ArticleRNA biology2013
RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.
Article in RNA biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- The Thermococcales as a model system: historical perspectives and emerging tools.Journal of bacteriology · 2025Review
- Archaea express circular isoforms of IS200/IS605-associated ωRNAs.Frontiers in microbiology · 2025Article
- Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing.Frontiers in molecular biosciences · 2022Article
- Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea.RNA biology · 2021Article
- Discovery of 20 novel ribosomal leader candidates in bacteria and archaea.BMC microbiology · 2020Article
- New proposal of nitrogen metabolism regulation by small RNAs in the extreme halophilic archaeon Haloferax mediterranei.Molecular genetics and genomics : MGG · 2020Article
- Recent Advances in Archaeal Translation Initiation.Frontiers in microbiology · 2020Review
- Start Codon Recognition in Eukaryotic and Archaeal Translation Initiation: A Common Structural Core.International journal of molecular sciences · 2019Review
- Next Generation DNA-Seq and Differential RNA-Seq Allow Re-annotation of theFrontiers in microbiology · 2019Article
- A Haloarchaeal Small Regulatory RNA (sRNA) Is Essential for Rapid Adaptation to Phosphate Starvation Conditions.Frontiers in microbiology · 2019Article
- Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq.PloS one · 2019Article
- Role of aIF1 in Pyrococcus abyssi translation initiation.Nucleic acids research · 2018Article
- Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!Microbiology spectrum · 2018Review
- Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.Genome research · 2018Article
- A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius.Nucleic acids research · 2018Article
- Review
- A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase.Nature microbiology · 2017Article
- Genome-wide primary transcriptome analysis of HScientific reports · 2017Article
- Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq).BMC genomics · 2016Article
- Transcription Regulation in Archaea.Journal of bacteriology · 2016Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 are less conserved 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.
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