piRNA-IPdb: a PIWI-bound piRNAs database to mining NGS sncRNA data and beyond.

BACKGROUND: PIWI-interacting RNAs (piRNAs) are an abundant single-stranded type of small non-coding RNAs (sncRNAs), which initially were discovered in gonadal cells, with a role as defenders of genomic integrity in the germline, acting against the transposable elements. With a regular size range of 21-35 nt, piRNAs are associated with a PIWI-clade of Argonaute family proteins. The most widely accepted mechanisms of biogenesis for piRNAs involve the transcription of longer precursors of RNAs to be processed, by complexes of proteins, to functional size, preferentially accommodating uridine residues at the 5' end and 3' methylation to increase the stability of these molecules. piRNAs have also been detected in somatic cells, with diverse potential functions, indicating their high plasticity and pleiotropic activity. Discovered about two decades ago, piRNAs are a large and versatile type of sncRNA and that remain insufficiently identified and analyzed, through next-generation sequencing (NGS), to evaluate their processing, functions, and biogenesis in different cell types and during development. piRNAs' distinction from other sncRNAs has led to controversial results and interpretation difficulties when using existing databases because of the heterogeneity of the criteria used in making the distinction. DESCRIPTION: We present "piRNA-IPdb", a database based uniquely on datasets obtaining after the defining characteristic of piRNAs: those small RNAs bound to PIWI proteins. We selected and analyzed sequences from piRBase that exclusively cover the binding to PIWI. We pooled a total of 18,821,815 sequences from RNA-seq after immunoprecipitation that included the binding to any of the mouse PIWI proteins (MILI, MIWI, or MIWI2). CONCLUSIONS: In summary, we present the characteristics and potential use of piRNA-IPdb database for the analysis of bona fide piRNAs.

Changes in vinexin expression patterns in the mouse testis induced by developmental exposure to 17beta-estradiol.

In the seminiferous epithelium, numerous cell interactions between Sertoli cells and Sertoli-germ cells are established by specialized proteins so as to maintain the functionality of the testis. Exogenous estrogen exposure can result in alterations to these interactions and cause pathologies, including impaired spermatogenesis and tumorigenesis. In the present study, with the aim of finding markers of the action of estrogenic compounds in the mammalian testis, we focused on investigating molecules that are linked to cellular junctions. We found that the testicular vinexin (sorbin and SH3 domain-containing protein 3, encoded by the Sorbs3 gene) pattern underwent significant changes after developmental exposure to 17beta-estradiol (E(2)). Vinexin is an adaptor protein that is implicated in cell adhesion and actin-cytoskeletal reorganization. We characterized, at the protein and mRNA levels, the expression patterns of vinexin isoforms during testis development and in defined cell types from the seminiferous tubule. The protein expression patterns of vinexin-interacting proteins flotillin 1 and vinculin were also analyzed. Thus, we have identified a novel association between a vinexin isoform and germ cells, which contrasts with the predominant localization of the gamma isoform in Sertoli cells. The effects of E(2) on the testes of developmentally exposed mice were evident, with total depletion of the germ-cell-associated vinexin isoform and a noticeable decrease in Sertoli-cell-related vinexin gamma.