Abstract
piRNAs are a class of noncoding RNAs that perform functions in epigenetic regulation and silencing of transposable elements, a mechanism conserved among most mammals. At present, there are more than 30,000 known piRNAs in humans, of which more than 80% are derived from intergenic regions, and approximately 20% are derived from the introns and exons of pre-mRNAs. It was observed that the expression of the piRNA profile is specific in several organs, suggesting that they play functional roles in different tissues. In addition, some studies suggest that changes in regions that encode piRNAs may have an impact on their function. To evaluate the conservation of these regions and explore the existence of a seed region, SNP and INDEL variant rates were investigated in several genomic regions and compared to piRNA region variant rates. Thus, data analysis, data collection, cleaning, treatment, and exploration were implemented using the R programming language with the help of the RStudio platform. We found that piRNA regions are highly conserved after considering INDELs and do not seem to present an identifiable seed region after considering SNPs and INDEL variants. These findings may contribute to future studies attempting to determine how polymorphisms in piRNA regions can impact diseases.
Highlights
There are over 30,000 PIWI-interacting RNAs (piRNAs) in humans, among which more than 80% are derived from intergenic regions, and approximately 20% are derived from introns and exons of pre-mRNAs [14,15]
It was observed that piRNA regions have higher conservation for INDEL variants and lower conservation for single-nucleotide polymorphism (SNP) variants relative to exonic regions
This suggests that piRNA regions are more permissive to SNP variations and less permissive to INDEL variations, indicating that SNPs may have little effect on piRNA regular activity, and that INDELs may have a significant impact on its structure and functions
Summary
The Encyclopedia of DNA Elements (ENCODE), a large consortium project to map all functional elements in the human genome, has suggested that up to 80% of the genome is biologically active and functional with an essential role in controlling DNA expression and spatial organization of the genome [1,2,3]. PiRNAs are a class of recently discovered sncRNAs that were described for the first time in germ cells [5,6,7,8] and identified later in somatic cells [9]. These sncRNAs have 24–31 nucleotides, interact with argonaut proteins of the PIWI subfamily, and form the PIWI–piRNA pathway, which plays roles in transcriptional and posttranscriptional silencing of transposable elements (TEs), epigenetic regulation, the maintenance of germ cell function, and the regulation of mRNA [9,10,11]. The silencing of TEs and other genetic elements in germlines, at both the transcriptional and the posttranscriptional levels, is highly conserved across animal species [12,13]
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