piRNAs and their associated proteins (PIWI) were initially discovered in Drosophila melanogaster as small non-coding RNAs essential for germline development (Lin, 2007). The PIWI proteins are crucial for piRNA biogenesis and are involved in forming the piRNA-induced silencing complex (piRISC) to induce DNA methylation for silencing of transposable elements in the germline, maintaining genomic integrity, and regulating transcription (Aravin et al., 2006; Thomson & Lin, 2009). piRNAs contain several characteristics including strong preference for a uridine signature at the 5’ end, an adenosine signature at position 10, and a 2'-O-methylation signature at the 3' end, appended by HEN1 methyltransferase (Zuo, Wang, Tan, Chen, & Luo, 2016). Traditionally, the piRNA class of small RNA was limited to sequence-specific de novo DNA methylation of transposable elements and genic regions of germ cells. However, recent studies reveal widespread PIWI and piRNA expression in somatic tissues, including the brain (Rajasethupathy et al., 2012; Ross, Weiner, & Lin, 2014). In mice, somatic piRNAs were also revealed to be shorter in length relative to their germline counterparts (B. P. U. Perera et al., 2019). The functional implications of somatic PIWI and piRNAs are poorly understood. Therefore, piOxi DB aims to carefully catalog samples categorized by species, tissue, developmental stage, sex, and piRNA detection method, to improve analysis and interpretation of piRNA-directed functions and mechanisms (B. P. Perera, Faulk, C., Svoboda, L.K., Goodrich, J.M., Dolinoy, D.C., 2019). The current database can be utilized for broad research applications in the fields of RNA biology, cancer biology, environmental toxicology, and beyond (B. P. U. Perera et al., 2022).

1. Aravin, A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., et al. (2006). A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442(7099), 203-207.
2. Lin, H. (2007). piRNAs in the germ line. Science, 316(5823), 397.
3. Perera, B. P., Faulk, C., Svoboda, L.K., Goodrich, J.M., Dolinoy, D.C. (2019). The Role of Environmental Exposures and the Epigenome in Helath and Disease. Environ Mol Mutagen.
4. Perera, B. P. U., Morgan, R. K., Polemi, K. M., Sala-Hamrick, K. E., Svoboda, L. K., & Dolinoy, D. C. (2022). PIWI-Interacting RNA (piRNA) and Epigenetic Editing in Environmental Health Sciences. Curr Environ Health Rep, 9(4), 650-660.
5. Perera, B. P. U., Tsai, Z. T., Colwell, M. L., Jones, T. R., Goodrich, J. M., Wang, K., et al. (2019). Somatic expression of piRNA and associated machinery in the mouse identifies short, tissue-specific piRNA. Epigenetics, 1-18.
6. Rajasethupathy, P., Antonov, I., Sheridan, R., Frey, S., Sander, C., Tuschl, T., et al. (2012). A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell, 149(3), 693-707.
7. Ross, R. J., Weiner, M. M., & Lin, H. (2014). PIWI proteins and PIWI-interacting RNAs in the soma. Nature, 505(7483), 353-359.
8. Thomson, T., & Lin, H. (2009). The biogenesis and function of PIWI proteins and piRNAs: progress and prospect. Annu Rev Cell Dev Biol, 25, 355-376.
9. Zuo, L. J., Wang, Z. R., Tan, Y. L., Chen, X. N., & Luo, X. G. (2016). piRNAs and Their Functions in the Brain. International Journal of Human Genetics, 16(1-2), 53-60.

Sodium periodate treatment method specifically enriches for small RNAs containing a periodate-resistant 2ʹ-O-methylation signature, a well-known modification typically found at the 3’ end of a mature piRNA transcript. Subsequent library preparation with PCR amplification, paired with comparisons between sodium periodate treated and untreated sample specimens by novel bioinformatics pipelines, can be incorporated for high-throughput sequencing of piRNA transcripts. The specific protocol for sodium periodate treatment can be found here.