Genome-wide analysis of polyadenylation events in Schmidtea mediterranea
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PROVIDER: PRJNA313150 | ENA |
REPOSITORIES: ENA
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Project description:Genome-wide analysis of polyadenylation events in Schmidtea mediterranea (I)
| PRJNA312800 | ENA
Project description:Genome-wide analysis of polyadenylation events in Schmidtea mediterranea (II)
| PRJNA313149 | ENA
Project description: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.
2022-10-01 | GSE78261 | GEO
Project description: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.
2022-10-01 | GSE78161 | GEO
Project description: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.
| S-EPMC5068929 | biostudies-literature
Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea
2011-07-15 | E-MTAB-607 | biostudies-arrayexpress
Project description:Identification of differentially expressed genes in intestinal phagocytes, compared to non-intestinal cells in Schmidtea mediterranea.
2012-10-01 | GSE35565 | GEO
Project description:Schmidtea mediterranea Raw sequence reads
| PRJNA276084 | ENA
Project description:Schmidtea mediterranea small RNA sequencing
| PRJNA187187 | ENA
Project description:Schmidtea mediterranea Raw sequence reads
| PRJNA318690 | ENA