{"doi":"10.7554/elife.49658","title":"Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification","abstract":"Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant <i>Arabidopsis thaliana</i> and a mutant defective in mRNA methylation (m<sup>6</sup>A). Here we show that m<sup>6</sup>A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m<sup>6</sup>A from 3' untranslated regions is associated with decreased relative transcript abundance and defective RNA 3' end formation. A functional consequence of disrupted m<sup>6</sup>A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode.","journal":"eLife","year":2020,"id":3020,"datarank":0.9327900179537595,"base_score":6.218600119691729,"endowment":6.218600119691729,"self_citation_contribution":0.9327900179537595,"citation_network_contribution":0.0,"self_endowment_contribution":0.9327900179537595,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":501,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0734,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-14","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":33799,"name":"Katarzyna Knop","orcid":"0000-0002-2636-9450","position":1,"is_corresponding":false},{"id":33800,"name":"Anna V. Sherwood","orcid":"0000-0001-7153-8420","position":2,"is_corresponding":false},{"id":33801,"name":"Nicholas J Schurch","orcid":"0000-0001-9068-9654","position":3,"is_corresponding":false},{"id":33802,"name":"Katarzyna Mackinnon","orcid":null,"position":4,"is_corresponding":false},{"id":33803,"name":"Peter D Gould","orcid":null,"position":5,"is_corresponding":false},{"id":33804,"name":"Anthony JW Hall","orcid":null,"position":6,"is_corresponding":false},{"id":33805,"name":"Geoffrey J. Barton","orcid":"0000-0002-9014-5355","position":7,"is_corresponding":false},{"id":7298,"name":"Gordon G. Simpson","orcid":"0000-0001-6744-5889","position":8,"is_corresponding":false},{"id":33806,"name":"Peter Gould","orcid":"0000-0002-0709-1190","position":9,"is_corresponding":false},{"id":33807,"name":"Anthony Hall","orcid":"0000-0002-1806-020X","position":10,"is_corresponding":false},{"id":33798,"name":"Matthew T. Parker","orcid":"0000-0002-0891-8495","position":0,"is_corresponding":true}],"reference_count":107,"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":[]}