# Understanding the full spectrum of epigenetic vulnerability in cancer through the delineation of DNA methylation function in gene 3' end

> **NIH NIH R01** · CLEVELAND CLINIC LERNER COM-CWRU · 2020 · $399,981

## Abstract

Abstract
DNA methylation abnormalities occur in all genomic contexts throughout the cancer genome, and studies of
such aberrant epigenetic patterns have led to seminal discoveries regarding tumor suppressor gene silencing
by promoter hypermethylation. While promoter hypermethylation causes transcriptional silencing, the functions
of non-promoter DNA methylation are poorly defined. Such lack of knowledge severely limits our ability to
contextualize the effects of abnormal DNA methylation on cancer biology and to realize the full potential of
epigenetic-based cancer therapy. In this proposal, we propose to investigate the impact of non-promoter DNA
methylation on the transcriptome and will focus 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 a robust 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
leveraging the Cancer Genome Atlas (TCGA) data, we could also observe the correlation between gene 3'
DNA methylation and APA at select loci in cancer patient samples. We hypothesize that differential DNA
methylation in gene 3' ends can result in cancer-promoting expression patterns through regulation of APA. In
Aim 1, we will define the mechanism of DNA methylation-regulated APA using a combination of computational,
biochemical, molecular biology, and genomic approaches. In Aim 2, we will validate our model and in vitro data
by mapping polyadenylation site usage in additional cancer cell lines and testing for disease-relevant APA
events across different cancer types using publically available RNA-seq and DNA methylation data from the
International Cancer Genome Consortium (ICGC). 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. We also envision that our findings
here can have broad impact on our knowledge of how epigenetic regulation shapes the transcriptome in
cancer as well as in other human healthy and pathological conditions.

## Key facts

- **NIH application ID:** 9856997
- **Project number:** 5R01CA230033-02
- **Recipient organization:** CLEVELAND CLINIC LERNER COM-CWRU
- **Principal Investigator:** Angela H Ting
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $399,981
- **Award type:** 5
- **Project period:** 2019-02-01 → 2024-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9856997

## Citation

> US National Institutes of Health, RePORTER application 9856997, Understanding the full spectrum of epigenetic vulnerability in cancer through the delineation of DNA methylation function in gene 3' end (5R01CA230033-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9856997. Licensed CC0.

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