Systematic identification and characterization of Aedes aegypti long noncoding RNAs

Abstract

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

Tetraspanins as Potential Therapeutic Candidates for Targeting Flaviviruses

“…Genome wide profiling of lncRNA expression identified MAGED1, STAT1, and IL12A genes that might play a key role as biomarkers for designing new strategies to prevent DHF (91). Transcriptomic analysis of lncRNAs profile of A. aegypti cells identified a set of differentially expressed immunerelated genes implicated in IMD and MAPK signaling pathway responsive to DENV infection (98). Collectively, these observations highlight the significance of ncRNA in viral replication, transmission, and immunity, but further research enhancement on this topic is needed to fully reveal the mechanism(s).…”

Identification and characterization of Aedes albopictus long noncoding RNAs provides insights into their roles in development and flavivirus infection

“…albopictus. To get high confident lncRNA transcripts, we applied a stringent identification pipeline that was adapted with slight alterations from lncRNA identification studies in other species (Azlan et al, 2018;Chen et al, 2016;Etebari et al, 2016;Hezroni et al, 2015;Wu et al, 2016;Young et al, 2012). An overview of lncRNA identification pipeline can be found in Figure 1.…”