Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution.

ABSTRACT:

Motivation

While promoter methylation is associated with reinforcing fundamental tissue identities, the methylation status of distant enhancers was shown by genome-wide association studies to be a powerful determinant of cell-state and cancer. With recent availability of long reads that report on the methylation status of enhancer-promoter pairs on the same molecule, we hypothesized that probing these pairs on the single-molecule level may serve the basis for detection of rare cancerous transformations in a given cell population. We explore various analysis approaches for deconvolving cell-type mixtures based on their genome-wide enhancer-promoter methylation profiles.

Results

To evaluate our hypothesis we examine long-read optical methylome data for the GM12878 cell line an

SUBMITTER: Margalit S 

PROVIDER: S-EPMC8275347 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature