ArticleBMC genomics2017
Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 63 citations in OpenAlex.
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- A novel transposable element-based authentication protocol for Drosophila cell lines.G3 (Bethesda, Md.) · 2022Article
- A review of strategies used to identify transposition events in plant genomes.Frontiers in plant science · 2022Review
- Genetic stability of Aedes aegypti populations following invasion by wMel Wolbachia.BMC genomics · 2021Article
- Uncovering the Worldwide Diversity and Evolution of the Virome of the MosquitoesMicroorganisms · 2021Article
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- AnViruses · 2021Article
- Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses.Cell host & microbe · 2021Article
- A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons.Genome research · 2021Article
- Imd pathway-specific immune assays reveal NF-κB stimulation by viral RNA PAMPs in Aedes aegypti Aag2 cells.PLoS neglected tropical diseases · 2021Article
- Measuring and interpreting transposable element expression.Nature reviews. Genetics · 2020Review
- Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein.Genome medicine · 2020Article
- Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.GigaScience · 2020Article
- Novel genome sequences of cell-fusing agent virus allow comparison of virus phylogeny with the genetic structure ofVirus evolution · 2020Article
- Aedes aegypti (Aag2)-derived clonal mosquito cell lines reveal the effects of pre-existing persistent infection with the insect-specific bunyavirus Phasi Charoen-like virus on arbovirus replication.PLoS neglected tropical diseases · 2019Article
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9 authors at 3 institutions in 3 countries.
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Abstract
backgroundAedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs. Furthermore, as for many non-model organisms, incomplete genome annotation has hampered proteomic studies on Ae. aegypti.
resultsWe analysed the Ae. aegypti proteome using our new proteomics informed by transcriptomics (PIT) technique, which bypasses the need for genome annotation by identifying proteins through matched transcriptomic (rather than genomic) data. Our data vastly increase the number of experimentally confirmed Ae. aegypti proteins. The PIT analysis also identified hotspots of incomplete genome annotation, and showed that poor sequence and assembly quality do not explain all annotation gaps. Finally, in a proof-of-principle study, we developed criteria for the characterisation of proteomically active TEs. Protein expression did not correlate with a TE's genomic abundance at different levels of classification. Most notably, long terminal repeat (LTR) retrotransposons were markedly enriched compared to other elements. PIT was superior to 'conventional' proteomic approaches in both our transposon and genome annotation analyses.
conclusionsWe present the first proteomic characterisation of an organism's repertoire of mobile genetic elements, which will open new avenues of research into the function of transposon proteins in health and disease. Furthermore, our study provides a proof-of-concept that PIT can be used to evaluate a genome's annotation to guide annotation efforts which has the potential to improve the efficiency of annotation projects in non-model organisms. PIT therefore represents a valuable new tool to study the biology of the important vector species Ae. aegypti, including its role in transmitting emerging viruses of global public health concern.
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