PROKRNA · Prokaryotic RNomics: Unravelling the RNA-mediated regulatory layers

Pioneering studies from the recent year, including those published by the PI of this proposal, are revolutionizing our perception of prokaryotic transcriptomes, and reveal unexpected regulatory complexity. Two central concepts are arising: the unanticipated abundance of cis-antisense RNAs overlapping protein coding genes, and alternative transcripts resulting from a dynamic behaviour of operon structures (where genes can be included or excluded from a polycistronic transcript in response to environmental cues). Understanding these phenomena holds a great potential for our ability to decipher how bacteria regulate their complex life styles and pathogenic behaviours, but their dynamics, regulatory roles, and effects on combinatorially increasing the regulatory capacity of the genome are completely unknown.The primary objectives of this proposed research are: i) to understand the extent, regulatory roles, and evolutionary consequences of cis-antisenseRNAs in prokaryotes; ii) to understand the regulatory code, combinatorial effects and dynamics of alternative operon structures; and, in parallel iii) to develop a unified framework for comparative prokaryotic transcriptomics.Our strategy is based on a combination of deep sequencing technologies, computational modelling and data analyses, systems biologyapproaches, and focused molecular biology experiments. We will identify the extent and the impact of these RNA-based regulatory layers in representative pathogenic and non-pathogenic species across the prokaryotic tree of life, study their functional and evolutionary consequences, and break the regulatory code controlling them. Our planned research has the potential of producingmethodological and conceptual breakthroughs in the emerging field of prokaryotic transcriptomics.