A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development

Betting, Valerie; Joosten, Joep; Halbach, Rebecca; Thaler, Melissa; Miesen, Pascal; Rij, Ronald P. van

doi:10.1261/rna.078876.121

Cited by 14 publications

(19 citation statements)

References 67 publications

(90 reference statements)

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“…The heat maps showing differential expression of glycolytic genes (based on log2transformed fold changes) were generated in Microsoft Excel using three colour scale option of the conditional formatting function. Expression analysis of helicases in published datasets was performed as described previously (43,44). Briefly, publicly available datasets were retrieved from NCBI Sequence Read Archive and mapped to the AaegL5 genome using STAR aligner version 2.5.2b (41).…”

Section: Bioinformatics Analysesmentioning

confidence: 99%

The DEAD-box RNA helicase Dhx15 controls glycolysis and arbovirus replication in Aedes aegypti mosquito cells

Miesen

Machado

et al. 2022

Preprint

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Aedes aegypti mosquitoes are responsible for the transmission of arthropod-borne (arbo)viruses including dengue and chikungunya virus (CHIKV), but in contrast to human hosts, arbovirus infected mosquitoes are able to efficiently control virus replication to sub-pathological levels. Yet, our knowledge about the molecular interactions of arboviruses with their mosquito hosts is largely incomplete. Here, we aimed to identify and characterize novel host genes that control arbovirus replication in Aedes mosquitoes. RNA binding proteins (RBPs) are well known to regulate immune signaling pathways in all kingdoms of life. We therefore performed a knockdown screen targeting 461 genes encoding predicted RBPs in Aedes aegypti Aag2 cells and identified 15 genes with antiviral activity against a Sindbis reporter virus. Amongst these, three DEAD-box RNA helicases, AAEL004419/Dhx15, AAEL008728 and AAEL004859 also acted as antiviral factors in dengue and CHIKV infections. Here, we explore the mechanism of Dhx15 in regulating an antiviral transcriptional response in mosquitoes by silencing Dhx15 in Aag2 cells followed by deep-sequencing of poly-A enriched RNAs. Dhx15 knockdown in uninfected or CHIKV-infected cells resulted in differential expression of 856 and 372 genes, respectively. Interestingly, amongst the consistently downregulated genes, glycolytic process was the most strongly enriched GO term as the expression of all core enzymes of the glycolytic pathway was reduced, suggesting that Dhx15 regulates glycolytic function. A decrease in lactate production supported the observation that Dhx15 silencing functionally impaired glycolysis. Modified rates of glycolytic metabolism have been implicated in controlling the replication of several classes of viruses and strikingly, infection of Aag2 cells with CHIKV by itself also resulted in the decrease of several glycolysis genes. Our data suggests that Dhx15 regulates replication of CHIKV, and possibly other arboviruses, by controlling glycolysis in mosquito cells.

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Section: Bioinformatics Analysesmentioning

confidence: 99%

The DEAD-box RNA helicase Dhx15 controls glycolysis and arbovirus replication in Aedes aegypti mosquito cells

Miesen

Machado

et al. 2022

Preprint

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“…In the tiger mosquito Ae. albopictus , a competent vector of multiple arboviruses, only a few studies regarding ncRNAs have been published so far ( Gu et al, 2019 ; Azlan et al, 2021 ; Betting et al, 2021 ) and none presented significant data related to the impact of particular lncRNAs in physiological systems. Our aim was to provide the first proof-of-evidence regarding the role of specific lncRNAs in a vital biological process of the mosquito with potential utility for pest control.…”

Section: Discussionmentioning

confidence: 99%

A species-specific lncRNA modulates the reproductive ability of the asian tiger mosquito

Belavilas-Trovas

Gregoriou

Tastsoglou

et al. 2022

Front. Bioeng. Biotechnol.

