A human microRNA, miR-122, promotes Hepatitis C virus RNA accumulation through three distinct mechanisms
Bibliographic record
Abstract
Hepatitis C virus (HCV) is a positive-sense single-stranded RNA virus.The 5' untranslated region (UTR) of the HCV genome interacts with a liver-specific microRNA, called miR-122.miR-122 binds to two sites (Site 1 and Site 2) on the 5' UTR of the viral genome and promotes HCV RNA accumulation, although the precise role(s) of miR-122 in the HCV life cycle have remained unclear until recently.Previous studies suggested two main mechanisms of miR-122-mediated viral RNA accumulation: 1) protection from pyrophosphatase and subsequent exoribonuclease activity; and2) suppression of an alternative secondary structure and promotion of the HCV internal ribosomal entry site (IRES) formation.Herein, we hypothesized that miR-122 binding to HCV genome alters the structure of 5' UTR in a manner that promotes HCV RNA accumulation.Using biophysical analyses and Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE), we provided a new model of Ago:miR-122 interactions with the HCV genome that suggests that miR-122 plays three roles in the HCV life cycle.Firstly, Ago:miR-122 binds to Site 2 of HCV RNA, suppressing a more energetically favorable secondary structure, termed SLII alt and promoting formation of the functional SLII structure which makes up part of the viral IRES (SLII-IV).Secondly, another Ago:miR-122 complex is recruited to Site 1, protecting the 5' terminus of the viral genome from cellular pyrophosphatase activity and subsequent exoribonuclease-mediated decay.Finally, in order to accommodate both Ago:miR-122 complexes in such close proximity, the Ago:miR-122 complex at Site 2 weakens its auxiliary base-pairing interactions, but is further stabilized by interacting with SLIIa of the HCV IRES, stabilizing the canonical SLII structure and promoting viral translation.Recent clinical trials using miR-122 inhibitors to treat chronic HCV-infected patients revealed the selection of several resistance associated variants (RAVs) in the 5' terminus of the iii HCV genome.We hypothesized that these RAVs result in changes to the secondary structure of the HCV genome that promote viral RNA accumulation, even in the absence of miR-122.We demonstrated that the RAVs could be classified into three main classes, with distinct mechanisms of action, all based on changes to the structure of the viral RNA.Specifically, Class I RAVs, including C2GC3U, U4C and G28A are 'riboswitched' and are able to form the functional SLII structure, even in the absence of miR-122.Class II RAVs, including C2GC3U, C3U and U4C result in additional base-pairing interactions at the 5' terminus of the HCV RNA that provide genome stability, independently of miR-122.Finally, the Class III RAV, C37U, alters the structure of the 3' terminus of the negative-strand intermediate, which is predicted to alter positive-strand RNA synthesis, as this region of the genome contains the positive-strand promoter.This research has uncovered the mechanism(s) of action of miR-122 in the HCV life cycle and revealed new paradigms for miRNA function.Moreover, it has revealed three distinct mechanisms of antiviral resistance all based on modifications in RNA structure.We anticipate that this research may be applicable to other important human or veterinary pathogens and will be relevant in the design, development, and evaluation of resistance to miRNA-based therapies more broadly.iv
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".