{"doi":"10.1093/nar/gkaa100","title":"Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA","abstract":"While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). Deep sequencing PSTVd genomes from plants inoculated with a cloned master sequence revealed naturally occurring variants, and showed that G/U pairs are maintained to the same extent as canonical WC base pairs. Comprehensive mutational analysis demonstrated that nearly all G/U pairs are critical for replication and/or systemic spread. Two selected G/U pairs were found to be required for PSTVd entry into, but not for exit from, the host vascular system. This study identifies critical roles for G/U pairs in the survival of an infectious RNA, and increases understanding of structure-based regulation of replication and trafficking of pathogen and cellular RNAs.","journal":"Nucleic Acids Research","year":2020,"id":100537,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":28,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9111,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":494642,"name":"Cuiji Zhou","orcid":null,"position":1,"is_corresponding":false},{"id":493593,"name":"James Li","orcid":"0000-0002-1248-6592","position":2,"is_corresponding":false},{"id":493594,"name":"Chun Li","orcid":"0000-0002-9370-1775","position":3,"is_corresponding":false},{"id":493595,"name":"Xiaorong Tao","orcid":"0000-0003-1259-366X","position":4,"is_corresponding":false},{"id":74715,"name":"Neocles B. Leontis","orcid":"0000-0003-3521-5119","position":5,"is_corresponding":false},{"id":493596,"name":"Craig L. Zirbel","orcid":"0000-0002-3281-918X","position":6,"is_corresponding":false},{"id":493597,"name":"David M. Bisaro","orcid":"0000-0002-6765-0548","position":7,"is_corresponding":false},{"id":493598,"name":"Biao Ding","orcid":"0000-0003-3431-5214","position":8,"is_corresponding":false},{"id":344935,"name":"Jian Wu","orcid":"0000-0001-9933-7364","position":0,"is_corresponding":true}],"reference_count":67,"raw_metadata":null,"created_at":"2026-07-18T22:39:01.863288Z","pmid":"32083649","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}