Description and detection of excludons as transcriptional regulators in gram-positive, gram-negative and archaeal strains of prokaryotes

Recent major studies have highlighted a newly discovered paradigm termed the “excludon”, which are overlapping transcripts that produce anticorrelated protein expression. These antisense overlapping transcripts are believed to act as common regulatory mechanisms in prokaryotes. Current research prevalence of excludons has only been demonstrated in Gram-positive bacteria and has not been explored in any Gram-negative or archaeal prokaryotes. To overcome this limitation, it is important to determine the frequency of excludons across all prokaryote domains in order to confirm its regulatory role in prokaryotes. With the recent advances in next-generation sequencing, it is now possible to define nucleic acid populations at an unprecedented depth and resolution. This study involves the evaluation of bioinformatics as a novel method to identify potential excludons and to investigate the occurrence of excludons in both bacterial (Gram-positive and Gram-negative) and archaeal strains. The paradigm of the excludons is mathematically represented using the Heaviside function to facilitate the identification of excludons with the help of computational algorithms. Based on the results, these excludons are likely to be common in both bacteria and archaea and may be a common regulatory system in prokaryotes.