because of computational difficulties. Most of the CpG islands on the X-chromosome are mono-allelically methylated in normal female cells and only present as a single copy in male cells. We treated two colorectal cancer cell lines from a male (HCT116) and a female (RKO) with increasing doses of a DNA methyltransferase 1 (DNMT1)-specific inhibitor (GSK3685032/GSK5032) over several months to remove as much non-essential CpG methylation as possible. Profiling of the remaining DNA methylome revealed an unexpected, enriched retention of DNA methylation on the X-chromosome. Strikingly, the identified retained X-chromosome DNA methylation patterns accurately predicted de novo DNA hypermethylation in colon cancer pa2022-01-01T00:00:00Z2022 Jun2025-04-25T19:45:03.892Z2025-04-06T08:08:22.935ZS-EPMC91630653565482610.1038/s42003-022-03509-3