{"doi":"10.1007/978-1-0716-0680-3_12","title":"Transcriptome-Wide Mapping of Protein–RNA Interactions","abstract":null,"journal":"Methods in Molecular Biology","year":2020,"id":593757,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":56484,"name":"Xiaohua Shen","orcid":"0000-0002-4590-1502","position":1,"is_corresponding":false},{"id":653307,"name":"Xianju Bi","orcid":"0000-0001-9061-2622","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Transcriptome-Wide Mapping of Protein–RNA Interactions","abstract":"RNA and RNA-binding proteins (RBPs) control multiple biological processes. The spatial and temporal arrangement of RNAs and RBPs underlies the delicate regulation of these processes. The strategy called CLIP-seq (cross-linking and immunoprecipitation) has been developed to capture endogenous protein-RNA interactions with UV cross-linking followed by immunoprecipitation. Despite the wide use of conventional CLIP-seq method in RBP study, the CLIP experiment is limited by the availability of the high-quality antibodies, potential contaminants from the co-purified RBPs, requirement of isotope manipulation, and potential loss of information during tedious experimental procedure. Here we described a modified CLIP-seq method called <sup>Fbio</sup>CLIP-seq using the FLAG-Biotin tag tandem purification. Through tandem purification and stringent wash condition, almost all the interacting RNA-binding proteins are removed; thus the indirect interacting RNAs mediated by these co-purified RBPs are also decreased. Our <sup>Fbio</sup>CLIP-seq method allows efficient detection of direct protein-bound RNAs without SDS-PAGE and membrane transfer procedure in an isotope-free and protein-specific antibody-free manner.","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"32681512","pmcid":null,"openalex_id":"https://openalex.org/W3042819199","authors":[],"funders":[],"total_grants":0,"fwci":0.0,"citation_percentile":0.12150992,"influential_citations":0,"citation_trend":[],"oa_status":"closed","license":"http://www.springer.com/tdm","oa_locations":[{"url":"http://link.springer.com/content/pdf/10.1007/978-1-0716-0680-3_12","host_type":"publisher"},{"url":"https://doi.org/10.1007/978-1-0716-0680-3_12","host_type":"book series"},{"url":"https://pubmed.ncbi.nlm.nih.gov/32681512","host_type":"repository"}],"fields_of_study":["RNA Research and Splicing","RNA and protein synthesis mechanisms","RNA modifications and cancer","Animals","Cell Line","Cells, Cultured","Cross-Linking Reagents","Humans","Immunoprecipitation","Nucleotide Motifs","Protein Binding","RNA","RNA-Binding Proteins","Sequence Analysis, RNA","Transcriptome","Ultraviolet Rays"],"mesh_terms":["Animals","Cell Line","Cells, Cultured","Cross-Linking Reagents","Humans","Protein Binding","RNA","Ultraviolet Rays","RNA-Binding Proteins","Sequence Analysis, RNA","Immunoprecipitation","Nucleotide Motifs","Transcriptome"],"keywords":["Immunoprecipitation","RNA-binding protein","RNA","Computational biology","Tandem","Biology","Tandem affinity purification","Chemistry","Biochemistry","Gene","Affinity chromatography","Enzyme","Lin28","Protein–rna Interaction","Wdr43","Fbioclip-seq"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-27T12:07:31.040513Z","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":[]}