Dnmt3bas coordinates transcriptional induction and alternative exon inclusion to promote catalytically active Dnmt3b expression

During mammalian embryogenesis, DNMT3B activity is critical for the genome-wide establishment of DNA methylation. Using naive ESC differentiation as a model, we elucidated the mechanism by which lncRNA, Dnmt3bas, controls the inducible expression and alternative splicing of Dnmt3b. Our data showed that Dnmt3bas knockdown increased transcriptional induction and decreased H3K27me3 at Dnmt3b cis-regulatory elements post-differentiation. Notably, transcriptional induction of Dnmt3b was accompanied by exon inclusion, switching the major isoform from catalytically inactive Dnmt3b6 to the active Dnmt3b1. While Dnmt3bas overexpression attenuated Dnmt3b induction, it increased the Dnmt3b1:Dnmt3b6 ratio. This observation was explained by a specific interaction of Dnmt3bas with hnRNPL, which promotes exon inclusion. These data suggest that Dnmt3bas coordinates alternative splicing and transcriptional induction of Dnmt3b by facilitating the interaction of hnRNPL and RNA Pol II at the Dnmt3b promoter. This two-pronged mechanism would tightly control DNMT3B activity, ensuring the fidelity and specificity of de novo DNA methylation during development.