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

Abstract

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.

Unraveling mitochondrial piRNAs in mouse embryonic gonadal cells

“…Considering the canonical characteristics of piRNAs, we also analyzed the sequences of the mito-piRNAs. In this context, a classic established hallmark for piRNAs is the bias of the presence of uridine at the 5' position of piRNAs (1U), clearly detected in the overall analysis of the piRNA database used in the present study as reference for piRNA consideration (piRNA-IPdb) 39 . However, neither the sequences nor reads of the specific mito-piRNAs that we have identified in gonadal cells showed such a hallmark, so that, rather than the classical uridine at the 5′ 1 position (1U), adenine (1A) was found by sequences or by reads (Fig.…”

“…By Bowtie aligner, two types of sncRNAs, miRNAs and piRNAs, were identified. Using miRBase version 22.1 102 , allowing two mismatches for miRNAs, and a custom database, to consider only those mouse sequences identified in the piRBase 40 detected after immunoprecipitation with PIWI proteins; the custom database, called piRNA-IPdb 39 , allowed 1 mismatch for piRNAs. The exact command passed to Bowtie was “-x < Bowtie Index of database > -f < Sample > -p 7 -v < mismatch > –sam-RG map_$mapping –best –strata -y –chunkmbs 256 –sam”.…”

“…Annotation of piRNAs has been controversial since each database uses different parameters to annotate a sequence as piRNA. To avoid this confusion, we built and use a custom database piRNA-IPdb 39 ( https://ipdb2.shinyapps.io/ipdb2/ ), restricting piRNA selection criteria from the piRBase 40 to those sequences that are immunoprecipitated, in mice, with any PIWI protein. This approach avoids the possibility of degradation products that were annotated as valid piRNAs.…”

Databases and computational methods for the identification of piRNA-related molecules: A survey

“…piRNA-IPdb [50] is a database based on PIWI protein-bound piRNA sequences for analyzing the data and functions of small ncRNA. This database provides a more accurate and reliable source of data on piRNAs.…”

Expression and Role of PIWI Proteins and piRNAs in Reproduction of Water Buffalo (Bubalus bubalis, Linn.)

“…Small non-coding RNAs (sncRNAs) circulated in the bloodstream are paracrine and endocrine messengers with prognostic value. PIWI-interacting RNAs (sncRNAs) are a common single-stranded type of small non-coding RNAs (sncRNAs) that protect genomic integrity in the germline by acting against transposable elements which they were first found in gonadal cells [73]. Abnormal epigenetic programming of the germ line is proposed as a possible mechanism for compromised spermatogenesis [74].…”