Antagonistic roles between Nibbler and Hen1 modulate piRNA 3' ends in Drosophila

Abstract

In eukaryotes, aberrant expression of transposable elements (TEs) is detrimental to the host genome. Piwi-interacting RNAs (piRNAs) of ∼23 to 30 nucleotides bound to PIWI clade Argonaute proteins silence transposons in a manner that is strictly dependent on their sequence complementarity. Hence, a key goal in understanding piRNA pathways is to determine mechanisms that modulate piRNA sequences. Here, we identify a protein-protein interaction between the 3′-to-5′ exoribonuclease Nibbler (Nbr) and Piwi that links Nbr activity with piRNA pathways. We show that there is a delicate balance in the interplay between Nbr and Hen1, a methyltransferase involved in 2′-O-methylation at the 3′ terminal nucleotides of piRNAs, thus connecting two genes with opposing activities in the biogenesis of piRNA 3′ ends. With age, piRNAs become shorter and fewer in number, which is coupled with the derepression of select TEs. We demonstrate that activities of Nbr and Hen1 inherently contribute to TE silencing and age-dependent profiles of piRNAs. We propose that antagonistic roles of Nbr and Hen1 define a mechanism to modulate piRNA 3′ ends.

piRNA Biogenesis in Drosophila melanogaster

“…In this case, a 3’-to-5’ exonuclease trims a longer precursor formed by cleavage by an endonuclease (slicer or Zuc) to make mature piRNAs of the correct size. Such ‘Trimmer’ activity was first observed in vitro using lysate from a silkworm cell line [78] and later associated with the exonuclease Nibbler (Nbr) [77, 79, 80]. Independently of the mechanism by which the 3’end of piRNAs is generated, the last step is the 2’OMe-modification of the last nucleotide by Hen1, which is thought to increase the stability of piRNAs [80–82].…”

Innate and intrinsic antiviral immunity in Drosophila

“…As implied by their name, piRNAs associate with Piwi and two related proteins named Aubergine and AGO3, which form a separate clade of AGO proteins. Like siRNA, their 3’ end is protected by 2’-O-methylation [40]. The synthesis of piRNAs does not depend on Dicer proteins, but rather involves the exonuclease Zucchini and the AGO proteins from the Piwi clade themselves.…”

Structural insights into the sequence-specific recognition of Piwi by Drosophila Papi

“…Similarly, in Drosophila, Papi may be involved in primary piRNA production. Zuc-mediated cleavage of prepiRNA directly generates mature piRNA, while prepiRNAs released from the ping-pong cycle require further resection by Nibbler, which belongs to another 3′-5′ exoribonuclease family (31,32). The depletion of Papi increases the length of Piwi-bound piRNA somewhat, leaving both Aub-bound and Ago3-bound piRNAs unaffected (31).…”