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Fig. 3 | BMC Genomics

Fig. 3

From: piRNA-like small RNAs mark extended 3’UTRs present in germ and somatic cells

Fig. 3

piRNA clusters mark extended 3’ UTRs. Potential precursors of extended 3’ UTR piRNA clusters are detectable as 3’ UTR isoforms in testis and in somatic tissues. a Representative example of a piRNA cluster that extends beyond an annotated 3’ UTR. The annotated 3’UTR is shown in purple and the piRNA cluster is shown in red. Individual piRNA alignments are in blue (sense strand) and red (antisense strand) at the bottom. Genomic features are visualized using the Integrative Genomics Viewer [51]. b Unannotated portions of 3’ UTR piRNA clusters are enriched for polyA+ RNA expression when compared to randomly selected unannotated regions. We used an adult testis RNA-Seq dataset [18] to determine expression of the unannotated portions of the extended 3’ UTR clusters (dark blue) or random intergenic regions of equal size (light blue). This indicates that the unannotated extended 3’UTRs are transcribed in the testis. c Expression of the unannotated portion of extended 3’ UTR clusters (X-axis) compared with expression of the corresponding annotated mRNA (Y-axis) in the adult testis RNA-Seq dataset [18]. The annotated portions of genes are generally expressed at higher RPKM than the unannotated portion of the 3’UTR. d Schematic of Northern blot probes, RT-PCR primers, and PCR amplicons. e Northern blot of Pdpr with an exonic probe (top) shows bands consistent with the length of the annotated mRNA, plus a band consistent with addition of the unannotated region corresponding to the piRNA cluster. The bands are visible only in brain. Probing of the same blot with the unannotated 3’UTR probe (bottom) shows a single band in the same position as the upper band in the exonic probe blot. f Representative RT-PCR results of the three Pdpr amplicons shown schematically in D and marked to the right, with (+) and without (−) reverse transcriptase during the cDNA synthesis step (top). g Summary of RT-PCR products obtained from 10 transcripts with extended 3’ UTR piRNA clusters. For each gene testis, brain, spleen, and liver were tested. All transcripts show evidence of an extended 3’UTR in testis and most also have the extended 3’ UTR in the other tissues as well

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