PGC methylome analysis revealed large, germline-specific mouse hypomethylated DNA domains with unique genomic and epigenomic features [DNA methylation_NimbleGen]

ABSTRACT: With the goal of understanding the epigenetic regulation required for germ cell-specific gene expression, we devised a method of DNA methylation analysis adapted for a small number of developing germ cells. This microarray-based method provides the genome-wide assay of DNA methylation using a sub-nanogram quantity of genomic DNA. Using this technique, we obtained DNA methylation profiles for mouse germ cells in various developmental stages including primordial germ cells (PGC) and for stem cells derived from embryos or germ cells. Cluster analysis of the data revealed that each cell type possesses its own characteristic DNA methylation profile, enabling classification of the cell types. This classification is generally consistent with that based on gene expression profiles except for primordial germ cells, whose genome is globally hypomethylated. Among the differentially methylated sites thus identified, we focused on a group of genomic sequences hypomethylated specifically in germline cells. These hypomethylated sequences tend to be clustered, forming large (10 kb to ~9 Mb) genomic domains. Most of these hypomethylated regions designated here as Large Hypomethylated Domain (LoD) correspond to segmentally duplicated regions that contain gene families showing germ cell-specific expression. These include mouse orthologues of human cancer testis antigen genes. Most LoDs appear to be enriched with H3 lysine 9 dimethylation (H3K9me2), usually regarded as a repressive histone modification. It thus appears t hat such a unique epigenomic state (i.e., DNA hypomethylation with H3K9me2 enrichment) may be a prerequisite for the expression of genes contained in these genomic domains. DNA methylation data sets from early developmenatal stage of mouse, cultured cell, and somatic tissue cells.

ORGANISM(S): Mus musculus

SUBMITTER: Rieko Ikeda 

PROVIDER: E-GEOD-39794 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress