Abstract
PIWI-interacting RNAs (piRNAs) are essential for transcriptional and post-transcriptional regulation of transposons and coding genes in germline. With the development of sequencing technologies, length variations of piRNAs have been identified in several species. However, the extent to which, piRNA isoforms exist, and whether these isoforms are functionally distinct from canonical piRNAs remain uncharacterized. Through data mining from 2154 datasets of small RNA sequencing data from four species (Homo sapiens, Mus musculus, Danio rerio and Drosophila melanogaster), we have identified 8 749 139 piRNA isoforms from 175 454 canonical piRNAs, and classified them on the basis of variations on 5′ or 3′ end via the alignment of isoforms with canonical sequence. We thus established a database named IsopiRBank. Each isoforms has detailed annotation as follows: normalized expression data, classification, spatiotemporal expression data and genome origin. Users can also select interested isoforms for further analysis, including target prediction and Enrichment analysis. Taken together, IsopiRBank is an interactive database that aims to present the first integrated resource of piRNA isoforms, and broaden the research of piRNA biology. IsopiRBank can be accessed at http://mcg.ustc.edu.cn/bsc/isopir/index.html without any registration or log in requirement. Database URL: http://mcg.ustc.edu.cn/bsc/isopir/index.html
Highlights
PIWI-interacting RNAs are small, 26–31 nt singlestranded RNAs that interact with the PIWI proteins, a clade of Argonaute protein family [1]
PiRNAs are reported to act like miRNAs to induce mRNA deadenylation or decay [13,14,15]. PIWI-interacting RNAs (piRNAs) that were produced from coding genes can regulate the ‘host’ gene expression [16]
We found a small fraction of piRNA isoforms with 30 or 50 NE (Supplementary Figure S3B), which are similar to isomiRs that resulted from variations in the Drosha and Dicer cleavage sites within pre-miRNA [53]
Summary
PIWI-interacting RNAs (piRNAs) are small, 26–31 nt singlestranded RNAs that interact with the PIWI proteins, a clade of Argonaute protein family [1]. In Drosophila, Nbr, an established 30–50 exoribonuclease, firstly discovered in miRNA isoform (isomiR) biogenesis, is found to be responsible for trimming piRNA 30 ends and functionally relevant with the repression of TEs [23, 26]. BmPAPI, a TUDOR domain-containing protein, can modulate the length of piRNAs via the cooperative working with PNLDC1 in silkworms [25, 27] Depleting both of them resulted in accumulation of $35–40 nt pre-piRNAs that were impaired for target cleavage and are prone to degradation [25]. In Drosophila, antagonistic roles between Hen and Nbr have been found in modulating piRNA 30 ends [23] These discoveries indicated the existence of piRNA isoforms, like already established known isomiRs. In contrast to well-studied isomiRs, the divergent nature of piRNA biogenesis and sequence, increases the complexity of studies on piRNA isoforms. IsopiRBank is implemented in PHP þ MySQL þ JavaScriptþ R and can be accessed at http://mcg.ustc.edu. cn/bsc/isopir/index.html without any registration (Figure 1)
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