Computational Analysis of Alternative Polyadenylation in Embryonic Stem Cells and Induced Pluripotent Cells

Abstract

The 3’ untranslated region (3’UTR) of mRNA plays important roles in posttranscriptional control of gene expression. Over half of the human genes have multiple polyadenylation sites in 3’UTRs, leading to 3’UTR isoforms containing different cis elements. Alternative polyadenylation (APA) has been found to be dynamically regulated in different tissue types and under various cellular conditions. Embryonic stem (ES) cells have the ability to self-renew and differentiate into any cell type in the adult body. Posttranscriptional gene regulation through cis elements in 3’UTRs is increasingly found to be important for these functions. In addition, various methods have recently been developed to induce differentiated cells to ES-like cells, called induced pluripotent stem (iPS) cells. Here we show a computational method to examine regulation of 3’UTR by APA using DNA microarray data. We applied this method to ES cells and iPS cells derived from different cell types.

Keywords: mRNA processing, alternative polyadenylation, 3' end formation, embryonic stem cells, induced pluripotent cells, 3'UTR, microRNA, development, proliferation, differentiation, mRNA isoform, post-transcriptional gene regulation.