The majority of the human genome is actively transcribed into RNAs with no obvious coding capacity, termed non-coding RNAs (ncRNAs). ncRNAs have been categorised into a number of species with varying features and functions, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs). We have investigated the roles of two types of ncRNAs, circRNAs and lncRNAs, during KSHV infection.
circRNAs are formed through a unique backsplice mechanism. Their best described function is their ability to sponge miRNAs, forming regulatory networks which allow them to regulate gene expression. This miRNA sponging function is known to be important during KSHV infection. We therefore aimed to gain an overview of the role of circRNA regulatory networks during KSHV infection. Transcriptomic data was used to identify circRNAs, miRNAs and mRNAs that are differentially expressed during KSHV lytic replication. Potential circRNA regulatory networks were identified by cross-referencing these lists of RNAs with a database of experimentally supported RNA:RNA interactions. Further analysis showed a high level of redundancy in these circRNA regulatory networks, and suggested they played a role in angiogenesis and cell proliferation. Two candidates for experimental validation, circISOC1 and circPRKAR1B, were identified.
Although research into ncRNA has focused on their non-coding roles, recent advances have shown that lncRNAs can be associated with ribosomes and contain small Open Reading Frames (smORFs) encoding functional micropeptides. As KSHV is known to dysregulate translation by inducing the production of specialised ribosomes, we asked if smORF translation is dysregulated during KSHV infection and if specialised ribosomes have a role. Analysis of a Ribo-Seq dataset from cells lytically infected with KSHV showed that lncRNA smORFs can be translated during KSHV lytic replication, and that KSHV-induced specialised ribosomes may promote their translation. Preliminary experimental evidence then further supported the translation of two candidate smORFs, encoded by GAS5 and LINC03057.
