{"doi":"10.3390/ijms24109033","title":"Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae","abstract":"<jats:p>As a master regulator in cells, RNA-binding protein (RBP) plays critical roles in organismal development, metabolism and various diseases. It regulates gene expression at various levels mostly by specific recognition of target RNA. The traditional CLIP-seq method to detect transcriptome-wide RNA targets of RBP is less efficient in yeast due to the low UV transmissivity of their cell walls. Here, we established an efficient HyperTRIBE (Targets of RNA-binding proteins Identified By Editing) in yeast, by fusing an RBP to the hyper-active catalytic domain of human RNA editing enzyme ADAR2 and expressing the fusion protein in yeast cells. The target transcripts of RBP were marked with new RNA editing events and identified by high-throughput sequencing. We successfully applied HyperTRIBE to identifying the RNA targets of two yeast RBPs, KHD1 and BFR1. The antibody-free HyperTRIBE has competitive advantages including a low background, high sensitivity and reproducibility, as well as a simple library preparation procedure, providing a reliable strategy for RBP target identification in Saccharomyces cerevisiae.</jats:p>","journal":"International Journal of Molecular Sciences","year":2023,"id":608790,"datarank":0.3453877639491069,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.0,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"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":1123657,"name":"Chong Li","orcid":"0000-0002-7496-4852","position":1,"is_corresponding":false},{"id":1563955,"name":"Pengkun Sun","orcid":null,"position":2,"is_corresponding":false},{"id":1563956,"name":"Miaomiao Yang","orcid":null,"position":3,"is_corresponding":false},{"id":1563957,"name":"Yansong Ding","orcid":null,"position":4,"is_corresponding":false},{"id":105748,"name":"Wei Song","orcid":"0000-0002-0983-0823","position":5,"is_corresponding":false},{"id":1563958,"name":"Yunxiao Jia","orcid":null,"position":6,"is_corresponding":false},{"id":621381,"name":"Liqun Yu","orcid":"0000-0002-1099-5860","position":7,"is_corresponding":false},{"id":1563959,"name":"Yanming Lu","orcid":null,"position":8,"is_corresponding":false},{"id":352541,"name":"Hua Jin","orcid":"0000-0001-9829-0306","position":9,"is_corresponding":false},{"id":1563954,"name":"Weilan Piao","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae","abstract":"<jats:p>As a master regulator in cells, RNA-binding protein (RBP) plays critical roles in organismal development, metabolism and various diseases. It regulates gene expression at various levels mostly by specific recognition of target RNA. The traditional CLIP-seq method to detect transcriptome-wide RNA targets of RBP is less efficient in yeast due to the low UV transmissivity of their cell walls. Here, we established an efficient HyperTRIBE (Targets of RNA-binding proteins Identified By Editing) in yeast, by fusing an RBP to the hyper-active catalytic domain of human RNA editing enzyme ADAR2 and expressing the fusion protein in yeast cells. The target transcripts of RBP were marked with new RNA editing events and identified by high-throughput sequencing. We successfully applied HyperTRIBE to identifying the RNA targets of two yeast RBPs, KHD1 and BFR1. The antibody-free HyperTRIBE has competitive advantages including a low background, high sensitivity and reproducibility, as well as a simple library preparation procedure, providing a reliable strategy for RBP target identification in Saccharomyces cerevisiae.</jats:p>","is_dataset_classified":null,"base_score":2.302585092994046,"endowment":2.302585092994046,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"37240377","pmcid":"PMC10218906","openalex_id":"https://openalex.org/W4377241107","authors":[],"funders":[{"funder_name":"National Natural Science Foundation of China","grant_id":"31970622","title":null}],"total_grants":1,"fwci":0.8426,"citation_percentile":0.69613571,"influential_citations":0,"citation_trend":[{"year":2024,"count":2},{"year":2025,"count":5},{"year":2026,"count":2}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.mdpi.com/1422-0067/24/10/9033/pdf?version=1684563899","host_type":"journal"},{"url":"https://www.mdpi.com/1422-0067/24/10/9033/pdf?version=1684563899","host_type":"publisher"},{"url":"https://www.mdpi.com/1422-0067/24/10/9033/pdf","host_type":"publisher"},{"url":"https://doi.org/10.3390/ijms24109033","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/37240377","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10218906","host_type":"repository"},{"url":"https://dx.doi.org/10.3390/ijms24109033","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10218906/pdf/ijms-24-09033.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC10218906","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC10218906?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["RNA Research and Splicing","RNA regulation and disease","RNA and protein synthesis mechanisms","Humans","Saccharomyces cerevisiae","Reproducibility of Results","Binding Sites","RNA-Binding Proteins","RNA","Repressor Proteins","Saccharomyces cerevisiae Proteins"],"mesh_terms":["Binding Sites","Humans","Repressor Proteins","RNA","Saccharomyces cerevisiae","Reproducibility of Results","RNA-Binding Proteins","Saccharomyces cerevisiae Proteins"],"keywords":["RNA","RNA-binding protein","Saccharomyces cerevisiae","Yeast","Biology","Computational biology","Transcriptome","RNA editing","Tandem affinity purification","Gene expression","Gene","Biochemistry","Enzyme","Affinity chromatography","Rna-binding Protein (Rbp)","Bfr1","Hypertribe","Khd1"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-30T22:13:09.435123Z","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":[]}