Abstract
A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in both eukaryotes and bacteria. Here, we provide evidence for existence of TSSaRNAs in several archaeal transcriptomes including: Halobacterium salinarum, Pyrococcus furiosus, Methanococcus maripaludis, and Sulfolobus solfataricus. We validated TSSaRNAs from the model archaeon Halobacterium salinarum NRC-1 by deep sequencing two independent small-RNA enriched (RNA-seq) and a primary-transcript enriched (dRNA-seq) strand-specific libraries. We identified 652 transcripts, of which 179 were shown to be primary transcripts (∼7% of the annotated genome). Distinct growth-associated expression patterns between TSSaRNAs and their cognate genes were observed, indicating a possible role in environmental responses that may result from RNA polymerase with varying pausing rhythms. This work shows that TSSaRNAs are ubiquitous across all domains of life.
Highlights
Molecular mechanisms that are conserved throughout evolution, or arise independently to perform similar tasks are of major interest to biology [1]
Discovery of TSSaRNAs in the third domain of life In the present work, we investigated whether TSSaRNAs do exist in archaea and, ubiquitous across all three domains of life
In this study we demonstrated that TSSaRNAs are present in archaea
Summary
Molecular mechanisms that are conserved throughout evolution, or arise independently to perform similar tasks are of major interest to biology [1]. Evolutionary conservation and convergence are strong indicators of important biological functions. Understanding commonalities and differences across organisms from all three domains of life have served as powerful means to discover and characterize important molecular mechanisms. The roles of non-coding RNA (ncRNA) molecules have proven to be especially elusive. High-throughput technologies have revealed that ncRNAs have important functions across diverse biological systems and processes [2,3]. Among the newly discovered ncRNAs is an intriguing class of transcription start site associated RNAs (TSSaRNAs) that have far been observed in eukaryotes and bacteria [4,5,6,7]
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