Abstract LB-091: CpG island DNA methylation regulates alternative cleavage and polyadenylation

Abstract

Abstract Abnormal DNA methylation pattern is a hallmark of human cancer, and our work in genomic profiling of DNA methylation patterns in prostate and colon cancers have identified the majority of unique DNA hypermethylation to occur outside of gene promoters. While promoter hypermethylation causes transcriptional silencing, the functions of non-promoter DNA methylation are poorly defined. Thus, we began investigating the impact of non-promoter DNA methylation on the transcriptome and specifically focused on studying the functions of DNA methylation near gene 3' ends. Using a pair of isogenic cancer cells (HCT116 and DKO cells) that differ specifically in their ability to maintain DNA methylation, we discovered an intriguing association between gene 3' end differential DNA methylation and alternative cleavage and polyadenylation (APA) events. Briefly, pre-mRNAs undergo cleavage and polyadenylation as part of normal mRNA 3' end formation, and alternative sites of cleavage and polyadenylation can be utilized to produce transcripts with varying regulatory sequences in the 3' untranslated regions (3' UTRs) or protein isoforms via APA within coding sequences. Previous studies have demonstrated that cancer cells can hijack the APA pathway to skew expression of short 3' UTRs in oncogenes to evade negative regulation, highlighting APA as an important process involved in cancer initiation and progression. By using pharmacologic inhibition of DNA methylation and reporter constructs, we demonstrated that CpG island DNA methylation near polyadenylation sites is necessary and sufficient for determining relative usage, most likely by modulating RNA polymerase II elongation rate. By leveraging the Cancer Genome Atlas (TCGA) and the Roadmap Epigenomics data, we could observe the correlation between gene 3' DNA methylation and APA at select loci in vivo. The results of our study will improve overall functional understanding of non-promoter DNA methylation, provide a novel mechanism for APA regulation, and ultimately accelerate discovery of novel targets for cancer management. Note: This abstract was not presented at the meeting. Citation Format: Thomas Sweet, Lihua Jin, Josephine Dermawan, Angela H. Ting. CpG island DNA methylation regulates alternative cleavage and polyadenylation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-091. doi:10.1158/1538-7445.AM2017-LB-091