The folding of the hepatitis C virus internal ribosome entry site depends on the 3′-end of the viral genome

Romero-López, Cristina; Barroso‐delJesus, Alicia; García‐Sacristán, Albino; Briones, Carlos; Berzal‐Herranz, Alfredo

doi:10.1093/nar/gks927

Cited by 36 publications

(85 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The present results, together with previously reported data (43,44,47), allow a working hypothesis to be envisioned in which, during early viral infection, the HCV IRES is occupied by the translational machinery, thus avoiding any contact with the 5BSL3.2 domain of the CRE region (Figure 8B). This would favor the establishment of the interaction 5BSL3.2-3′SLII, thus occluding the DLS motif.…”

Section: Discussionsupporting

confidence: 81%

See 1 more Smart Citation

End-to-end crosstalk within the hepatitis C virus genome mediates the conformational switch of the 3′X-tail region

Romero-López¹,

Barroso‐delJesus²,

García‐Sacristán³

et al. 2013

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

The hepatitis C virus (HCV) RNA genome contains multiple structurally conserved domains that make long-distance RNA–RNA contacts important in the establishment of viral infection. Microarray antisense oligonucelotide assays, improved dimethyl sulfate probing methods and 2′ acylation chemistry (selective 2’-hydroxyl acylation and primer extension, SHAPE) showed the folding of the genomic RNA 3′ end to be regulated by the internal ribosome entry site (IRES) element via direct RNA–RNA interactions. The essential cis-acting replicating element (CRE) and the 3′X-tail region adopted different 3D conformations in the presence and absence of the genomic RNA 5′ terminus. Further, the structural transition in the 3′X-tail from the replication-competent conformer (consisting of three stem-loops) to the dimerizable form (with two stem-loops), was found to depend on the presence of both the IRES and the CRE elements. Complex interplay between the IRES, the CRE and the 3′X-tail region would therefore appear to occur. The preservation of this RNA–RNA interacting network, and the maintenance of the proper balance between different contacts, may play a crucial role in the switch between different steps of the HCV cycle.

show abstract

Section: Discussionsupporting

confidence: 81%

“…Transcripts were purified as previously described (47). RNA yield was determined by ultraviolet spectrophotometry (A 260 ) and the extent of protein and carbohydrate contaminations assessed by the A 260 /A 280 and A 260 /A 230 ratios, respectively.…”

Section: Methodsmentioning

confidence: 99%

End-to-end crosstalk within the hepatitis C virus genome mediates the conformational switch of the 3′X-tail region

Romero-López¹,

Barroso‐delJesus²,

García‐Sacristán³

et al. 2013

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…Other RNA elements within the NS5B-coding region upstream of 5BSL3.2 also appear essential for efficient replication 53, 64 . Longer-range interactions between the CRE, the 3′UTR and the IRES have been identified, and may influence the structure of both the IRES and the 3′ X-tail 58, 65 . Thus, a network of variably conserved RNA-RNA interactions exists across the HCV RNA genome and between its 5′ and 3′ ends that may modulate various steps of the replication cycle.…”

Section: The Yin Of Hepatitis C: Hcv Rna Synthesismentioning

confidence: 99%

The yin and yang of hepatitis C: synthesis and decay of hepatitis C virus RNA

Yamane

Masaki

et al. 2015

Nat Rev Microbiol

View full text Add to dashboard Cite

PREFACE Hepatitis C virus (HCV) is an unusual RNA virus that possesses a striking capacity to persist for life in the majority of infected individuals. In order to persist, HCV must balance viral RNA synthesis and decay in infected cells. In this Review, we focus on interactions between the positive-sense RNA genome of HCV and host RNA-binding proteins and microRNAs (miRNAs) that influence the competing processes of viral RNA synthesis and decay to achieve stable, long-term persistence of the viral genome. We discuss how these processes impact HCV pathogenesis and therapeutic strategies against the virus.

show abstract

“…Preliminary experiments based on our previous experience [51,61–63] were conducted to compare the performance of control microarrays that were hybridized using different experimental parameters (data not shown). Regarding the preparation of the target molecules, control experiments advised against the use of streptavidin-coated magnetic beads to obtain ssDNA by discarding the biotin-labelled strain.…”

Section: Resultsmentioning

confidence: 99%

An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies

et al. 2016

Self Cite

View full text Add to dashboard Cite

The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice. Here we describe the development and testing of a HIV-1 genotyping DNA microarray that detects and quantifies, in majority and minority viral subpopulations, relevant mutations and amino acid insertions in 42 codons of the pol gene associated with drug- and multidrug-resistance to protease (PR) and reverse transcriptase (RT) inhibitors. A customized bioinformatics protocol has been implemented to analyze the microarray hybridization data by including a new normalization procedure and a stepwise filtering algorithm, which resulted in the highly accurate (96.33%) detection of positive/negative signals. This microarray has been tested with 57 subtype B HIV-1 clinical samples extracted from multi-treated patients, showing an overall identification of 95.53% and 89.24% of the queried PR and RT codons, respectively, and enough sensitivity to detect minority subpopulations representing as low as 5–10% of the total quasispecies. The developed genotyping platform represents an efficient diagnostic and prognostic tool useful to personalize antiviral treatments in clinical practice.

show abstract

The folding of the hepatitis C virus internal ribosome entry site depends on the 3′-end of the viral genome

Cited by 36 publications

References 62 publications

End-to-end crosstalk within the hepatitis C virus genome mediates the conformational switch of the 3′X-tail region

End-to-end crosstalk within the hepatitis C virus genome mediates the conformational switch of the 3′X-tail region

The yin and yang of hepatitis C: synthesis and decay of hepatitis C virus RNA

An Efficient Microarray-Based Genotyping Platform for the Identification of Drug-Resistance Mutations in Majority and Minority Subpopulations of HIV-1 Quasispecies

Contact Info

Product

Resources

About