Variants of DNMT3A cause transcript-specific gene expression changes

The de novo DNA methyltransferase 3A (DNMT3A) plays a pivotal role in hematopoietic differentiation. In this study, we followed the hypothesis that alternative splicing of DNMT3A has characteristic epigenetic and functional sequels. Various transcripts of DNMT3A were either knocked down or overexpressed in human hematopoietic stem and progenitor cells resulting in complementary and transcript-specific DNA methylation (DNAm) and gene expression changes. Our results demonstrate that different splice variants of DNMT3A have distinct epigenetic and functional sequels. Six biological replicas of cord blood-derived CD34+ hematopoietic stem and progenitor cells (HSPCs; #1-6) were isolated for the knockdown (KD; #1-3) and the overexpression (OE; #4-6) of DNMT3A transcripts. HSPCs were lentivirally infected with either shRNA or overexpression vectors 1 day after isolation. Control HSPCs were infected with a scrambled or empty vector. Genomic DNA was isolated at day 12 after infection, bisulfite converted and hybridized to the Illumina Infinium 450k Human Methylation Beadchip.