{"doi":"10.1101/2025.08.05.668543","title":"CLASHub: an integrated database and analytical platform for microRNA-target interactions","abstract":"Abstract MicroRNAs (miRNAs) are ∼22-nucleotide RNAs that regulate gene expression, critical for development and disease. Residing in Argonaute (AGO) proteins, miRNAs target messenger RNAs via complementary base-pairing. Current miRNA-target databases rely on indirect data from AGO crosslinking immunoprecipitation (AGO-CLIP). In contrast, CLASH (Crosslinking, Ligation, and Sequencing of Hybrids) employs proximity ligation within AGO complexes, providing direct miRNA-target interaction evidence. Existing CLASH datasets remain limited to few human and mouse samples. CLASHub integrates CLASH-defined interactions with gene and miRNA expression data from human, mouse, Drosophila , and C. elegans , covering over 20 cell types and tissues. The datasets also include samples with ZSWIM8-knockout, an essential component in target RNA-directed miRNA degradation (TDMD)—a specialized mechanism for miRNA turnover triggered by basepairing with specific target RNA—thereby providing unique insights into miRNA turnover mechanisms. CLASHub also features a user-friendly Analyzer interface for CLASH, RNA-seq, miRNA-seq, and cumulative fraction curve analysis. Leveraging these tools, we uncovered a novel TDMD “trigger” for miR-335-3p degradation in ATP6V1G1 ’s 3ʹ UTR. Thus, CLASHub offers an online platform for miRNA research, enabling discovery of novel miRNA targets and triggers across diverse contexts. Graphical abstract","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":558719,"datarank":0.10998406793578726,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.006011990851795443,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.006011990851795443,"corpus_percentile":27.663030865630077,"corpus_rank":9352,"citation_count":1,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9092,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":720320,"name":"Peike Sheng","orcid":"0000-0003-1324-8606","position":1,"is_corresponding":false},{"id":720318,"name":"Nicholas M. Hiers","orcid":"0000-0003-0996-364X","position":2,"is_corresponding":false},{"id":720319,"name":"Tianqi Li","orcid":"0000-0003-3919-0211","position":3,"is_corresponding":false},{"id":1178398,"name":"Acadia L. Grimme","orcid":"0000-0003-1474-015X","position":4,"is_corresponding":false},{"id":1056002,"name":"Yuzhi Wang","orcid":"0000-0002-3443-9527","position":5,"is_corresponding":false},{"id":1060841,"name":"Conner M. Traugot","orcid":"0009-0001-9550-6754","position":6,"is_corresponding":false},{"id":720323,"name":"Mingyi Xie","orcid":"0000-0001-7955-197X","position":7,"is_corresponding":false},{"id":1454501,"name":"Lu Li","orcid":"0000-0002-3097-1954","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":null,"created_at":"2026-07-19T02:55:30.312295Z","pmid":"40799581","pmcid":"PMC12340844","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":[]}