{"doi":"10.1016/j.isci.2025.113299","title":"SELEX identifies high-affinity RNA targets for chromatin-binding proteins PARP1 and MeCP2","abstract":"Recent discoveries showed that some chromatin-binding proteins also interact with RNA to regulate gene expression. Poly (ADP-ribose) polymerase 1 (PARP1) and methyl-CpG binding protein 2 (MeCP2) are two chromatin-associated, DNA-binding proteins that play central roles in gene expression, DNA damage response, and epigenetic regulation. Both proteins possess RNA-binding properties, but the mechanism by which PARP1 and MeCP2 recognize RNA-binding sites remains unclear. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach with a random 70-mer RNA library, we uncovered that PARP1 preferentially binds guanine-rich RNAs, while MeCP2 favors cytosine-rich targets. However, neither protein recognizes a consensus (linear) RNA sequence motif. Instead, PARP1 targets RNAs with long stems and small loops, while MeCP2 targets RNAs with large loops or bulges and intricate multi-stem structures. These findings suggest that both proteins rely on distinct RNA structural features, highlighting the structural versatility of RNA as a regulatory element.","journal":"iScience","year":2025,"id":524072,"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":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9548,"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":1112384,"name":"Kalpani de Silva","orcid":"0000-0001-5652-4741","position":1,"is_corresponding":false},{"id":882271,"name":"Darrell P. Chandler","orcid":"0000-0002-6462-0941","position":2,"is_corresponding":false},{"id":1397567,"name":"Richard N Cassidy","orcid":null,"position":3,"is_corresponding":false},{"id":75067,"name":"Kalina Andreeva","orcid":"0000-0002-5206-532X","position":4,"is_corresponding":false},{"id":948100,"name":"Héjer Dhahri","orcid":"0009-0007-8607-2222","position":5,"is_corresponding":false},{"id":250188,"name":"Eric C. Rouchka","orcid":"0000-0003-3487-6572","position":6,"is_corresponding":false},{"id":17129,"name":"Yvonne Fondufe‐Mittendorf","orcid":"0000-0002-2551-9920","position":7,"is_corresponding":false},{"id":1397566,"name":"Manana Melikishvili","orcid":null,"position":0,"is_corresponding":true}],"reference_count":73,"raw_metadata":null,"created_at":"2026-07-19T02:50:07.396155Z","pmid":"40894892","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":[]}