Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation

Daniel Gebert,Lena K Neubert,Catrin Lloyd,Jinghua Gui,Ruth Lehmann,Felipe Karam Teixeira

doi:10.1016/j.molcel.2021.07.011

Daniel Gebert, Lena K Neubert + Show 4 more

Open Access

https://doi.org/10.1016/j.molcel.2021.07.011

Copy DOI

Abstract

SummaryPIWI proteins and their guiding Piwi-interacting small RNAs (piRNAs) are crucial for fertility and transposon defense in the animal germline. In most species, the majority of piRNAs are produced from distinct large genomic loci, called piRNA clusters. It is assumed that germline-expressed piRNA clusters, particularly in Drosophila, act as principal regulators to control transposons dispersed across the genome. Here, using synteny analysis, we show that large clusters are evolutionarily labile, arise at loci characterized by recurrent chromosomal rearrangements, and are mostly species-specific across the Drosophila genus. By engineering chromosomal deletions in D. melanogaster, we demonstrate that the three largest germline clusters, which account for the accumulation of >40% of all transposon-targeting piRNAs in ovaries, are neither required for fertility nor for transposon regulation in trans. We provide further evidence that dispersed elements, rather than the regulatory action of large Drosophila germline clusters in trans, may be central for transposon defense.

Highlights

In the germline of animals, the piwi-interacting small RNA pathway is an essential defense mechanism against transposable elements (TEs) (Aravin et al, 2007; Brennecke et al, 2007; Czech et al, 2018)
Evolution of germline-expressed Piwi-interacting small RNAs (piRNAs) clusters in the Drosophila genus To study the evolutionary dynamics of germline piRNA clusters through relatively short periods of time, we focused on ten species closely related to D. melanogaster, representing $73 million years (My) of evolution within the Drosophila genus (Figure 1A)
Unbiased identification of germline-expressed piRNA clusters was conducted by combining previously annotated genome drafts (Adams et al, 2000; Drosophila 12 Genomes Consortium et al, 2007; Hoskins et al, 2015), recently published Nanopore long-readbased genome assemblies (Miller et al, 2018; Shah et al, 2019), and species-specific, high-throughput small RNA sequencing (RNA-seq) data obtained from mixed-aged embryos, which contain maternally deposited small RNAs generated during oogenesis as well as small RNAs zygotically produced during embryogenesis

Summary

Introduction

In the germline of animals, the piwi-interacting small RNA (piRNA) pathway is an essential defense mechanism against transposable elements (TEs) (Aravin et al, 2007; Brennecke et al, 2007; Czech et al, 2018). PiRNA biogenesis relies on the activity of conserved endonucleases and PIWI proteins, but unlike other small RNA pathways, it operates independently of Dicer proteins (Brennecke et al, 2007; Gunawardane et al, 2007). Silencing is mediated by piRNA-loaded effector complexes that either induce target transcript slicing by PIWI-mediated cleavage or recruit additional complexes that direct chromatin modification at the target loci (Czech et al, 2018)

Results

Discussion

Conclusion