Abstract
PIWI-interacting RNAs (piRNAs) and their partnering PIWI proteins defend the animal germline against transposable elements and play a crucial role in fertility. Numerous studies in the past have uncovered many additional functions of the piRNA pathway, including gene regulation, anti-viral defense, and somatic transposon repression. Further, comparative analyses across phylogenetic groups showed that the PIWI/piRNA system evolves rapidly and exhibits great evolutionary plasticity. However, the presence of so-called piRNA clusters as the major source of piRNAs is common to nearly all metazoan species. These genomic piRNA-producing loci are highly divergent across taxa and critically influence piRNA populations in different evolutionary lineages. We launched the initial version of the piRNA cluster database to facilitate research on regulation and evolution of piRNA-producing loci across tissues und species. In recent years the amount of small RNA sequencing data that was generated and the abundance of species that were studied has grown rapidly. To keep up with this recent progress, we have released a major update for the piRNA cluster database (https://www.smallrnagroup.uni-mainz.de/piRNAclusterDB), expanding it from 12 to a total of 51 species with hundreds of new datasets, and revised its overall structure to enable easy navigation through this large amount of data.
Highlights
PIWI proteins and PIWI-interacting RNAs (piRNAs) represent a mainly metazoan system for the regulation of a range of target sequences [1,2,3,4], including transposable elements [5,6], protein-coding genes [7,8,9,10,11] and long noncoding RNAs [12]
While in vertebrates the PIWI/piRNA pathway is mostly restricted to the germline, in invertebrate groups such as arthropods and mollusks, piRNAs are in addition ubiquitously found in somatic tissues [15,16]
We further significantly improved our small RNA transcriptome analysis, which includes an extensive set of non-coding RNAs, and we provide bibliographic information, as well as easy access to reference data used in our analysis
Summary
PIWI proteins and piRNAs represent a mainly metazoan system for the regulation of a range of target sequences [1,2,3,4], including transposable elements [5,6], protein-coding genes [7,8,9,10,11] and long noncoding RNAs [12]. Though these regions make up overall only small portions of a genome with 0.1 to 5%, they produce the vast majority of piRNAs. In Drosophila, over 90% of all sequenced germline piRNAs can be derived from these genomic loci [19]. The first release of the piRNA cluster database [27], which was launched to as a central resource for piRNA cluster research, comprised more than 100 Sequence Read Archive (SRA) datasets from 12 species.
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