Identification and comparison of circular RNAs in archaeal transcriptome data

Abstract

Circular RNAs (circRNAs) are closed RNA molecules with their 5' and 3' ends covalently ligated. They were first discovered in viruses and viroids and then in eukaryotes. CircRNAs are progressively being understood as functional molecules and not as mere splicing by-products: their functions range from acting as genetic regulators to being translated. Next generation sequencing experiments have been used to identify circRNAs (Circ-Seq) in a wide range of organisms, however, we know little about this class of molecules in prokaryotes. Archaea, a group of well placed organisms in the tree of life with both bacterial and eukaryotic features, can help us elucidate the evolutionary paths that established circRNAs. Halobacterium salinarum NRC-1 is a Systems Biology model halophilic archaeon for which we have Circ-Seq data with thorough Bioinformatics analysis still pending. In this project we aim (1) to identify and characterize H. salinarum circRNAs, and (2) to investigate circRNAs evolutionary history and conservation through reanalysis of other archaeal Circ-Seq published data. To reach theses goals, we will: develop a computational pipeline to identify prokaryotic circRNAs; verify circRNA expression levels in different conditions; experimentally validate some candidates that may be important for H. salinarum; study circRNA interaction with relevant biomolocules; and investigate the evolutionary history of circRNAs comparing them among archaea. We hope to help elucidate why there are few and/or none circRNAs in bacteria while they are abundant and relevant in eukaryotes. (AU)