A heterochromatin-specific RNA export pathway facilitates piRNA production

Abstract

Interactive data links: High-throughput sequencing (UCSC browser session); Mass spectrometry (interactive plots) PIWI-interacting RNAs (piRNAs) guide transposon silencing in animals. The 22-30nt piRNAs are processed in the cytoplasm from long non-coding RNAs. How piRNA precursors, which often lack RNA processing hallmarks of export-competent transcripts, achieve nuclear export is unknown. Here, we uncover the RNA export pathway specific for piRNA precursors in the Drosophila germline. This pathway requires Nxf3-Nxt1, a variant of the hetero-dimeric mRNA export receptor Nxf1-Nxt1. Nxf3 interacts with UAP56, a nuclear RNA helicase essential for mRNA export, and CG13741/Bootlegger, which recruits Nxf3-Nxt1 and UAP56 to heterochromatic piRNA source loci. Upon RNA cargo binding, Nxf3 achieves nuclear export via the exportin Crm1, and accumulates together with Bootlegger in perinuclear nuage, suggesting that after export, Nxf3-Bootlegger delivers precursor transcripts to the piRNA processing sites. Our findings indicate that the piRNA pathway bypasses nuclear RNA surveillance systems to achieve export of heterochromatic, unprocessed transcripts to the cytoplasm, a strategy also exploited by retroviruses.

Specialization of theDrosophilanuclear export family protein, Nxf3, for piRNA precursor export

“…We further find that Nxf3mediated export depends on Crm1. These findings are all in agreement with those of ElMaghraby and colleagues who also identified Nxf3 and Bootlegger as critical facilitators of piRNA precursor export (ElMaghraby et al 2019).…”

“…The work presented here, and other emerging realizations (Batki et al 2019;ElMaghraby et al 2019;Fabry et al 2019;Murano et al 2019;Zhao et al 2019) begin to paint a picture in which the evolutionary pressures exerted by the need to control mobile genetic elements have resulted in exaptation and dedication of nuclear export factor family members to the piRNA pathway. This specialization has taken different forms.…”

“…This specialization has taken different forms. The most easily understood is the adaptation of Nxf3 to export a specific class of non-canonically transcribed RNAs (ElMaghraby et al 2019), whereas the precise mechanism by which Nxf2 acts as a co-transcriptional silencing factor remains more mysterious (Batki et al 2019;Fabry et al 2019;Murano et al 2019;Zhao et al 2019). Ultimately, an understanding of how these proteins have assumed new roles through evolution will require a detailed understanding of how they are recruited to particular transcripts and how they mediate their downstream effects.…”

“…2D,E), whereas Nxf3 in turn could promote translocation of some CG13741 protein outside of the nucleus. Given the involvement of CG13741 in the biology of dual-strand piRNA clusters, we have, by mutual agreement, named CG13741 Bootlegger (ElMaghraby et al 2019).…”

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation

“…In flies, the three NXF variants exhibit gonad-specific expression with Nxf2 and Nxf3 being expressed predominantly in ovaries, and Nxf4 being testis-specific (Gramates et al, 2017). Besides Nxf2 (this study), Drosophila Nxf3 is also an essential piRNA pathway component as it is required for the nuclear export of un-processed piRNA cluster transcripts in the germline (ElMaghraby et al, 2019). In mice and humans, several NXF variants are preferentially expressed in testes.…”