The hepatitis delta (δ) virus possesses a circular RNA

A, Kos; Dijkema, R.; Arnberg, Annika C.; Meide, P. H. Van Der; Schellekens, Huub

doi:10.1038/323558a0

Cited by 600 publications

(417 citation statements)

References 16 publications

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“…Known circular RNAs include the genomes of a very few subviral agents such as hepatitis delta virus and the viroids (33,34). In addition, in cellular organisms, some RNA processing pathways give rise to circular RNA byproducts or intermediates.…”

Section: Resultsmentioning

confidence: 99%

Circular box C/D RNAs in Pyrococcus furiosus

Starostina

Marshburn

Johnson

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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In eukaryotes, box C͞D modification guide RNAs are made by two primary pathways (2, 5, 10, 11). Some are found in the introns of host genes, and the linear box C͞D RNAs are processed from debranched lariats. In other cases, linear box C͞D RNAs are processed from mono-or polycistronic transcripts synthesized from independent promoters. Box C͞D RNAs were found only recently in archaea (12, 13). The pathway by which archaeal box C͞D RNAs are made is unknown. The archaeal box C͞D RNAs are located primarily in intergenic regions of the genome, sometimes overlapping the 3Ј or 5Ј end of flanking ORFs (1, 4, 12, 13). Independent promoters have not been identified.In the course of analyzing a cDNA library of small RNAs from P. furiosus, we observed an interesting incongruence between the linear sequence of some box C͞D RNA clones

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Section: Resultsmentioning

confidence: 99%

Circular box C/D RNAs in Pyrococcus furiosus

Starostina

Marshburn

Johnson

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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“…12,64 The high self-complementarity of the genome enables it to assumes a rod-like structure. [65][66][67][68] A double-rolling-circle mechanism is exploited by HDV to replicate via the host RNA polymerase II, yielding linear multimers of both genomic and antigenomic senses 64,68 .The multimers are subsequently self-cleaved into monomers via a trans-esterification reaction catalyzed by the HDV ribozyme in cis. 64,68 The linear monomers are then ligated into a circular genome via a host factor, which harbours the ribozyme-targeting cleavage site again.…”

Section: Hdv Ribozymementioning

confidence: 99%

Four RNA families with functional transient structures

Zhu

Meyer

2015

RNA Biology

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P rotein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since RFAM annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing RFAM families or introduce a new RNA family to RFAM. For each of the four RNA families, we compile a multiplesequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5 0 flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5 0 UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All transient and dominant structures are mapped to our new alignments introduced here.

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“…Hepatitis delta antigen (HDAg), the only protein coded by hepatitis delta virus (HDV), is essential for viral replication and virion assembly [15][16][17][18][19][20]. HDAg has an RNA chaperone activity in vivo [21] and in vitro [22,23].…”

Section: Introductionmentioning

confidence: 99%

Characterization and application of the selective strand annealing activity of the N terminal domain of hepatitis delta antigen

Huang

Chen

2004

FEBS Letters

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We used synthetic DNA oligos to investigate the nucleic acid chaperone properties of the N terminal domain of hepatitis delta antigen (NdAg). We found that NdAg possessed a bona fide chaperone activity. NdAg could distinguish subtle differences in the thermal stability of the base pairing region, and enabled DNA oligos to form a more stable duplex among competing sequences through facilitating strand annealing selectively, stimulating duplex conversion selectively, and stabilizing the more stable duplex. The property of NdAg identified in this study could be applied to improve the efficiency and specificity of dot blot hybridization under conditions of low stringency.

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The hepatitis delta (δ) virus possesses a circular RNA

Cited by 600 publications

References 16 publications

Circular box C/D RNAs in Pyrococcus furiosus

Circular box C/D RNAs in Pyrococcus furiosus

Four RNA families with functional transient structures

Characterization and application of the selective strand annealing activity of the N terminal domain of hepatitis delta antigen

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