Abstract Long noncoding RNAs (lncRNAs) play diverse roles in biological processes. Aedes aegypti ( Ae . aegypti ), a blood-sucking mosquito, is the principal vector responsible for replication and transmission of arboviruses including dengue, Zika, and Chikungunya virus. Systematic identification and developmental characterisation of Ae . aegypti lncRNAs are still limited. We performed genome-wide identification of lncRNAs, followed by developmental profiling of lncRNA in Ae . aegypti . We identified a total of 4,689 novel lncRNA transcripts, of which 2,064, 2,076, and 549 were intergenic, intronic, and antisense respectively. Ae . aegypti lncRNAs share many characteristics with other species including low expression, low GC content, short in length, and low conservation. Besides, the expression of Ae . aegypti lncRNAs tend to be correlated with neighbouring and antisense protein-coding genes. A subset of lncRNAs shows evidence of maternal inheritance; hence, suggesting potential role of lncRNAs in early-stage embryos. Additionally, lncRNAs show higher tendency to be expressed in developmental and temporal specific manner. The results from this study provide foundation for future investigation on the function of Ae . aegypti lncRNAs.
Dengue virus (DENV) is a single-stranded, positive-strand RNA virus that belongs to the family of Flaviviridae, and it is mainly transmitted by the mosquito Aedes aegypti (Ae. aegypti). Understanding the interaction of the virus with mosquito vector is vital for devising new strategies for preventing virus transmission. Although protein-coding genes have been the central focus, many reports indicated that long non-coding RNAs (lncRNAs) were also involved in virus-host interaction. Recently, the latest version of Ae. aegypti genome (AaegL5) was released, and the assembly was up to chromosome level. This prompted us to perform lncRNA identification and characterization using the latest genome release as reference. In this study, we investigated the transcriptome profiles of both protein-coding and lncRNA genes in Aedes aegypti cells upon DENV infection. By combining RNA-seq libraries generated in this study with publicly available datasets, we identified a total of 7,221 novel lncRNA transcripts, of which 3,052 and 3,620 were intronic and intergenic respectively, while 549 were antisense to the reference genes. A total of 2,435 differentially expressed transcripts, of which 956 of them were lncRNAs. Overall, the distribution of lncRNA expression and fold change upon virus infection were lower than that of protein-coding genes. We found that the expression of immune-related genes involved in IMD and MAPK signaling pathways were altered. In addition, the expression of major genes involved in RNA-interference (RNAi) pathway that confers antiviral resistance in mosquitoes were found to be unchanged upon DENV infection. Gene ontology analysis suggests that differentially expressed transcripts, either upregulated or downregulated, generally belong to the same functional categories or working in similar signaling pathways. Taken together, besides providing a new set of lncRNA repertoire, the outcomes of our study offer basic understanding of Ae. aegypti responses to DENV infection at gene level.
Abstract The Asian tiger mosquito, Aedes albopictus ( Ae. albopictus ), is an important vector that transmits arboviruses such as dengue (DENV), Zika (ZIKV) and Chikungunya virus (CHIKV). On the other hand, long noncoding RNAs (lncRNAs) are known to regulate various biological processes. Knowledge on Ae. albopictus lncRNAs and their functional role in virus-host interactions are still limited. Here, we identified and characterized the lncRNAs in the genome of an arbovirus vector, Ae. albopictus , and evaluated their potential involvement in DENV and ZIKV infection. We used 148 public datasets, and identified a total of 10, 867 novel lncRNA transcripts, of which 5,809, 4,139, and 919 were intergenic, intronic and antisense respectively. The Ae. albopictus lncRNAs shared many characteristics with other species such as short length, low GC content, and low sequence conservation. RNA-sequencing of Ae. albopictus cells infected with DENV and ZIKV showed that the expression of lncRNAs was altered upon virus infection. Target prediction analysis revealed that Ae. albopictus lncRNAs may regulate the expression of genes involved in immunity and other metabolic and cellular processes. To verify the role of lncRNAs in virus infection, we generated mutation in lncRNA loci using CRISPR-Cas9, and discovered that two lncRNA loci mutations, namely XLOC_029733 (novel lncRNA transcript id: lncRNA_27639.2) and LOC115270134 (known lncRNA transcript id: XR_003899061.1) resulted in enhancement of DENV and ZIKV replication. The results presented here provide an important foundation for future studies of lncRNAs and their relationship with virus infection in Ae. albopictus . Author summary Ae. albopictus is an important vector of arboviruses such as dengue and Zika. Studies on virus-host interaction at gene expression and molecular level are crucial especially in devising methods to inhibit virus replication in Aedes mosquito. Previous reports showed that, besides protein-coding genes, noncoding RNAs such as lncRNAs are also involved in virus-host interaction. In this study, we report a comprehensive catalog of novel lncRNA transcripts in the genome of Ae. albopictus . We also show that the expression of lncRNAs was altered upon infection with dengue and Zika. Additionally, depletion of certain lncRNAs resulted in increased replication of dengue and Zika; hence, suggesting potential association of lncRNAs in virus infection. Results of this study provide a new avenue to the investigation of mosquito-virus interactions that may potentially pave way to the development of novel methods in vector control.
