Systematic identification of regions where DNA methylation is correlated with transcription refines regulatory logic in normal and tumour tissues.

ABSTRACT: DNA methylation at gene promoters is generally considered to be associated with transcriptional repression in vertebrates. However, lack of a clear picture of where promoter methylation is most important for transcriptional regulation has hindered our understanding of this relationship and resulted in the use of a wide variety of arbitrary promoter definitions. We demonstrate here that the use of different promoter definitions can lead to contradictory results between studies of promoter methylation. In response, we have developed Methodical, a computational method that combines RNA-seq and whole genome bisulfite sequencing (WGBS) data to identify genomic regions where DNA methylation is highly correlated with transcriptional activity. We refer to these regions as transcript-proximal methy

SUBMITTER: Heery R 

PROVIDER: S-EPMC12481017 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature