The completion of a telomere-to-telomere human reference genome,T2T-CHM13,has resolved complex regions of the genome,including repetitive and homologous regions.Here,we present a high-resolution epigenetic study of previously unresolved sequences,representing entire acrocentric chromosome short arms,gene family expansions,and a diverse collection of repeat classes.This resource precisely maps CpG methylation(32.28 million CpGs),DNA accessibility,and short-read datasets(166,058 previously unresolved chromatin immunoprecipitation sequencing peaks)to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation.Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization.This analysis provides a framework with which to investigate the most elusive regions of the human genome,granting insights into epigenetic regulation.
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