A single unidirectional piRNA cluster similar to the flamenco locus is the major source of EVE-derived transcription and small RNAs in Aedes aegypti mosquitoes
- Eric R G R Aguiar1,
- João Paulo P Almeida1,
- Lucio Rezende Queiroz1,
- Liliane S Oliveira2,
- Roenick P Olmo1,
- Isaque João S Faria1,
- Jean-Luc Imler3,
- Arthur Gruber2,
- Benjamin J Matthews4 and
- João T Marques1,5
- 1 Universidade Federal de Minas Gerais;
- 2 Universidade de São Paulo;
- 3 Université de Strasbourg, CNRS UPR9022, Inserm U1257;
- 4 University of British Columbia
- ↵* Corresponding author; email: jtm{at}ufmg.br
Abstract
Endogenous viral elements (EVEs) are found in many eukaryotic genomes. Despite considerable knowledge about genomic elements such as transposons (TEs) and retroviruses, we still lack information about non-retroviral EVEs. Aedes aegypti mosquitoes have a highly repetitive genome that is covered with EVEs. Here, we identified 129 non-retroviral EVEs in the AaegL5 version of the A. aegypti genome. These EVEs were significantly associated with TEs and preferentially located in repeat-rich clusters within intergenic regions. Genome-wide transcriptome analysis showed that most EVEs generated transcripts although only around 1.4% were sense RNAs. The majority of EVE transcription was antisense and correlated with the generation of EVE-derived small RNAs. A single genomic cluster of EVEs located in a 143 kb repetitive region in chromosome 2 contributed with 42% of antisense transcription and 45% of small RNAs derived from viral elements. This region was enriched for TE-EVE hybrids organized in the same coding strand. These generated a single long antisense transcript that correlated with the generation of phased primary PIWI-interacting RNAs (piRNAs). The putative promoter of this region had a conserved binding site for the transcription factor Cubitus interruptus, a key regulator of the flamenco locus in Drosophila melanogaster. Here, we have identified a single unidirectional piRNA cluster in the A. aegypti genome that is the major source of EVE transcription fueling the generation of antisense small RNAs in mosquitoes. We propose that this region is a flamenco-like locus in A. aegypti due to its relatedness to the major unidirectional piRNA cluster in Drosophila melanogaster.
Keywords
- Received November 14, 2019.
- Accepted January 22, 2020.
- Published by Cold Spring Harbor Laboratory Press for the RNA Society
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