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.
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.
26The Asian tiger mosquito, Aedes albopictus (Ae. albopictus), is an important vector that transmits 27 arboviruses such as dengue (DENV), Zika (ZIKV) and Chikungunya virus (CHIKV). On the other hand, 28 long noncoding RNAs (lncRNAs) are known to regulate various biological processes. Knowledge on Ae.29 albopictus lncRNAs and their functional role in virus-host interactions are still limited. Here, we 30 identified and characterized the lncRNAs in the genome of an arbovirus vector, Ae. albopictus, and 31 evaluated their potential involvement in DENV and ZIKV infection. We used 148 public datasets, and 32 identified a total of 10, 867 novel lncRNA transcripts, of which 5,809, 4,139, and 919 were intergenic, 33 intronic and antisense respectively. The Ae. albopictus lncRNAs shared many characteristics with other 34 species such as short length, low GC content, and low sequence conservation. RNA-sequencing of Ae.35 albopictus cells infected with DENV and ZIKV showed that the expression of lncRNAs was altered upon 36 virus infection. Target prediction analysis revealed that Ae. albopictus lncRNAs may regulate the 37 expression of genes involved in immunity and other metabolic and cellular processes. To verify the role 38 of lncRNAs in virus infection, we generated mutation in lncRNA loci using CRISPR-Cas9, and 39 discovered that two lncRNA loci mutations, namely XLOC_029733 (novel lncRNA transcript id: 40 lncRNA_27639.2) and LOC115270134 (known lncRNA transcript id: XR_003899061.1) resulted in 41 enhancement of DENV and ZIKV replication. The results presented here provide an important 42 foundation for future studies of lncRNAs and their relationship with virus infection in Ae. albopictus. 43 44 45 46 47 Author summary 48 49 Ae. albopictus is an important vector of arboviruses such as dengue and Zika. Studies on virus-50 host interaction at gene expression and molecular level are crucial especially in devising methods to 51 inhibit virus replication in Aedes mosquito. Previous reports showed that, besides protein-coding genes, 52 noncoding RNAs such as lncRNAs are also involved in virus-host interaction. In this study, we report a 53 comprehensive catalog of novel lncRNA transcripts in the genome of Ae. albopictus. We also show that 54 the expression of lncRNAs was altered upon infection with dengue and Zika. Additionally, depletion of 55 certain lncRNAs resulted in increased replication of dengue and Zika; hence, suggesting potential 56 association of lncRNAs in virus infection. Results of this study provide a new avenue to the investigation 57 of mosquito-virus interactions that may potentially pave way to the development of novel methods in 58 vector control. 59 60 Introduction 61 The Asian tiger mosquito, Aedes albopictus (Ae. albopictus) is an important vector of arboviruses 62 such as dengue virus (DENV), Chikungunya virus (CHIKV), and Zika virus (ZIKV). Due to its 63 invasiveness and aggressive spread, Ae. albopictus has widespread geographic distribution; hence, poses 64 serious health threat globally. Althou...
24Long noncoding RNAs (lncRNAs) play diverse roles in biological process including 25 developmental regulation and host-pathogen interactions. Aedes aegypti (Ae. aegypti), a blood-sucking 26 mosquito, is the principal vector responsible for replication and transmission of arboviruses including 27 dengue, zika, and chikungunya virus. Systematic identification and developmental characterisation of 28Ae. aegypti lncRNAs are still limited. We performed genome-wide identification of lncRNAs followed 29 by developmental profiling of lncRNA expression in Ae. aegypti. We identified a total of 4,689 novel 30 lncRNA transcripts, of which 2,064, 2,076, and 549 were intergenic, intronic, and antisense 31 respectively. Ae. aegypti lncRNAs shared many of the characteristics with other species including low 32 expression, low GC content, short in length, low conservation, and their expression tended to be 33 correlated with neighbouring and antisense protein-coding genes. Subsets of lncRNAs showed 34 evidence that they were maternally inherited, suggesting potential roles in early-stage embryos. 35Additionally, lncRNAs showed higher tendency to be expressed in developmental and temporal 36 specific manner. Upon infection of Ae. aegypti cells with dengue virus serotype 1, we identified 2,335 37 differentially expressed transcripts, 957 of which were lncRNA transcripts. The systematic annotation, 38 developmental profiling, and transcriptional response upon virus infection provide foundation for 39 future investigation on the function of Ae. aegypti lncRNAs. 40 41 42 43 44 45 46 47 regulate the activity of chromatin modifying proteins; hence, modulating gene expression. In Ae. 65 aegypti, it had been reported that lncRNA was involved in virus-host interaction. Knockdown of 66 lincRNA_1317 in Ae. aegypti cells caused higher replication of DENV 1 . Although lncRNAs have been 67 systematically identified in many organisms, most lncRNAs have not been functionally characterised. 68Recently, the latest version of Ae. aegypti genome (AaegL5) was released, and the assembly 69 was up to chromosome-length scaffolds, which is more contiguous than the previous AaegL3 and 70 AaegL4 assemblies 5 . This prompted us to perform novel lncRNA identification and characterisation 71
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