title: Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea.
abstract: In eukaryotes, 3' untranslated regions (UTRs) play important roles in regulating posttranscriptional gene expression. The 3'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'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'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.
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, NCBS campus, GKVK, Bellary Road, Bangalore 560065, Karnataka, India SASTRA University, Thirumalaisamudram, Thanjavur 613401, Tamil Nadu, India.
authors.forename: Vairavan
authors.identifier: 0000-0001-9468-9571
authors.initials: V
authors.lastname: Lakshmanan
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, NCBS campus, GKVK, Bellary Road, Bangalore 560065, Karnataka, India Manipal University, Madhav Nagar, Near Tiger Circle, Manipal 576104, Karnataka, India.
authors.forename: Dhiru
authors.initials: D
authors.lastname: Bansal
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, NCBS campus, GKVK, Bellary Road, Bangalore 560065, Karnataka, India.
authors.forename: Jahnavi
authors.initials: J
authors.lastname: Kulkarni
authors.affiliation: University of Bergen, Department of Clinical Science, Bergen 5020, Norway.
authors.forename: Deepak
authors.initials: D
authors.lastname: Poduval
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, NCBS campus, GKVK, Bellary Road, Bangalore 560065, Karnataka, India SASTRA University, Thirumalaisamudram, Thanjavur 613401, Tamil Nadu, India.
authors.forename: Srikar
authors.initials: S
authors.lastname: Krishna
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, NCBS campus, GKVK, Bellary Road, Bangalore 560065, Karnataka, India Manipal University, Madhav Nagar, Near Tiger Circle, Manipal 576104, Karnataka, India.
authors.forename: Vidyanand
authors.initials: V
authors.lastname: Sasidharan
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, NCBS campus, GKVK, Bellary Road, Bangalore 560065, Karnataka, India dasaradhip@instem.res.in.
authors.forename: Praveen
authors.identifier: 0000-0003-2219-4785
authors.initials: P
authors.lastname: Anand
authors.affiliation: National Centre for Biological Sciences, GKVK Campus, Bangalore 560065, Karnataka, India dasaradhip@instem.res.in.
authors.forename: Aswin
authors.identifier: 0000-0001-7028-1803
authors.initials: A
authors.lastname: Seshasayee
authors.affiliation: Institute for Stem Cell Biology and Regenerative Medicine, NCBS campus, GKVK, Bellary Road, Bangalore 560065, Karnataka, India dasaradhip@instem.res.in.
authors.forename: Dasaradhi
authors.identifier: 0000-0003-2219-4785
authors.initials: D
authors.lastname: Palakodeti
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D019295:Computational Biology / Q000379:methods; D049751:Genome, Helminth; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics; D058977:Molecular Sequence Annotation; D010986:Platyhelminths / Q000235:genetics*; D011061:Poly A; D026723:Polyadenylation; D034622:RNA Interference; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D012333:RNA, Messenger; D011061:Poly A
keywords: 3P-Seq (poly(A)-position profiling); alternate polyadenylation; planaria; polyadenylation; posttranscriptional regulation