Biology subjects

Azzam, G.

Publications and source records attributed to Azzam, G..

4 recordsLinked to original sources

bioRxiv2018

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

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.

genetics↗

bioRxiv2018

Transcriptome profiles and novel lncRNA identification of Aedes aegypti cells in response to dengue virus serotype 1

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 better understanding of Ae. aegypti responses to DENV infection at gene level.\n\nAuthor SummaryDengue virus (DENV), a single-stranded and positive-strand RNA virus of the family Flaviviridae, is primarily transmitted by Aedes aegypti (Ae. aegypti) mosquitoes. There are four closely related but antigenically different serotypes of dengue virus namely DENV1-4. Our understanding on the interaction of each serotype of DENV with its mosquito vector is still very limited. Since vector-borne viruses pose significant burden to public health, knowledge on the virus-host interaction at the molecular level is essential, especially in developing effective strategies to control virus transmission. In this study, we embarked on investigating the transcriptional response of long non-coding RNAs (lncRNAs) and protein-coding genes upon dengue virus serotype 1 (DENV1) infection. Besides, we also generate a comprehensive list of novel lncRNAs identified from the latest and improved genome version of Ae. aegypti. Similar to protein-coding genes, we discovered that the overall expression of lncRNA was significantly altered, suggesting that lncRNAs were involved in virus-host interaction. The results of this study provide basic understanding on the interaction between DENV1 and Ae. aegypti vector at the transcriptional level.

genetics↗

bioRxiv2018

CTP synthase regulation by miR-975 controls cell proliferation and differentiation in Drosophila melanogaster

CTP synthase (CTPsyn) is an essential metabolic enzyme. As a key regulator of the nucleotide pool, the protein has been found to be elevated in cancer models. In many organisms, CTPsyn compartmentalizes into filaments termed cytoophidia. For D. melanogaster, it is only its Isoform C i.e. CTPsynIsoC which forms the structure. The fruit flys testis is home to somatic and germline stem cells. Both micro and macro-cytoophidia are normally seen in the transit amplification regions close to its apical tip, where the stem-cell niche is located and development is at its most rapid. Here, we report that CTPsynIsoC overexpression causes the lengthening of cytoophidia throughout the entirety of the testicular body. A bulging apical tip is found in approximately one-third of like-genotyped males. Immunostaining shows that the cause of this tumour-like phenotype is most likely due to increased numbers of both germline cells and spermatocytes. We also report that under conditions whereby miR-975 is overexpressed, greater incidences of the same bulged-phenotype coincides with induced upregulation of CTPsynIsoC. However, RT-qPCR assays reveal that either overexpression genotype provokes a differential response in expression of a number of genes concurrently associated with CTPsyn and cancer, showing that the pathways CTPsynIsoC affect and miR-975 regulate may be completely independent of each other. This study presents the first instance of consequences of miRNA-asserted regulation upon CTPsyn in D. melanogaster, and further reaffirms the enzymes close ties to cancer and carcinogenesis.

cell biology↗

bioRxiv2018

MicroRNA regulation of CTP synthase and cytoophidium in Drosophila melanogaster

CTPsyn is a crucial metabolic enzyme which synthesizes CTP molecules through the de novo or salvage pathway. It has the extraordinary ability to compartmentalize into filaments termed cytoophidia. Although this property is retained amongst orthologues, and cytoophidia are therefore found across kingdoms, the mechanisms behind their formation remain unknown. Micro-RNAs (miRNAs) are single-stranded RNA with length of 20 - 22 nucleotides, capable of exerting mRNA silencing and degradation as a form of regulation. D. melanogaster itself has a high total gene count to miRNA gene number ratio, alluding to the possibility that CTPsyn may too come under the regulatory effects of these small RNAs. A thorough miRNA overexpression involving 123 UAS-miRNA lines, followed by staining of ovarian cytoophidia dme-egg chambers, revealed a small group of candidates which confer either a lengthening or truncating effect on the structure. Prime candidates are identified on the basis of consistency. MiR-975 and miR-1014 are both cytoophidia-elongating, whereas miR-190 and miR-932 are cytoophidia-shortening. Though target prediction shows that miR-975 and miR-932 do indeed have binding sites on CTPsyn mRNA, in vitro assays instead revealed that none of the four candidates may actually do so. This suggests that the effects asserted by overexpressed miRNAs indirectly reach CTPsyn and its cytoophidia through the actions of middling elements. In silico target prediction and qPCR quantification indicated that, at least for miR-932 and miR-1014, these undetermined elements may be players in fat metabolism. This is the first study to thoroughly investigate miRNAs in connection to CTPsyn expression and activity in any species. The findings presented could serve as a basis for further queries into not only the fundamental aspects of the enzymes regulation, but may uncover new facets of closely related pathways as well.

cell biology↗