Integrative Genome-Wide Analysis of DNA Methyltransferase 3A Reveals a Novel Model of Transcriptional Regulation Modulated by Long Non-coding RNAs

Abstract

LncRNAs are a class of nucleic acids that have been widely demonstrated to be involved in transcriptional regulation through epigenetic regulation via DNA methylation and chromatin remodeling. Though previously shown to be directly involved in histone modification by conferring loci specificity to histone methyltransferases and acetylases, their involvement in DNA methylation is largely unappreciated. Our group has previously demonstrated that a lncRNA interacts with the de novo methyltransferase DNMT3A, and mediates its recruitment. We hypothesized that this mechanism may regulate DNMT3A recruitment globally in the genome. By integrating ChIP-seq, RNA-seq, and RIP-seq genome-wide assays, I identify two genes – BIM and PDCD4 – that demonstrate bivalent modes of DNMT3A regulation through antisense lncRNAs emanating from their first intron, BIM-as and PDCD4-as1. Truncation of BIM-as and PDCD4-as1 of the mRNA-overlapping region results in decreased DNMT3A localization, without affecting promoter methylation or cognate mRNA expression. Surprisingly, RNAi suppression of PDCD4-as1 results in increased DNMT3A recruitment and PDCD4 mRNA expression without affecting PDCD4 promoter methylation. Finally, I demonstrate that loss of DNMT3A can occur despite accumulation of H3K9me3. My results support previous findings that DNMT3A has a wide breadth of context-dependent activity, but demonstrate novel molecular mechanisms that govern its function.