Cellular abundance shapes function in piRNA-guided genome defense

Abstract

Defense against genome invaders universally relies on RNA-guided immunity. Prokaryotic CRISPR-Cas and eukaryotic RNA interference pathways recognize targets by complementary base-pairing, which places the sequences of their guide RNAs at the center of self/nonself discrimination. Here, we explore the sequence space of PIWI-interacting RNAs (piRNAs), the genome defense of animals, and establish functional priority among individual sequences. Our results reveal that only the topmost abundant piRNAs are commonly present in every cell, whereas rare sequences generate cell-to-cell diversity in flies and mice. We identify a skewed distribution of sequence abundance as a hallmark of piRNA populations and show that quantitative differences of more than a 1000-fold are established by conserved mechanisms of biogenesis. Finally, our genomics analyses and direct reporter assays reveal that abundance determines function in piRNA-guided genome defense. Taken together, we identify an effective sequence space and untangle two classes of piRNAs that differ in complexity and function. The first class represents the topmost abundant sequences and drives silencing of genomic parasites. The second class sparsely covers an enormous sequence space. These rare piRNAs cannot function in every cell, every individual, or every generation but create diversity with potential for adaptation in the ongoing arms race with genome invaders.

Hierarchical length and sequence preferences establish a single major piRNA 3′-end

“…Longer piRNAs have the potential for stronger and more specific interactions, and precision of a major 3′end might be required to control specificity. The notion that every piRNA has a single major 3′end contributes to our emerging understanding that the functional piRNA sequence space is regulated to ensure effective genome defense ( Genzor et al., 2021 ).…”

Exosomes/microvesicles target SARS-CoV-2 via innate and RNA-induced immunity with PIWI-piRNA system

“…A limitation of this study was that piRNA sequences entirely relied on the information available in public depository while many of them have not been verified. What makes it more challenging is, defining piRNAs, perhaps in particular mammalian piRNAs, might not be clearly based on sequence information, for example, although piRNAs have strong bias for uridine at the five end and/or for adenosine at position 10, exceptions to these features are also reported ( 33 , 35 , 36 ). In this work, among piRNAs that we analyzed, some species fit with these features, whereas others do not, so future biochemical and functional assessment are anticipated to characterize these small RNA species.…”

Hierarchical length and sequence preferences establish a single major piRNA 3’-end

“…Longer piRNAs have the potential for stronger interactions, and precision of a major 3'end might be required to control specificity. The notion that every piRNA has a single major 3'end contributes to our emerging understanding that the functional piRNA sequence space is regulated to ensure effect genome defense [30]. .…”

“…. Datasets were initially processed as previously described [30]. All computational code is available in 'Supplemental Code'.…”

“…Mouse data were obtained from [NCBI BioProject accession number PRJNA421205]. Datasets were initially processed as previously described [30]. All computational code is available in ‘Supplemental Code’.…”