Genome-wide analysis of polyadenylation events in Schmidtea mediterranea (II)

This study is the first to report genome-scale polyadenylation events in S.mediterranea using poly-A position profiling (3P-Seq).Various cis-acting elements such as hexameric PAS & U/GU enrichment after cleavage site were observed to be conserved in planaria.The cleavage site derived from 3P-Seq could be successfully associated with ~38-60% of transcripts (Makers -38%, oxford- 60% and Dresden- 44%).We also investigated the functional consequences of altered 3’UTRs arising from ApA. Around 97 transcripts were observed to undergo coding region alternate polyadenylation (CR-ApA) that resulted in loss of specific domains from proteins (as inferred from pfam domain search). In this study, we also demonstrated that microRNA-mediated regulation might be one of the key factors playing an important role in selection/evolution of alternate 3’UTRs. The 3’ UTR is one of the key regulatory element that decides the fate of mRNA inside a cell. Switching isoforms according to the need of cell and environmental cues could help the cell to adapt. In this study, we also attempted to study the tissue-specific role of ApA pattern in planaria. Due to the limitations associated with isolation of different tissue-specific cells from planaria, we performed a high-throughput microarray analysis across X1, X2 and Xins cell populations. We were clearly able to identify the differential expression pattern of the ApA events across cell population. Expression pattern of alternate polyadenylated transcripts in planarian stem cells (X1), Progenitor cells (X2) and differentiated cell (Xins) populations. All the samples were done in duplicates