@article {1170,
	title = {Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea.},
	journal = {G3 (Bethesda)},
	volume = {6},
	year = {2016},
	month = {2016 10 13},
	pages = {3035-3048},
	abstract = {<p>In eukaryotes, 3{\textquoteright} untranslated regions (UTRs) play important roles in regulating posttranscriptional gene expression. The 3{\textquoteright}UTR is defined by regulated cleavage/polyadenylation of the pre-mRNA. The advent of next-generation sequencing technology has now enabled us to identify these events on a genome-wide scale. In this study, we used poly(A)-position profiling by sequencing (3P-Seq) to capture all poly(A) sites across the genome of the freshwater planarian, Schmidtea mediterranea, an ideal model system for exploring the process of regeneration and stem cell function. We identified the 3{\textquoteright}UTRs for \~{}14,000 transcripts and thus improved the existing gene annotations. We found 97 transcripts, which are polyadenylated within an internal exon, resulting in the shrinking of the ORF and loss of a predicted protein domain. Around 40\% of the transcripts in planaria were alternatively polyadenylated (ApA), resulting either in an altered 3{\textquoteright}UTR or a change in coding sequence. We identified specific ApA transcript isoforms that were subjected to miRNA mediated gene regulation using degradome sequencing. In this study, we also confirmed a tissue-specific expression pattern for alternate polyadenylated transcripts. The insights from this study highlight the potential role of ApA in regulating the gene expression essential for planarian regeneration.</p>
},
	keywords = {3{\textquoteright} Untranslated Regions, Animals, Computational Biology, Genome, Helminth, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing, MicroRNAs, Molecular Sequence Annotation, Platyhelminths, Poly A, Polyadenylation, Reproducibility of Results, RNA Interference, RNA Processing, Post-Transcriptional, RNA, Messenger},
	issn = {2160-1836},
	doi = {10.1534/g3.116.031120},
	author = {Lakshmanan, Vairavan and Bansal, Dhiru and Kulkarni, Jahnavi and Poduval, Deepak and Krishna, Srikar and Sasidharan, Vidyanand and Anand, Praveen and Seshasayee, Aswin and Palakodeti, Dasaradhi}
}
