Targets and genomic constraints of ectopic Dnmt3b expression

DNA methylation plays an essential role in mammalian genomes, hence DNA methyltransferase expression is tightly controlled. Deregulation of the de novo enzyme DNMT3B is frequently observed in many diseases, yet little is known about its ectopic genomic targets. Here we used an inducible transgenic mouse model to identify rules delineating abnormal DNMT3B targeting and explore the constraints of its activity across different cell types. Our results explain the preferential susceptibility of certain CpGs to aberrant methylation and point to transcriptional state and the associated chromatin landscape as the strongest predictors. Although DNA methylation and H3K27me3 are usually antagonistic at CpG islands, H3K27me3 can transiently co-occur with DNMT3B-induced DNA methylation and its depletion has minimal affect on ectopic methylation targets or levels in mouse embryonic fibroblasts. Our multilayered genome-wide data combined with ultra-deep locus-specific bisulfite sequencing suggest a hit-and-run model that induces hypermethylation and provides insights for interpreting the cancer methylome. To systematically study the impact of Dnmt3b deregulation, we generated ESCs containing a heterozygous inducible Dnmt3b1 construct and derived transgenic mice. We induced ectopic expression of Dnmt3b through doxycycline supplied in drinking water for 1.5 or 3 months and harvested six different tissues (liver, lung, muscle, intestine, kidney, heart) and several blood cell types (B cells, helper T cells, cytotoxic T cells, monocytes, granulocytes) from both induced and control (Dnmt3b1 construct, non-induced) mice. We also performed ChIP for H3K27me3 and H3K4me3 on control and induced liver tissue from mice treated for 3 months after birth. To compare our in vivo findings to an in vitro system, we isolated MEFs from E13.5 embryos and performed RNAseq, H3K27me3 ChIP, H3K4me3 ChIP and H3K27me3-ChIP-BS on control and induced MEFs at 1 and 7 days. Please note that the following processed data files were generated by merging two sample raw (bam) data for CpG calling or peak data; mouse_mef_control_noshRNA_RRBS.bed (mouse_mef_7day_control_RRBS_r1 and r2) mouse_mef_dox_noshRNA_RRBS.bed (mouse_mef_7day_dox_RRBS_r1 and r2) mouse_mef_7day_control_H3K27me3_ChIP_peaks.txt peak file (mouse_mef_7day_control_H3K27me3_ChIP_1.bam and _2.bam) and are linked to the corresponding *_r1 or *_ChIP_1 sample records.