bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/448852

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

Azlan, A.·Yunus, M. A.·Azzam, G.
View original source ↗Export metadata ↓

Abstract

Aedes albopictus (Ae. albopictus) is an important vector of arboviruses such as Dengue virus (DENV), Chikungunya virus (CHIKV), and Zika virus (ZIKV). Long noncoding RNA (lncRNAs) have been identified in other vectors including Aedes aegypti and Anopheles mosquitoes, few of which have been implicated in immunity and viral replication. To identify lncRNAs with potential biological functions in Ae. albopictus, we performed RNA-seq on Ae. albopictus cells infected with DENV and ZIKV, and analyzed them together with public datasets. We identified a total of 23,899 transcripts, 16,089 were intergenic while 3,126 and 4,183 of them were antisense and intronic to annotated genes respectively. Ae. albopictus lncRNAs shared many of the characteristics with their invertebrate and vertebrate counterparts, such as low expression, low GC content, short in length, and low conservation even among closely related species. Compared to protein-coding genes, lncRNAs exhibited higher tendency to be expressed in a stage-specific manner. Besides, expression of lncRNAs and nearest protein-coding genes tended to be correlated, especially for the gene pairs within 1kb from each other. We also discovered that Ae. albopictus lncRNAs have the potential to act as precursors for miRNA and piRNAs, both of which have been implicated in antiviral defense in Aedes mosquito. Upon flavivirus infection, lncRNAs were observed to be differentially expressed, which possibly indicates the involvement of lncRNAs in the host-antiviral defense. Our study provides the first systematic identification of lncRNAs in Ae. albopictus, hence, offering a foundation for future studies of lncRNA functions.

Explore related subjects

geneticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Azlan, A., Yunus, M. A., Azzam, G.. 2018-10-22. Identification and characterization of Aedes albopictus long noncoding RNAs provides insights into their roles in development and flavivirus infection. https://doi.org/10.1101/448852

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Host control and regulation of human anellovirus persistence

Anelloviruses are the most abundant and diverse eukaryotic viruses known to infect humans and can persist throughout our lifetimes. Despite their ubiquity, the host factors governing their physiologic distribution and abundance remain poorly understood. Here, we construct a viral pangenome of 2,023 strains to quantify anellovirus DNA in >1.1 million participants spanning three genetic biobanks. Genome-wide association studies identify 121 loci linked to viral persistence, predominantly via immune regulation by NF-kB signaling. Further, we associate variable anellovirus detection with conditions characterized by immune dysfunction, including lymphoid malignancies. By screening 3.2 petabases of human single-cell sequencing data, we identify myeloid progenitors in the bone marrow as a prominent site of anellovirus transcription in vivo. Finally, Perturb-seq of anellovirus proteins reveals that anellovirus ORF2, particularly from Alphatorquevirus, attenuates TNF-a-induced NF-kB signaling, connecting host genetic variation, cellular context, and viral immunomodulation to characterize the persistence of the eukaryotic human virome's most abundant component.

genetics↗
bioRxiv2026

SARDINE unlocks EWAS summary statistics for large-scale epigenetic biomarker analysis

Epigenetic clocks are increasingly used to study biological aging, yet their interpretation and utility remain uncertain. Meanwhile, the growing wealth of epigenome-wide association study (EWAS) summary statistics remains largely untapped for evaluating these biomarkers. Here, we introduce SARDINE, a statistical framework that estimates epigenetic clock-phenotype associations using EWAS summary statistics, clock weights, and reference methylation covariance, without individual-level data. SARDINE accurately reproduced individual-level association estimates across 38 epigenetic biomarkers and four phenotypes in 15,677 individuals. Applying SARDINE to diverse EWAS datasets revealed substantial heterogeneity in biomarker associations with aging, diseases, and lifestyle factors. By transforming CpG-level EWAS results into interpretable biomarker-level associations, SARDINE unlocks a largely underutilized data resource and establishes a scalable paradigm for systematic biomarker evaluation and discovery in aging research.

genetics↗
bioRxiv2026

Deep transcriptomic analysis of molecular mediators of complex traits in heterogeneous stock (HS) rats

Rats are a powerful model organism for genome-wide association studies (GWAS) of physiological and behavioral traits. Heterogeneous Stock (HS) rats, which were created by intercrossing 8 inbred rat strains, are heavily used for this purpose because of their genetic diversity and accumulated recombinations due to over 100 generations of outbreeding, which improves mapping precision. However, functional genomics resources for post-GWAS interpretation of genomic findings have been limited. We processed 3,160 RNA-seq samples, 1,932 of which were previously unpublished, from 13 tissues as part of RatGTEx. We used Pantry to quantify six modalities of transcriptome regulation (expression, isoform ratio, intron excision ratio, alternative transcription start site (TSS), alternative poly(A), and RNA stability) in each sample, which allowed us to identify 144,876 independent quantitative trait loci (QTL) for 22,599 genes. We performed a transcriptome-wide association study (TWAS) with 19,796 unique genes across tissues and transcriptional modalities and 308 traits collected from 14 studies using FUSION, which identified 7,473 significant gene-trait associations. This work presents a significant expansion of the RatGTEx resource in terms of samples, modes of transcriptome regulation, and genetic analyses. Our findings provide molecular evidence for the involvement of specific genes in mediating GWAS signals through a range of transcriptome regulatory mechanisms. These gene-to-phenotype relationships can be easily applied to genetic analyses in humans and other species. Further experiments can use this evidence to confirm these molecular mediators and target them for the treatment of behavioral and physiological traits and disorders. To facilitate use of these results, we have updated results on RatGTEx.org and provided a new interactive TWAS web portal (twas.ratgtex.org).

genetics↗