piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation

AbstractPIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly expressed and extensively studied from the germline. piRNAs associate with PIWI proteins to maintain DNA methylation for transposon silencing and transcriptional gene regulation for genomic stability. Mature germline piRNAs have distinct characteristics including a 24- to 32-nucleotide length and a 2 ʹ-O-methylation signature at the 3ʹ end. Although recent studies have identified piRNAs in somatic tissues, they remain poorly characterized. For example, we recently demonstrated notable expression of piRNA in the murine soma, and while overall expression was lower than that of the germline, uniq ue characteristics suggested tissue-specific functions of this class. While currently available databases commonly use length and association with PIWI proteins to identify piRNA, few have included a chemical oxidation method that detects piRNA based on its 3ʹ modification. This method leads to rep roducible and rigorous data processing when coupled with next-generation sequencing and bioinformatics analysis. Here, we introduce piOxi DB, a user-friendly web resource that provides a comprehensive analysis of piRNA, generated exclusively through sodium periodate treatment of small RNA. The curre nt version of piOxi DB includes 435 749 germline and 9828 somatic piRNA sequences robustly identified fromM. musculus, M. fascicularis andH. sapiens. The database provides species- and tissue-specific ...
Source: Database : The Journal of Biological Databases and Curation - Category: Databases & Libraries Source Type: research