{"doi":"10.1101/274290","title":"mRNA structure dynamics identifies the embryonic RNA regulome","abstract":"RNA folding plays a crucial role in RNA function. However, our knowledge of the global structure of the transcriptome is limited to steady-state conditions, hindering our understanding of how RNA structure dynamics influences gene function. Here, we have characterized mRNA structure dynamics during zebrafish development. We observe that on a global level, translation guides structure rather than structure guiding translation. We detect a decrease in structure in translated regions, and we identify the ribosome as a major remodeler of RNA structure in vivo . In contrast, we find that 3’-UTRs form highly folded structures in vivo , which can affect gene expression by modulating miRNA activity. Furthermore, we find that dynamic 3’-UTR structures encode RNA decay elements, including regulatory elements in nanog and cyclin A1 , key maternal factors orchestrating the maternal-to-zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2018,"id":6986,"datarank":0.11685116642740523,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.012879089343413416,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.012879089343413416,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.057,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2018-03-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":39887,"name":"Eva Maria Novoa","orcid":"0000-0002-9367-6311","position":1,"is_corresponding":false},{"id":39888,"name":"Charles E. Vejnar","orcid":"0000-0002-7132-4534","position":2,"is_corresponding":false},{"id":39889,"name":"Valeria Yartseva","orcid":null,"position":3,"is_corresponding":false},{"id":14693,"name":"Sharon L. R. Kardia","orcid":"0000-0002-9853-3379","position":5,"is_corresponding":false},{"id":3237,"name":"Carter M. Takacs","orcid":null,"position":7,"is_corresponding":false},{"id":3244,"name":"Antonio J. Giráldez","orcid":"0000-0002-6823-137X","position":8,"is_corresponding":false},{"id":39886,"name":"Jean-Denis Beaudoin","orcid":"0000-0003-4932-1668","position":0,"is_corresponding":true}],"reference_count":71,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"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":[]}