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

• Published in: Cell reports (Cambridge) 2023-06, Vol.42 (6), p.112587-112587, Article 112587
• Main Authors: Dar, Mohd Saleem, Mensah, Isaiah K., He, Ming, McGovern, Sarah, Sohal, Ikjot Singh, Whitlock, Hannah Christian, Bippus, Nina Elise, Ceminsky, Madison, Emerson, Martin L., Tan, Hern J., Hall, Mark C., Gowher, Humaira
• Format: Article
• Language: English
• Subjects: alternative splicing; Cell Differentiation; chromatin modifications; CP: Molecular biology; DNA (Cytosine-5-)-Methyltransferases - genetics; DNA (Cytosine-5-)-Methyltransferases - metabolism; DNA methylation; DNA Methylation - genetics; DNA Methyltransferase 3B; dnmt3b; Dnmt3bas; Embryonic Stem Cells - metabolism; enhancers; Exons - genetics; hnRNPL; lncRNA; Mice; Polycomb Repressive Complex 2 - metabolism; PRC2 complex; promoters
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2023.112587

Embryonic expression of DNMT3B is critical for establishing de novo DNA methylation. This study uncovers the mechanism through which the promoter-associated long non-coding RNA (lncRNA) Dnmt3bas controls the induction and alternative splicing of Dnmt3b during embryonic stem cell (ESC) differentiation. Dnmt3bas recruits the PRC2 (polycomb repressive complex 2) at cis-regulatory elements of the Dnmt3b gene expressed at a basal level. Correspondingly, Dnmt3bas knockdown enhances Dnmt3b transcriptional induction, whereas overexpression of Dnmt3bas dampens it. Dnmt3b induction coincides with exon inclusion, switching the predominant isoform from the inactive Dnmt3b6 to the active Dnmt3b1. Intriguingly, overexpressing Dnmt3bas further enhances the Dnmt3b1:Dnmt3b6 ratio, attributed to its interaction with hnRNPL (heterogeneous nuclear ribonucleoprotein L), a splicing factor that promotes exon inclusion. Our data suggest that Dnmt3bas coordinates alternative splicing and transcriptional induction of Dnmt3b by facilitating the hnRNPL and RNA polymerase II (RNA Pol II) interaction at the Dnmt3b promoter. This dual mechanism precisely regulates the expression of catalytically active DNMT3B, ensuring fidelity and specificity of de novo DNA methylation. [Display omitted] •Dnmt3bas is a spliced and polyadenylated lncRNA•Dnmt3bas fine-tunes Dnmt3b transcriptional induction by regulating PRC2 activity•Dnmt3bas promotes exon inclusion to express catalytically active Dnmt3b1 isoform•Dnmt3bas recruits hnRNPL and coordinates transcription with alternative splicing Dar et al. report the regulatory role of Dnmt3bas lncRNA and cis-regulatory regions in Dnmt3b expression. By interacting with and recruiting the PRC2 complex and hnRNPL to the Dnmt3b promoter, Dnmt3bas regulates transcriptional induction and alternative splicing of Dnmt3b, dictating the prevalence of catalytically active DNMT3B, required for global de novo methylation.