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Long non-coding RNA (lncRNA) research has emerged as an independent scientific field in recent years. Despite their association with critical cellular and metabolic processes in plenty of organisms, lncRNAs are still a largely unexplored area in mosquito research. We propose that they could serve as exceptional tools for pest management due to unique features they possess. These include low inter-species sequence conservation and high tissue specificity. In the present study, we investigated the role of ovary-specific lncRNAs in the reproductive ability of the Asian tiger mosquito, Aedes albopictus. Through the analysis of transcriptomic data, we identified several lncRNAs that were differentially expressed upon blood feeding; we called these genes Norma (NOn-coding RNA in Mosquito ovAries). We observed that silencing some of these Normas resulted in significant impact on mosquito fecundity and fertility. We further focused on Norma3 whose silencing resulted in 43% oviposition reduction, in smaller ovaries and 53% hatching reduction of the laid eggs, compared to anti-GFP controls. Moreover, a significant downregulation of 2 mucins withing a neighboring (∼100 Kb) mucin cluster was observed in smaller anti-Norma3 ovaries, indicating a potential mechanism of in-cis regulation between Norma3 and the mucins. Our work constitutes the first experimental proof-of-evidence connecting lncRNAs with mosquito reproduction and opens a novel path for pest management.

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“…The majority of piRNAs in D. melanogaster are generated from TE-rich regions despite an overall low genomic TE content [14, 45, 46], whereas it is the opposite for Aedes mosquitoes [47]. Moreover, the mosquito piRNA pathway processes a broader repertoire of substrates including transcripts from protein-coding genes and satellite repeats as well as cytoplasmic viral RNA, and, thus, has important functions beyond transposon silencing [10, 35, 36, 38, 39, 48–50].…”

Section: Introductionmentioning

confidence: 99%

“…While hallmark features are conserved (Betting et al, 2021; Halbach et al, 2020; Joosten et al, 2019; Joosten et al, 2021a; Miesen et al, 2015), the piRNA pathway in Aedes mosquitoes differs significantly from D. melanogaster in terms of an expanded PIWI gene family and ubiquitously expressed piRNAs in somatic tissues (Akbari et al, 2013; Campbell et al, 2008; Ma et al, 2021; Marconcini et al, 2019; Miesen et al, 2016b). The majority of piRNAs in D. melanogaster are generated from TE-rich regions despite an overall low genomic TE content (Bergman et al, 2006; Brennecke et al ., 2007; Mérel et al, 2020), whereas it is the opposite for Aedes mosquitoes (Arensburger et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA cluster biogenesis in mosquitoes

Betting

Iterson

et al. 2022

Preprint

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The PIWI-interacting RNA (piRNA) pathway in culicine mosquitoes differs substantially from other model organisms in terms of an expanded PIWI gene family and ubiquitously expressed piRNAs in somatic tissues. Here, through comprehensive analyses of endogenous piRNAs in Aedes aegypti, we defined core piRNA clusters as small RNA source loci that showed ubiquitous expression in both somatic and germline tissues. These core piRNA clusters produced piRNAs from a single genomic strand and were enriched for non-retroviral endogenous viral elements (nrEVEs) in antisense orientation. Biogenesis of cluster-derived piRNAs depended on key factors, the mRNA exporter Nxf1, three Tudor proteins, Veneno, Tejas, and Yb, as well as the evolutionarily conserved cochaperone Shutdown. Combined transcriptional and chromatin state analyses showed that these core piRNA clusters do not have independent promoters, but instead depended on readthrough transcription from upstream genes for piRNA biogenesis. This biogenesis mechanism was evolutionarily conserved in other vector mosquito species, Aedes albopictus, Culex quinquefasciatus, and Anopheles gambiae. Interestingly, the upstream genes of many core piRNA clusters of the two Aedes mosquitoes were orthologous, but the downstream piRNA clusters differed both in size and sequence, especially evident by distinct nrEVE insertions from different virus families. We propose a model in which a conserved set of genes determine the loci for piRNA biogenesis, while the downstream piRNA clusters function as traps for nrEVEs, allowing adaptation to environmental challenges such as virus infection. Our systematic analyses of piRNA cluster expression and chromatin state lay a solid foundation for future studies of piRNA and genome evolution in these important vector species.

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A piRNA-lncRNA regulatory network initiates responder and trailer piRNA formation during mosquito embryonic development

Cited by 14 publications

References 67 publications

The DEAD-box RNA helicase Dhx15 controls glycolysis and arbovirus replication in Aedes aegypti mosquito cells

The DEAD-box RNA helicase Dhx15 controls glycolysis and arbovirus replication in Aedes aegypti mosquito cells

A species-specific lncRNA modulates the reproductive ability of the asian tiger mosquito

Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA cluster biogenesis in mosquitoes

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