RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi

The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transc...

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Main Authors:	Toffano-Nioche, Claire, Ott, Alban, Crozat, Estelle, Nguyen, An N., Zytnicki, Matthias, Leclerc, Fabrice, Forterre, Patrick, Bouloc, Philippe, Gautheret, Daniel
Format:	Online
Language:	English
Published:	Landes Bioscience 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849170/

id	pubmed-3849170
recordtype	oai_dc
spelling	pubmed-38491702013-12-12 RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi Toffano-Nioche, Claire Ott, Alban Crozat, Estelle Nguyen, An N. Zytnicki, Matthias Leclerc, Fabrice Forterre, Patrick Bouloc, Philippe Gautheret, Daniel Research Paper The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. Antisense transcription is widespread (215 transcripts) and targets protein-coding genes that appear to evolve more rapidly than average genes. We identify at least three novel H/ACA-like guide RNAs among the newly characterized non-coding RNAs. Long 5′ UTRs in mRNAs of ribosomal proteins and amino-acid biosynthesis genes strongly suggest the presence of cis-regulatory leaders in these mRNAs. We selected a high-interest subset of non-coding RNAs based on their strong promoters, high GC-content, phylogenetic conservation, or abundance. Some of the novel small RNAs and long 5′ UTRs display high GC contents, suggesting unknown structural RNA functions. However, we were surprised to observe that most of the high-interest RNAs are AU-rich, which suggests an absence of stable secondary structure in the high-temperature environment of P. abyssi. Yet, these transcripts display other hallmarks of functionality, such as high expression or high conservation, which leads us to consider possible RNA functions that do not require extensive secondary structure. Landes Bioscience 2013-07-01 2013-07-02 /pmc/articles/PMC3849170/ /pubmed/23884177 http://dx.doi.org/10.4161/rna.25567 Text en Copyright © 2013 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
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	Toffano-Nioche, Claire Ott, Alban Crozat, Estelle Nguyen, An N. Zytnicki, Matthias Leclerc, Fabrice Forterre, Patrick Bouloc, Philippe Gautheret, Daniel
spellingShingle	Toffano-Nioche, Claire Ott, Alban Crozat, Estelle Nguyen, An N. Zytnicki, Matthias Leclerc, Fabrice Forterre, Patrick Bouloc, Philippe Gautheret, Daniel RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi
author_facet	Toffano-Nioche, Claire Ott, Alban Crozat, Estelle Nguyen, An N. Zytnicki, Matthias Leclerc, Fabrice Forterre, Patrick Bouloc, Philippe Gautheret, Daniel
author_sort	Toffano-Nioche, Claire
title	RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi
title_short	RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi
title_full	RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi
title_fullStr	RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi
title_full_unstemmed	RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi
title_sort	rna at 92°c: the non-coding transcriptome of the hyperthermophilic archaeon pyrococcus abyssi
description	The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. Antisense transcription is widespread (215 transcripts) and targets protein-coding genes that appear to evolve more rapidly than average genes. We identify at least three novel H/ACA-like guide RNAs among the newly characterized non-coding RNAs. Long 5′ UTRs in mRNAs of ribosomal proteins and amino-acid biosynthesis genes strongly suggest the presence of cis-regulatory leaders in these mRNAs. We selected a high-interest subset of non-coding RNAs based on their strong promoters, high GC-content, phylogenetic conservation, or abundance. Some of the novel small RNAs and long 5′ UTRs display high GC contents, suggesting unknown structural RNA functions. However, we were surprised to observe that most of the high-interest RNAs are AU-rich, which suggests an absence of stable secondary structure in the high-temperature environment of P. abyssi. Yet, these transcripts display other hallmarks of functionality, such as high expression or high conservation, which leads us to consider possible RNA functions that do not require extensive secondary structure.
publisher	Landes Bioscience
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849170/
_version_	1612033676945653760

RNA at 92°C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi

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