{"id":"https://openalex.org/W7225261986","doi":"https://doi.org/10.64898/2026.11.02.763788","title":"RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure","display_name":"RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure","publication_year":2026,"publication_date":"2026-11-03","ids":{"openalex":"https://openalex.org/W7225261986","doi":"https://doi.org/10.64898/2026.11.02.763788"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.02.763788","doi":"https://doi.org/10.64898/2026.11.02.763788","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.02.763788","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.11.02.763788","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5140131977","display_name":"Yang Li","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Li","raw_affiliation_strings":["University of Chicago;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Chicago;","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101100203","display_name":"Chang Ye","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chang Ye","raw_affiliation_strings":["The University of Chicago;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Chicago;","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029083198","display_name":"Ruiqi Ge","orcid":"https://orcid.org/0000-0002-8529-3070","observed_orcids":["https://orcid.org/0000-0002-8529-3070"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruiqi Ge","raw_affiliation_strings":["The University of Chicago;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Chicago;","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025372898","display_name":"Cheng\u2010Wei Ju","orcid":"https://orcid.org/0000-0002-2250-8548","observed_orcids":["https://orcid.org/0000-0002-2250-8548","https://orcid.org/0000-0003-0236-5671"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cheng-Wei Ju","raw_affiliation_strings":["The University of Chicago;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Chicago;","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160722639","display_name":"Yu Xiao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Xiao","raw_affiliation_strings":["The University of Chicago;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Chicago;","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081170071","display_name":"Weixin Tang","orcid":"https://orcid.org/0000-0002-5739-5416","observed_orcids":["https://orcid.org/0000-0002-5739-5416"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weixin Tang","raw_affiliation_strings":["The University of Chicago;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Chicago;","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101488791","display_name":"Mengjie Chen","orcid":"https://orcid.org/0000-0003-1579-087X","observed_orcids":["https://orcid.org/0000-0003-1579-087X"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mengjie Chen","raw_affiliation_strings":["University of Chicago;"],"raw_orcid":"https://orcid.org/0000-0003-1579-087X","affiliations":[{"raw_affiliation_string":"University of Chicago;","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5160630595","display_name":"Chuan He","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chuan He","raw_affiliation_strings":["Univ. Chicago"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Univ. Chicago","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5160630595"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.7685999870300293,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.7685999870300293,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.14669999480247498,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12610","display_name":"RNA regulation and disease","score":0.029999999329447746,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7594000101089478},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6037999987602234},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.507099986076355},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.4618000090122223},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3898000121116638},{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.37369999289512634},{"id":"https://openalex.org/C21786251","wikidata":"https://www.wikidata.org/wiki/Q14886350","display_name":"RNA editing","level":4,"score":0.36469998955726624},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.35350000858306885},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.32739999890327454},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3260999917984009},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.31369999051094055},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.31150001287460327},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30889999866485596},{"id":"https://openalex.org/C158730165","wikidata":"https://www.wikidata.org/wiki/Q24768845","display_name":"RNA recognition motif","level":5,"score":0.30000001192092896},{"id":"https://openalex.org/C2778323267","wikidata":"https://www.wikidata.org/wiki/Q21118028","display_name":"ADAR","level":5,"score":0.29649999737739563},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.2913999855518341},{"id":"https://openalex.org/C2191507","wikidata":"https://www.wikidata.org/wiki/Q7277185","display_name":"RNA silencing","level":5,"score":0.2906999886035919},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.2833999991416931},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.26489999890327454},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.2515000104904175}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.02.763788","doi":"https://doi.org/10.64898/2026.11.02.763788","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.02.763788","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.02.763788","doi":"https://doi.org/10.64898/2026.11.02.763788","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.02.763788","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"We":[0],"introduce":[1,133],"RAD\u2011seq":[2,22,57],"(RNA":[3],"Accessibility":[4],"via":[5],"Deamination":[6],"sequencing),":[7],"a":[8,54,115,159,168,185],"simple":[9],"and":[10,48,74,83,126,177],"scalable":[11],"method":[12],"that":[13,118,138],"quantifies":[14],"RNA":[15,46,72,79,90,99,120,175,182],"accessibility":[16,80,121,183],"by":[17],"protein":[18,50,112,178],"binding":[19,146],"in":[20,53],"vivo.":[21],"uses":[23],"TadA8.20-mediated":[24],"adenosine":[25,34],"deamination":[26],"to":[27,35,122,144,188],"report":[28,67],"the":[29,40,69,98,108,152],"local":[30,95],"exposure":[31],"of":[32,43,71,78,97,107,174],"each":[33],"its":[36],"molecular":[37],"environment,":[38],"integrating":[39,87],"combined":[41],"effects":[42],"base":[44],"pairing,":[45],"folding,":[47],"RNA\u2011binding":[49],"(RBP)":[51],"occupancy":[52],"single":[55,160],"experiment.":[56,162],"profiles":[58],"recapitulate":[59],"known":[60],"structural":[61],"signatures,":[62],"reveal":[63],"high\u2011resolution":[64],"RBP":[65],"footprints,":[66],"on":[68,192],"influence":[70],"modifications,":[73],"capture":[75],"dynamic":[76],"remodeling":[77],"during":[81],"oxidative":[82],"heat\u2011shock":[84],"stress.":[85],"By":[86],"RAD-seq":[88,140,161,166],"with":[89,141],"Bind-n-Seq":[91],"motifs,":[92],"we":[93,132],"detected":[94],"enrichment":[96],"N6-methyladenosine":[100],"(m6A)":[101],"methyltransferase":[102],"recruiter":[103],"TRA2A":[104,124],"following":[105],"knockdown":[106],"exon":[109],"junction":[110],"anchor":[111],"EIF4A3,":[113],"revealing":[114],"potential":[116],"mechanism":[117],"links":[119],"enhanced":[123],"recruitment":[125],"m6A":[127],"deposition.":[128],"Extending":[129],"this":[130],"framework,":[131],"an":[134],"unsupervised":[135],"statistical":[136],"model":[137],"combines":[139],"motif":[142],"priors":[143],"infer":[145],"landscapes":[147],"for":[148,171],"multiple":[149],"RBPs,":[150],"reproducing":[151],"information":[153],"from":[154,158],"numerous":[155],"CLIP-seq":[156],"datasets":[157],"These":[163],"results":[164],"indicate":[165],"as":[167,184],"generalizable":[169],"approach":[170],"joint":[172],"profiling":[173],"structure":[176],"occupancy,":[179],"defining":[180],"enzymatic":[181],"new":[186],"dimension":[187],"investigate":[189],"regulatory":[190],"elements":[191],"RNA.":[193]},"counts_by_year":[],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2026-11-05T00:00:00"}
