Structure, sequence and expression of the hepatitis delta (δ) viral genome

Wang, Kang-Sheng; Choo, Qui‐Lim; Weiner, Amy J.; Ou, Jing-Hsiung; Najarian, Richard C.; Thayer, Richard M.; Mullenbach, Guy T.; Denniston, Katherine J.; Gerin, John L.; Houghton, Michael

doi:10.1038/323508a0

Cited by 655 publications

(400 citation statements)

References 45 publications

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“…CircRNAs are long non-coding RNAs (lncRNAs) with circular forms and are widely observed in virus-like infectious particles, such as viroids, circular satellite viruses, or hepatitis delta virus. [1][2][3] Seemingly the result of mistaken RNA splicing, the crucial roles and functions of circRNAs have not be well recognized until very recently and such discovery have permanently altered our perspectives toward cancer, especially in carcinogenesis and cancer progression. [4][5][6] To date, investigators have discovered 2 major kinds of circRNAs, the intronic and exonic circRNAs.…”

Section: Introductionmentioning

confidence: 99%

Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

2016

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Circular RNAs (circRNAs) are long, non-coding RNAs that result from the non-canonical splicing of linear premRNAs. However, the characteristics and the critical role of circRNA in co-/post-transcriptional regulation were not well recognized until the "microRNA sponge" function of circRNA is discovered. Recent studies have mainly been devoted to the function of the circular RNA sponge for miR-7 (ciRS-7) and sex-determining region Y (SRY) by targeting microRNA-7 (miR-7) and microRNA-138 (miR-138), respectively. In this review, we illustrate the specific role of circRNAs in a wide variety of cancers and in regulating the biological behavior of cancers via miR-7 or miR-138 regulation. Furthermore, circRNA, together with its gene silencing ability, also shows its potential in RNA interference (RNAi) therapy by binding to target RNAs, which provides a novel perspective in cancer treatment. Thus, this review concerns the biogenesis, biological function, oncogenesis, progression and possible therapies for cancer involving circRNAs.

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Section: Introductionmentioning

confidence: 99%

Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

2016

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“…\ 18mer is the dissociated labeled top strand and \ duplex is the remaining labeled duplex. (d18m2/cd18 and d18m2T 5 /cd18) progressively converted to three perfectly matched duplexes (d18T 10 /cd18, d18T 15 /cd18, and T 10 d18T 10 /cd18), and the labeled cd18 hybridized predominantly to completely complementary DNA oligos after 60 min incubation with NdAg regardless of the location and the length of dT tail (Fig. 4A, lanes 5-8).…”

Section: Ndag Stimulated Duplex Conversionmentioning

confidence: 99%

“…The assay included six DNA oligos with labeled cd18 as the bottom strand (2.5 nM) and five competing oligos that were either completely complementary to cd18 or contained a substitution, that causes a mismatched base pair in cd18 duplex, and had a dT tail of different lengths at the 3 0 terminus or both termini (d18m2, d18m2T 5 , d18T 10 , d18T 15 , and T 10 d18 T 10 , and T n represents the length of dT tail) as the top strands (10 nM of each). Almost all cd18 participated in duplex formation in the absence of NdAg probably due to the relatively high DNA concentration, while two shorter DNA oligos (the ones with substitution) hybridized to cd18 more efficiently than three longer DNA oligos (the ones without substitution) with no obvious duplex conversion during the 60 min incubation period (Fig.…”

Section: Ndag Stimulated Duplex Conversionmentioning

confidence: 99%

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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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“…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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Structure, sequence and expression of the hepatitis delta (δ) viral genome

Cited by 655 publications

References 45 publications

Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

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

Four RNA families with functional transient structures

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