At least half of human genes use alternative cleavage and polyadenylation to generate mRNA transcripts that differ in the length of their 3’ untranslated regions (3’UTRs) while producing the same protein (Figure 1). We developed a tag-based sequencing method called 3’-seq that allows us to map all the 3’ ends of the transcriptome in a quantitative manner (Lianoglou et al., 2013
). Our study was chosen by Science Signaling
as one of the Signaling Breakthroughs of 2013 (Science Signaling)
We observed that during the transition from one cell type to another, genes change either their mRNA expression levels or their 3’UTR ratios (Figure 2). Our study also revealed that alternative 3’UTRs are expressed in a cell type– and gene-specific manner, meaning that each gene can have different 3’UTR expression ratios in different cell types. This motivated us to investigate how the highly complex 3’UTR isoform expression pattern is regulated. Because promoters are known to regulate gene expression in a cell type– and gene-specific manner, we focused our analyses on the influence of promoters and enhancers on polyadenylation (pA) site usage. To investigate pA site usage in living cells in the context of transcription, we established a reporter assay and found that regulatory elements located in the DNA and outside of mRNAs regulate proximal pA site usage (Patel et al., in review).
mRNAs are known as the template for protein synthesis. Furthermore, 3’UTRs are known to regulate protein abundance by influencing mRNA stability and translational efficiency. We recently discovered a new role for 3’UTRs. We found that 3’UTRs can mediate protein-protein interactions and thus can determine protein localization and protein functions (Berkovits & Mayr, 2015). For example, CD47 can promote both cell survival and death, depending on the death stimulus. We showed that CD47 protein that was generated by the long 3’UTR (CD47-LU) has a pro-survival role, whereas CD47 that was generated by the short 3’UTR (CD47-SU) promotes cell death (Figure 3)
The current focus of the lab is the investigation of 3’UTR-mediated protein complex formation. We have already shown that alternative 3’UTRs can determine alternative protein functions. As 3’UTRs became substantially longer during animal evolution, we hypothesize that 3’UTR-mediated protein complex formation contributes to the increased functional complexity seen in higher organisms. We are interested in studying the role of 3’UTR-dependent protein complex formation during evolution. We also investigate the regulation of protein multi-functionality by alternative 3’UTRs in normal and cancer cells and examine the mechanism of 3’UTR-dependent protein complex formation at a molecular level.