Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.

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 (TSSaR...

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Autores principales:	Livia S Zaramela, Ricardo Z N Vêncio, Felipe ten-Caten, Nitin S Baliga, Tie Koide
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/be604c511158458895a15130b5fb02a7
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spelling	oai:doaj.org-article:be604c511158458895a15130b5fb02a72021-11-25T05:59:57ZTranscription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.1932-620310.1371/journal.pone.0107680https://doaj.org/article/be604c511158458895a15130b5fb02a72014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0107680https://doaj.org/toc/1932-6203A 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.Livia S ZaramelaRicardo Z N VêncioFelipe ten-CatenNitin S BaligaTie KoidePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 9, p e107680 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Livia S Zaramela Ricardo Z N Vêncio Felipe ten-Caten Nitin S Baliga Tie Koide Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.
description	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.
format	article
author	Livia S Zaramela Ricardo Z N Vêncio Felipe ten-Caten Nitin S Baliga Tie Koide
author_facet	Livia S Zaramela Ricardo Z N Vêncio Felipe ten-Caten Nitin S Baliga Tie Koide
author_sort	Livia S Zaramela
title	Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.
title_short	Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.
title_full	Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.
title_fullStr	Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.
title_full_unstemmed	Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.
title_sort	transcription start site associated rnas (tssarnas) are ubiquitous in all domains of life.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/be604c511158458895a15130b5fb02a7
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Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life.

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