Yip, C.-W. | bioRxiv Science

bioRxiv2021

Down-regulation of A Human Herpesvirus 1 (HHV-1) MicroRNA in Infected Cells by Goniothalamin Treatment

Goniothalamin (GTN) has been proven to cause cell cycle arrest and apoptosis in human herpesvirus 1 (HHV-1) infected cells, but interestingly our preliminary transcriptomic analysis revealed other possible modes of action. The data showed that GTN treatment of HHV-1 clinical strain infected cells induced expression of the KLHL24 gene that encodes the Kelch-like 24 protein (KLHL24), a transcriptional inhibitor of HHV-1 immediate-early and early genes. An miRNA, hsv1-miR-H27, produced by HHV-1 has also been discovered to control the expression of KLHL24. In order to understand the cause of KLHL24 up-regulation, a time point study was conducted to investigate the effect of GTN on KLHL24 and hsv1-miR-H27 expression. Through RT-qPCR analysis, we found that HHV-1 down-regulated KLHL24 significantly (p < 0.05) starting from 12 hpi, while a significant up-regulation (p < 0.05) was observed upon GTN treatment of the infected cells at 4 and 8 hpi. For protein level analysis, significant down-regulation of KLHL24 (p < 0.05) was observed at all time points in HHV-1 infected cells. Intriguingly, treatment with GTN on HHV-1 infected cells showed no significant changes in protein expression compared to cells without any treatment. In addition, the miRNA hsv1-miR-H27 was detected from 16 hpi and treatment with GTN on infected cells showed down-regulation of the miRNA. This was in congruity with the recovery of KLHL24 down-regulation in GTN treated HHV-1 infected cells, confirming that GTN caused down-regulation of hsv1-miR-H27 that governs the expression of KLHL24. This study provides insights that GTN could be a potential multifaceted antiviral. ImportanceThis study provides evidence that GTN possesses a distinct mode of antivirus against HHV-1 compared to currently available antivirals. Our findings showed that GTN caused the down-regulation of a viral miRNA, which inhibits the expression of a cellular protein known as KLHL24. This protein serves as a transcriptional inhibitor of HHV-1 immediate-early and early genes. The down-regulation of this miRNA lead to the up-regulation of KLHL24 and eventually halted HHV-1 replication. With the previously reported antiviral mechanism and the outcome of this study, GTN is a potential multifaceted anti-HHV-1 agent.

microbiology↗

bioRxiv2019

Recounting the FANTOM Cage Associated Transcriptome

Long non-coding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes including human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly-defined human transcriptome, inclusive of over 109,000 coding and non-coding genes, as described in the FANTOM CAGE-Associated Transcriptome (FANTOM-CAT) study. This atlas greatly extends the gene annotation used in the original recount2 resource. We demonstrate the utility of the FC-R2 atlas by reproducing key findings from published large studies and by generating new results across normal and diseased human samples. In particular, we (a) identify tissue specific transcription profiles for distinct classes of coding and non-coding genes, (b) perform differential expression analyses across thirteen cancer types, providing new insights linking promoter and enhancer lncRNAs expression to tumor pathogenesis, and (c) confirm the prognostic value of several enhancers in cancer. Comprised of over 70,000 samples, the FC-R2 atlas will empower other researchers to investigate functions and biological roles of both known coding genes and novel lncRNAs. Most importantly, access to the FC-R2 atlas is available from https://jhubiostatistics.shinyapps.io/recount/, the recount Bioconductor package, and http://marchionnilab.org/fcr2.html.

genomics↗