PolA-Seq: A pipeline for the analysis of mRNA isoforms from alternative polyadenylation.

MARTIN GARCIA SOLÁ; EDITH C. KORDON; ALBANA GATELLI,; COSO, OMAR A; ABBA M

Bariloche

Congreso; The Fourth South American Symposium in Signal Transduction and Molecular Medicine? (SISTAM 2018)  ; 2018

More than half of human genes contain alternative polyadenylation (pA) sites, which allow the creation of various 3´ untranslated regions (3´UTRs). Alternative pA sites can be localized in internal introns or exons, allowing the formation of different protein isoforms, or they may be localized in the 3´UTR resulting in transcripts with variable 3´ UTRs encoding the same protein. It has been reported that cancer cells often express significant increased number of mRNA isoforms with shorter 3´UTRs than differentiated non transformed cells. It is also known than higher gene expression is tightly linked to cellular proliferation and short 3´UTR isoforms are more abundant in proliferating cells. Here, we report a pipeline named PolA-Seq to analyze the differential expression of genes than present alternative pA sites based on RNA- seq data. This new tool allows the use of transcriptomic public and private data for searching specific mRNA isoforms. The pipeline consists in the implementation of STAR, R/Bioconductor and deeptools packages, for data analysis and visualization. This pipeline allowed us to identify different 3´UTRs of previously non-reported genes with alternative polyadenylation based on RNA-Seq data. From an annotated genome, PolA-seq uses the DaPars algorithm to infer both the presence of de novo proximal PAS and the dynamics of the differential use of PAS between two conditions. With this new tool we seek to analyze different isoforms of mRNA involved in the development of mammary tumors and in differented stages of normal mammary cells. PolA-Seq was employed to compare gene expression data from mammary tumors and their normal counterparts. We identified a increased number of short 3´UTRs of the mRNA in the tumors cells. PolA-seq is shown to be a useful tool for the analysis of alternative polyadenylation from RNA-Seq. In addition, preliminary data allowed us to verify this pattern in other relevant genes with alternative pA sites.