Proper spatio-temporal control of gene activity is vital for animal development. In the C. elegans germline and early embryo, this occurs mainly by post-transcriptional regulation (PTR) via the three-prime untranslated region (3'UTR). PTR depends on cis-regulatory sequences and trans-acting factors, including RNA binding proteins (RBPs) and small regulatory RNAs, which influence the stability, translation, and localization of mRNA. Experimental analysis of PTR is technically challenging, and in vivo studies of the molecular mechanisms by which 3' UTRs regulate gene activity are limited. Sequence analysis of the 3'UTR landscape in C. elegans indicates that about half of the protein-coding genes are alternatively polyadenylated (Mangone et al., Science 2010; Jan et al., Nature 2011). Therefore, alternative polyadenylation (APA) can result in mRNA transcripts with 3'UTRs of varying lengths and regulatory potential. In the germline, 3'UTR-mediated PTR is the primary mechanism of gene regulation (Merritt et al., Curr Biol 2008). In addition, a number of key RBPs whose activities are crucial for development are expressed in spatio-temporally restricted regions. Our goal is to address the question of correlation between the availability of regulatory elements within the 3'UTR and their cognate trans-acting factors. By combining data on 3'UTR isoforms with iPAR-CLIP of GLD-1 (Jungkamp et al., Mol Cell 2011), we found 38 genes that experience APA and contain binding sites for GLD-1 in the variable 3'UTR region. To test the idea that individual transcripts may escape PTR by selective expression and/or degradation of alternative 3'UTRs in the germline and early embryo, we developed assays to detect and quantify them during development. We have cloned a subset of these 3'UTRs into a two-color in vivo reporter system that will provide a readout of 3'UTR-mediated PTR. Combining these expression assays with mutational analysis of 3'UTRs will allow us to assay the relative contributions of alternative isoforms and regulatory elements to specific spatio-temporal expression patterns during development.

Affiliations:
- Inserm, Marseille, FRA
- NYUAD, Abu Dhabi, UAE
- NYU, New York, USA
- MDC, Berlin, DEU