UMR-LMR-PMD-detection

To identify UMRs, LMRs, and PMDs from WGBS data, run a genome-wide segmentation pipeline using MethylSeekR on CpG methylation data to annotate unmethylated regions, low-methylated regions, and partially methylated domains.

CpG methylation segmentation requires whole-genome bisulfite sequencing methylation data provided in a BED-like format, along with a corresponding genome annotation, to produce BED outputs and summary tables.

You can use WGBS methylation data to identify PMDs and regulatory hypomethylation patterns in cancer or aging methylomes, allowing you to link these CpG methylation states to specific chromatin states.

MethylSeekR segmentation outputs BED annotations for UMRs, LMRs, and PMDs that directly support integration with other epigenomic data like ATAC-seq and ChIP-seq to analyze overlapping regulatory elements.

In genome segmentation, UMRs are unmethylated regions often associated with active promoters, while LMRs are low-methylated regions typically linked to enhancer-like hypomethylated areas, both identified from WGBS methylation patterns.

To output BED annotations for partially methylated domains, run the UMR-LMR-PMD detection workflow on your WGBS methylation data, which generates BED files and summary tables for PMDs.