Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

Farley, Elise J; Eggleston, Heather; Riehle, Michelle M.

doi:10.3390/insects12020186

Cited by 8 publications

(9 citation statements)

References 149 publications

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“…The term non-coding RNA encompasses multiple species of RNA. The four ncRNAs we detected are all longer than 200 bp, consistent with what would be considered long noncoding (lncRNAs) (reviewed in [ 106 ]). Studies in vertebrates and invertebrates have demonstrated that lncRNAs have regulatory roles in gene expression in a variety of cellular and biological processes (reviewed in [ 106 , 107 ]).…”

Section: Resultssupporting

confidence: 69%

“…The four ncRNAs we detected are all longer than 200 bp, consistent with what would be considered long noncoding (lncRNAs) (reviewed in [ 106 ]). Studies in vertebrates and invertebrates have demonstrated that lncRNAs have regulatory roles in gene expression in a variety of cellular and biological processes (reviewed in [ 106 , 107 ]). Thus, the putative lncRNAs we identified could be interesting targets to explore for potential roles in modulating post-mating responses.…”

Section: Resultssupporting

confidence: 69%

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Seminal fluid proteins induce transcriptome changes in the Aedes aegypti female lower reproductive tract

et al. 2021

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Background Mating induces behavioral and physiological changes in the arbovirus vector Aedes aegypti, including stimulation of egg development and oviposition, increased survival, and reluctance to re-mate with subsequent males. Transferred seminal fluid proteins and peptides derived from the male accessory glands induce these changes, though the mechanism by which they do this is not known. Results To determine transcriptome changes induced by seminal proteins, we injected extract from male accessory glands and seminal vesicles (MAG extract) into females and examined female lower reproductive tract (LRT) transcriptomes 24 h later, relative to non-injected controls. MAG extract induced 87 transcript-level changes, 31 of which were also seen in a previous study of the LRT 24 h after a natural mating, including 15 genes with transcript-level changes similarly observed in the spermathecae of mated females. The differentially-regulated genes are involved in diverse molecular processes, including immunity, proteolysis, neuronal function, transcription control, or contain predicted small-molecule binding and transport domains. Conclusions Our results reveal that seminal fluid proteins, specifically, can induce gene expression responses after mating and identify gene targets to further investigate for roles in post-mating responses and potential use in vector control.

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Section: Resultssupporting

confidence: 69%

Section: Resultssupporting

confidence: 69%

Seminal fluid proteins induce transcriptome changes in the Aedes aegypti female lower reproductive tract

et al. 2021

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“…To test this hypothesis, genome-wide lncRNA screening was conducted to compare A. aegypti Aag2 cells (W-cells) and W-Aag2 cells (W + cells) carrying Wolbachia wAlbB. Because A. aegypti lncRNAs display a highly temporal expression pattern (Azlan et al, 2019;Farley et al, 2021), the total RNA collected from day 1 to day 5 post passage was pooled as three biological replicates per cell line. This ensured the richness of generated lncRNA libraries.…”

Section: Wolbachia Walbb Induces Differential Expression Of Lncrna In Aedes Aegyptimentioning

confidence: 99%

Wolbachia Utilizes lncRNAs to Activate the Anti-Dengue Toll Pathway and Balance Reactive Oxygen Species Stress in Aedes aegypti Through a Competitive Endogenous RNA Network

Mao

Zeng

She

et al. 2022

Front. Cell. Infect. Microbiol.

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Long non-coding RNAs (lncRNA), a class of RNA molecules without protein coding potential, are more than 200 nucleotides in length and widely present in a variety of species. Although increasing progress in regard to the determination of lncRNA function has been made in vertebrates, Aedes aegypti lncRNAs were only identified recently and the functions of few lncRNAs have been annotated so far. Herein, the genome-wide alteration of the lncRNA expression profile trigged by Wolbachia wAlbB infection was investigated by comparing A. aegypti Aag2 cells and W-Aag2 cells infected with Wolbachia wAlbB. Based on lncRNA sequencing, 3035 differentially expressed lncRNAs (DE lncRNAs) in total were identified upon Wolbachia infection, which were further validated by quantitative PCR. The constructed co-expression network of DE lncRNAs and mRNAs revealed that Wolbachia-induced DE lncRNAs were highly enriched in the oxidative phosphorylation pathway via trans-activity, according to the KEGG pathway enrichment analyses. In addition, the established competitive endogenous RNA (ceRNA) network identifies the DE lncRNAs enriched in cellular oxidant detoxification based on GO enrichment analysis. Furthermore, silencing of aae-lnc-7598, the significantly up-regulated lncRNA with the highest fold change induced by Wolbachia, caused a significant reduction of antioxidant catalase 1B (CAT1B) gene expression as well as the enhancement of mitochondrial reactive oxygen species (ROS) production in living cells. These findings indicate that Wolbachia manipulates lncRNA to balance intracellular ROS stress and ensure its endosymbiosis in host A. aegypti. Notably, the function assay demonstrated that aae-lnc-0165 suppressed by Wolbachia could induce expression of the REL1 gene, the key regulator of downstream Toll pathway, through the sequence-specific binding of aae-miR-980-5p, which contributes to the activation of Toll pathway. Moreover, the depletion of aae-lnc-0165 caused the suppression of mitochondrial ROS levels in living cells. Our data reveal that Wolbachia activates the anti-dengue Toll pathway through a lncRNA-ceRNA pattern. Taken together, our finding suggested that Wolbachia utilizes lncRNAs to activate host anti-dengue Toll pathway via a ceRNA network. Moreover, Wolbachia employs lncRNAs to ensure ROS homeostasis for ROS-based anti-dengue defense through either trans-regulation or the ceRNA network. This study identifies novel potential molecular biomarkers for prevention and control of epidemic dengue.

