Premature polyadenylation of MAGI3 is associated with diminished N6-methyladenosine in its large internal exon

Thomas K Ni,Jessica S Elman,Piyush B Gupta,Dexter X Jin,Charlotte Kuperwasser

doi:10.1038/s41598-018-19916-8

Abstract

In cancer, tumor suppressor genes (TSGs) are frequently truncated, causing their encoded products to be non-functional or dominant-negative. We previously showed that premature polyadenylation (pPA) of MAGI3 truncates the gene, switching its functional role from a TSG to a dominant-negative oncogene. Here we report that MAGI3 undergoes pPA at the intron immediately downstream of its large internal exon, which is normally highly modified by N6-methyladenosine (m6A). In breast cancer cells that upregulate MAGI3pPA, m6A levels in the large internal exon of MAGI3 are significantly reduced compared to cells that do not express MAGI3pPA. We further find that MAGI3pPA transcripts are significantly depleted of m6A modifications, in contrast to highly m6A-modified full-length MAGI3 mRNA. Finally, we analyze public expression data and find that other TSGs, including LATS1 and BRCA1, also undergo intronic pPA following large internal exons, and that m6A levels in these exons are reduced in pPA-activated breast cancer cells relative to untransformed mammary cells. Our study suggests that m6A may play a role in regulating intronic pPA of MAGI3 and possibly other TSGs, warranting further investigation.

Highlights

Polyadenylation is an essential process controlling gene expression, yet how cancer cells deregulate this process to drive malignancy is only beginning to be appreciated
This event leads to the expression of a truncated, dominantly-acting oncogene (Fig. 1B), which can be detected by both 3′ rapid amplification of cDNA ends (RACE) and immunoblotting in MDA-MB-231 human breast cancer cells but not in MCF10A non-transformed human mammary cells (Fig. 1C and D)[4]
We hypothesized that a molecular mechanism which normally limits the usage of the intronic poly(A) signal (PAS) downstream of the large internal exon of MAGI3 may be deregulated in cancer

Summary

Introduction

Polyadenylation is an essential process controlling gene expression, yet how cancer cells deregulate this process to drive malignancy is only beginning to be appreciated. Intronic PAS are prevented from triggering cleavage and polyadenylation by ribonucleoprotein complexes that bind to suppressive RNA sequence elements, such as U1 snRNA-binding sites[2,3]. Despite these molecular safeguards, we previously showed that instances of intronic PAS activation do occur in cancer[4]. Pre-mRNAs from pPA, results in activation of multiple intronic PAS in the 5′ regions of most genes[3], with a strong bias for PAS in intron 15 These results cannot account for the focal pPA event occurring in intron 10 of MAGI34, yet not in upstream introns that are more likely to be affected by trans-acting factors. Intrigued by the specific occurrence of pPA following exon 10 of MAGI3 but not following other exons of the gene, we hypothesized that novel cis-acting elements may mark and render this gene region, and possibly others like it, susceptible to focal pPA events

Methods

Results

Conclusion