Mapping the RNA-Seq trash bin

Doose, Gero; Alexis, Maria S.; Kirsch, Rebecca; Findeiß, Sven; Langenberger, David; Machné, Rainer; Mörl, Mario; Hoffmann, Steve; Stadler, Peter F.

doi:10.4161/rna.24972

Cited by 14 publications

(17 citation statements)

References 57 publications

(53 reference statements)

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“…rRNAs, including P. abyssi 5S rRNA, and some coding RNAs did not show obvious enrichment in RNase R experiments, but have been observed in a circular form also in previous studies [Table S1. 10,30 ]. Formation of the circular 5S rRNA could be compatible with the proposed processing mechanism of the archaeal pre-5S-RNA possibly 31 but it is unclear whether this potential circular form corresponds to an additional processing intermediate or the mature 5S rRNA.…”

Section: Discussionmentioning

confidence: 99%

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

et al. 2017

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It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in P. abyssi. The large majority of these loci interacted with Pab1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that Pab1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of Pab1020 may facilitate the development of new biotechnological applications e.g. in ligation of preadenylated adaptors to RNA molecules.

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Section: Discussionmentioning

confidence: 99%

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

et al. 2017

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“…Some box C/D snoRNAs seem to be present predominantly or possibly exclusively as circular RNAs [9][10][11]. This is also true for assorted other small RNA species, among them the 5S rRNA [9].…”

Section: Introductionmentioning

confidence: 74%

“…Publicly available RNA-seq data of S. acidocaldarius [44,45], S. solfataricus [40], Nanoarchaeum equitans and Ignicoccus hospitalis [39], and M. kandleri [27] were mapped and analyzed as outlined in [11]. In brief, read data sets for each species were pooled, the reads were quality-trimmed and then mapped to the corresponding genome using segemehl [46,47] with the option --splits that forces reads that do not acceptably match as a single substring to be split and matched across splice sites.…”

Section: Circular Transcriptsmentioning

confidence: 99%

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Processed Small RNAs in Archaea and BHB Elements

Berkemer

Siederdissen

Amman

et al. 2015

Genomics Comput Biol

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Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piecewise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB elements of a phylogenetically diverse set of archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.

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“…They are ubiquitous and have been detected in various speciеs across kingdoms [1]- [7]. CircRNAs may consist of transcribed exons with or without introns that are scrambled (e.g.…”

Section: Introductionmentioning

confidence: 99%

Circular RNAs: New Players in Gene Regulation

Andreeva¹,

Cooper²

2015

ABB

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The existence of circular RNAs (circRNAs) was demonstrated over 30 years ago. They did not gain much interest at the time because they appeared to be relatively rare when compared to the abundance of the canonical linear RNAs. However, more recent evidence suggests that circRNAs are abundant in cells and tissues and possess intriguing biological properties. These recent developments have renewed our interest in this novel class of molecules. This report will provide an overview of circRNAs, discuss how they may modify our understanding of gene regulation and indicate their most likely relevance to health. The circRNAs from viruses, bacteria and archaea are not in the scope of this report, and we focused this review on circRNAs in eukaryotes.

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Mapping the RNA-Seq trash bin

Cited by 14 publications

References 57 publications

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

High-throughput sequencing reveals circular substrates for an archaeal RNA ligase

Processed Small RNAs in Archaea and BHB Elements

Circular RNAs: New Players in Gene Regulation

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