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“…Transcriptional enhancers can be identified by either direct or indirect experimental approaches ( Farley et al, 2021 ). Direct approaches measure enhancer activity of nucleotide sequence through assays such as manual luciferase reporter assays.…”

Section: Introductionmentioning

confidence: 99%

“…In contrast, indirect approaches identify enhancers as correlates of genomic regions differing in their chromatin accessibility or histone modification markers. The indirect strategies such as ChIP-seq and ATAC-seq ( Gomez-Diaz et al, 2017 ; Ruiz et al, 2019 ; Farley et al, 2021 ; Ruiz et al, 2021 ) infer enhancer presence based on chromatin properties such as chromatin accessibility and histone modifications, but do not directly or functionally test or confirm enhancer activity. Methods used to survey histone signatures and chromatin accessibility may also detect transcriptional silencers, insulators and other features in addition to enhancers, and the functional category of detected elements is not necessarily distinguishable without additional work, for example direct functional assays.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii

et al. 2022

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Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters. Enhancer locations cannot be accurately predicted bioinformatically because of the absence of a defined sequence code, and thus functional assays are required for their direct detection. Here we used a massively parallel reporter assay, Self-Transcribing Active Regulatory Region sequencing (STARR-seq), to generate the first comprehensive genome-wide map of enhancers in Anopheles coluzzii, a major African malaria vector in the Gambiae species complex. The screen was carried out by transfecting reporter libraries created from the genomic DNA of 60 wild A. coluzzii from Burkina Faso into A. coluzzii 4a3A cells, in order to functionally query enhancer activity of the natural population within the homologous cellular context. We report a catalog of 3,288 active genomic enhancers that were significant across three biological replicates, 74% of them located in intergenic and intronic regions. The STARR-seq enhancer screen is chromatin-free and thus detects inherent activity of a comprehensive catalog of enhancers that may be restricted in vivo to specific cell types or developmental stages. Testing of a validation panel of enhancer candidates using manual luciferase assays confirmed enhancer function in 26 of 28 (93%) of the candidates over a wide dynamic range of activity from two to at least 16-fold activity above baseline. The enhancers occupy only 0.7% of the genome, and display distinct composition features. The enhancer compartment is significantly enriched for 15 transcription factor binding site signatures, and displays divergence for specific dinucleotide repeats, as compared to matched non-enhancer genomic controls. The genome-wide catalog of A. coluzzii enhancers is publicly available in a simple searchable graphic format. This enhancer catalogue will be valuable in linking genetic and phenotypic variation, in identifying regulatory elements that could be employed in vector manipulation, and in better targeting of chromosome editing to minimize extraneous regulation influences on the introduced sequences.Importance: Understanding the role of the non-coding regulatory genome in complex disease phenotypes is essential, but even in well-characterized model organisms, identification of regulatory regions within the vast non-coding genome remains a challenge. We used a large-scale assay to generate a genome wide map of transcriptional enhancers. Such a catalogue for the important malaria vector, Anopheles coluzzii, will be an important research tool as the role of non-coding regulatory variation in differential susceptibility to malaria infection is explored and as a public resource for research on this important insect vector of disease.

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Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

Cited by 8 publications

References 149 publications

Seminal fluid proteins induce transcriptome changes in the Aedes aegypti female lower reproductive tract

Seminal fluid proteins induce transcriptome changes in the Aedes aegypti female lower reproductive tract

Wolbachia Utilizes lncRNAs to Activate the Anti-Dengue Toll Pathway and Balance Reactive Oxygen Species Stress in Aedes aegypti Through a Competitive Endogenous RNA Network

Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii

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