title: Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.
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.
authors.affiliation: Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
authors.forename: Livia S
authors.initials: LS
authors.lastname: Zaramela
authors.affiliation: Department of Computing and Mathematics, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.
authors.forename: Ricardo Z N
authors.initials: RZ
authors.lastname: Vêncio
authors.affiliation: Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
authors.forename: Felipe
authors.initials: F
authors.lastname: ten-Caten
authors.affiliation: Institute for Systems Biology, Seattle, Washington, United States of America.
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
authors.affiliation: Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
authors.forename: Tie
authors.initials: T
authors.lastname: Koide
mesh_terms: D001105:Archaea / Q000235:genetics*; D019848:Gene Expression Regulation, Archaeal; D019617:Halobacterium salinarum / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D017017:Methanococcus / Q000235:genetics; D020027:Pyrococcus furiosus / Q000235:genetics; D019642:RNA, Archaeal / Q000502:physiology*; D022661:RNA, Untranslated / Q000502:physiology*; D017423:Sequence Analysis, RNA; D048229:Sulfolobus solfataricus / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D019642:RNA, Archaeal; D022661:RNA, Untranslated