Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m⁶A detection efficiency and calling bias correcting pipeline.

ABSTRACT: Recent studies have combined DNA methyltransferase footprinting of genomic DNA in nuclei with long-read sequencing, resulting in detailed chromatin maps for multi-kilobase stretches of genomic DNA from one cell. Theoretically, nucleosome footprints and nucleosome-depleted regions can be identified using M.EcoGII, which methylates adenines in any sequence context, providing a high-resolution map of accessible regions in each DNA molecule. Here we report PacBio long-read sequence data for budding yeast nuclei treated with M.EcoGII and a bioinformatic pipeline which corrects for three key challenges undermining this promising method. First, detection of m⁶A in individual DNA molecules by the PacBio software is inefficient, resulting in false footprints predicted by random gaps of s

SUBMITTER: Dennis AF 

PROVIDER: S-EPMC10705563 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature