Circular RNA forms had been described in all domains of life. Such RNAs were shown to have diverse biological functions, including roles in the life cycle of viral and viroid genomes, and in maturation of permuted tRNA genes. Despite their potentially important biological roles, discovery of circular RNAs has so far been mostly serendipitous. We have developed circRNA-seq, a combined experimental/computational approach that enriches for circular RNAs and allows profiling their prevalence in a whole-genome, unbiased manner. Application of this approach to the archaeon Sulfolobus solfataricus P2 revealed multiple circular transcripts, a subset of which was further validated independently. The identified circular RNAs included expected forms, such as excised tRNA introns and rRNA processing intermediates, but were also enriched with non-coding RNAs, including C/D box RNAs and RNase P, as well as circular RNAs of unknown function. Many of the identified circles were conserved in Sulfolobus acidocaldarius, further supporting their functional significance. Our results suggest that circular RNAs, and particularly circular non-coding RNAs, are more prevalent in archaea than previously recognized, and might have yet unidentified biological roles. Our study establishes a specific and sensitive approach for identification of circular RNAs using RNA-seq, and can readily be applied to other organisms.
Transcriptome-wide discovery of circular RNAs in Archaea
Miri Danan,Schraga Schwartz,Sarit Edelheit,R. Sorek
Published 2011 in Nucleic Acids Research
ABSTRACT
PUBLICATION RECORD
- Publication year
2011
- Venue
Nucleic Acids Research
- Publication date
2011-12-02
- Fields of study
Biology, Medicine, Environmental Science
- Identifiers
- External record
- Source metadata
Semantic Scholar, PubMed
CITATION MAP
EXTRACTION MAP
CLAIMS
CONCEPTS
- c/d box rnas
Small non-coding RNAs with C/D box motifs involved in RNA modification, included among the circular transcripts identified here.
Aliases: C/D box small RNAs
- circrna-seq
A combined experimental and computational RNA-seq approach used here to enrich for circular RNAs and profile them genome-wide.
Aliases: circular RNA sequencing, circRNA sequencing
- circular non-coding rnas
Circular RNA species that do not encode proteins and include several of the enriched transcripts reported here.
Aliases: circular ncRNAs
- circular rnas
RNA molecules with covalently closed circular structure that are the main target of the profiling approach in this paper.
Aliases: circRNAs, circle RNAs
- excised trna introns
Circular RNA products generated from introns removed during tRNA maturation.
Aliases: tRNA intron circles
- rnase p
A non-coding RNA component of the RNase P ribonucleoprotein complex, found among the circular RNAs reported in this work.
Aliases: RNase P RNA
- rrna processing intermediates
Circular RNA forms associated with intermediate steps in ribosomal RNA maturation or processing.
Aliases: rRNA circles
- sulfolobus acidocaldarius
A related archaeal species used for conservation comparison of identified circular RNAs.
Aliases: S. acidocaldarius
- sulfolobus solfataricus p2
The archaeal species used as the primary organism for transcriptome-wide circular RNA discovery in this study.
Aliases: S. solfataricus P2
REFERENCES
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