Long noncoding RNAs (lncRNAs) play diverse roles in biological process including developmental regulation and host-pathogen interactions. Aedes aegypti (Ae. aegypti), a blood-sucking mosquito, is the principal vector responsible for replication and transmission of arboviruses including dengue, zika, and chikungunya virus. Systematic identification and developmental characterisation of Ae. aegypti lncRNAs are still limited. We performed genome-wide identification of lncRNAs followed by developmental profiling of lncRNA expression in Ae. aegypti. We identified a total of 4,689 novel lncRNA transcripts, of which 2,064, 2,076, and 549 were intergenic, intronic, and antisense respectively. Ae. aegypti lncRNAs shared many of the characteristics with other species including low expression, low GC content, short in length, low conservation, and their expression tended to be correlated with neighbouring and antisense protein-coding genes. Subsets of lncRNAs showed evidence that they were maternally inherited, suggesting potential roles in early-stage embryos. Additionally, lncRNAs showed higher tendency to be expressed in developmental and temporal specific manner. Upon infection of Ae. aegypti cells with dengue virus serotype 1, we identified 2,335 differentially expressed transcripts, 957 of which were lncRNA transcripts. The systematic annotation, developmental profiling, and transcriptional response upon virus infection provide foundation for future investigation on the function of Ae. aegypti lncRNAs.
The Asian tiger mosquito, Aedes albopictus ( Ae . albopictus ), is an important vector that transmits arboviruses such as dengue (DENV), Zika (ZIKV) and Chikungunya virus (CHIKV). Long noncoding RNAs (lncRNAs) are known to regulate various biological processes. Knowledge on Ae . albopictus lncRNAs and their functional role in virus-host interactions are still limited. Here, we identified and characterized the lncRNAs in the genome of an arbovirus vector, Ae . albopictus , and evaluated their potential involvement in DENV and ZIKV infection. We used 148 public datasets, and identified a total of 10, 867 novel lncRNA transcripts, of which 5,809, 4,139, and 919 were intergenic, intronic and antisense respectively. The Ae . albopictus lncRNAs shared many characteristics with other species such as short length, low GC content, and low sequence conservation. RNA-sequencing of Ae . albopictus cells infected with DENV and ZIKV showed that the expression of lncRNAs was altered upon virus infection. Target prediction analysis revealed that Ae . albopictus lncRNAs may regulate the expression of genes involved in immunity and other metabolic and cellular processes. To verify the role of lncRNAs in virus infection, we generated mutations in lncRNA loci using CRISPR-Cas9, and discovered that two lncRNA loci mutations, namely XLOC_029733 (novel lncRNA transcript id: lncRNA_27639.2) and LOC115270134 (known lncRNA transcript id: XR_003899061.1) resulted in enhancement of DENV and ZIKV replication. The results presented here provide an important foundation for future studies of lncRNAs and their relationship with virus infection in Ae . albopictus .
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