Profiling plant circRNAs as a guide for expression of plant genes involved in viral infection.
Bibliographic record
Abstract
In this study, we explore the changes in the expression of plant circRNAs as a guide to trace plant gene expression during viral/viral component infections, focusing on the circRNAs dysregulation and their role in triggering plant cell responses. Our investigation distinguishes host-virus (TRoV) determinants versus non-host virus (RYMV) in Arabidopsis thaliana (A. thalian) plants. We identified 760 plant circRNAs with varying abundances, primarily encoded in exonic regions, and further analyzed their distribution across all A. thaliana chromosomes. Notably, the chloroplast chromosome exhibits the highest number of circRNAs compared to other chromosomes, suggesting the chloroplast as a circRNA hotspot in response to viruses and/or viral genes. Gene ontology (GO) analysis indicates that most host genes encoding these circR-NAs are primarily associated with plant development and protein binding activity, suggesting a potential role for circRNAs in the regulation of their host genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis highlights photosynthesis as the most enriched pathway among the identified circRNAs. While some circRNAs are anticipated to function as decoys for miRNA binding, such as circRNA AT1G01520 targeting ath-miR396b-5p, it is noteworthy that the major-ity of identified circRNAs do not correspond with miRNA sequences. Additionally, the non-coding exogenous circular satellite RNA (scLTSV) (virusoid) is shown to affect specific genes. Our results demonstrate that numerous cellular circRNAs (e.g., ATCG00030 (ciRNA106) and ATCG00130 (ciRNA11)) are induced solely by scLTSV. One circRNA (circRNA2) with an open reading frame (ORF) codes for a protein similar to a described wheat protein with monooxy-genase activity. CircRNA205, displaying significant expression changes between non-host and host viruses, also contains a translatable ORF. RYMV genomic RNA is transcribed in transgenic A. thaliana by the 35S promoter but is unable to replicate (non-host), impacting host eIF4G ex-pression (AT3G60240). Intriguingly, expression of transgenic scLTSV (satellite RNA) in A. thali-ana enhances plant resistance to TRoV infection. These findings contribute to our understand-ing of circRNA-mediated mechanisms in plant-virus interactions, shedding light on potential av-enues for improving plant resistance to viral infections.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".