Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life

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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Main Authors: Zaramela, Livia S., Vêncio, Ricardo Z. N., ten-Caten, Felipe, Baliga, Nitin S., Koide, Tie
Format: Online
Language:English
Published: Public Library of Science 2014
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169567/
id pubmed-4169567
recordtype oai_dc
spelling pubmed-41695672014-09-22 Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life Zaramela, Livia S. Vêncio, Ricardo Z. N. ten-Caten, Felipe Baliga, Nitin S. Koide, Tie Research Article 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. Public Library of Science 2014-09-19 /pmc/articles/PMC4169567/ /pubmed/25238539 http://dx.doi.org/10.1371/journal.pone.0107680 Text en © 2014 Zaramela et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Zaramela, Livia S.
Vêncio, Ricardo Z. N.
ten-Caten, Felipe
Baliga, Nitin S.
Koide, Tie
spellingShingle Zaramela, Livia S.
Vêncio, Ricardo Z. N.
ten-Caten, Felipe
Baliga, Nitin S.
Koide, Tie
Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life
author_facet Zaramela, Livia S.
Vêncio, Ricardo Z. N.
ten-Caten, Felipe
Baliga, Nitin S.
Koide, Tie
author_sort Zaramela, Livia S.
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
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.
publisher Public Library of Science
publishDate 2014
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169567/
_version_ 1613135653008048128

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