Base-resolution analysis of DNA methylation patterns downstream of Dnmt3a in mouse naïve B cells

Background: The DNA methyltransferase, Dnmt3a, is one of the most commonly mutated genes in adult hematologic malignancies and is dynamically regulated throughout normal B cell development and upon activation by antigenic stimulation. Dnmt3a inactivation in hematopoietic stem cells has been shown to drive B cell-related malignancies, including chronic lymphocytic leukemia, and associates with specific DNA methylation patterns in transformed cells. While a cell-type specific role for Dnmt3a has been proposed in carcinogenesis, the role of Dnmt3a in directing specific DNA methylation patterns in B cell development has not been characterized. Results: We selectively inactivated Dnmt3a early in B cell development and then utilized Whole Genome Bisulfite Sequencing to generate base-resolution profiles of Dnmt3a+/+ and Dnmt3a−/− mouse naïve splenic B cells. Although overall methylation level distribution was largely consistent between Dnmt3a+/+ and Dnmt3a−/− B cells, we identified site-specific and regional differences corresponding to both gains and losses of methylation in Dnmt3a−/− cells relative to Dnmt3a+/+ cells. Hypomethylated regions (N = 313) in Dnmt3a−/− cells, however, were more frequently observed than were hypermethylated regions (N = 136) by over 2-fold, consistent with loss of methyltransferase activity. Conclusions: We have identified a set of CpG sites that require Dnmt3a to maintain normal methylation levels in naïve B cells. These CpGs are associated with genes expressed in B cells that undergo dysregulation in leukemias. Base-resolution methylomes for splenic naïve B cells from adult Dnmt3a+/+ and Dnmt3a−/− mice using Whole Genome Bisulfite Sequencing