{"doi":"10.1093/nar/gkac414","title":"Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats","abstract":"Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on the RNA tertiary structure. Previous studies have determined the two-dimensional secondary structures of the sense and antisense human LincRNA-p21 AluSx1 IRs using SHAPE. However, there were no insights into its three-dimensional structure. Therefore, we in vitro transcribed the sense and antisense regions of LincRNA-p21 AluSx1 Inverted Repeats (IRs) and performed analytical ultracentrifugation, size exclusion chromatography, light scattering, and small angle X-ray scattering (SAXS) studies. Based on these studies, we determined low-resolution, three-dimensional structures of sense and antisense LincRNA-p21. By adapting previously known two-dimensional information, we calculated their sense and antisense high-resolution models and determined that they agree with the low-resolution structures determined using SAXS. Thus, our integrated approach provides insights into the structure of LincRNA-p21 Alu IRs. Our study also offers a viable pipeline for combining the secondary structure information with biophysical and computational studies to obtain high-resolution atomistic models for long noncoding RNAs.","journal":"Nucleic Acids Research","year":2022,"id":256487,"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":19,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9458,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":301765,"name":"Tyler Mrozowich","orcid":"0000-0002-1077-9682","position":1,"is_corresponding":false},{"id":818957,"name":"Maulik D. Badmalia","orcid":"0000-0002-3384-6550","position":2,"is_corresponding":false},{"id":819418,"name":"Mitchell Geeraert","orcid":null,"position":3,"is_corresponding":false},{"id":818958,"name":"Angela Frederickson","orcid":"0009-0008-2967-4769","position":4,"is_corresponding":false},{"id":416051,"name":"Amy Henrickson","orcid":"0000-0003-3266-5202","position":5,"is_corresponding":false},{"id":399433,"name":"Borries Demeler","orcid":"0000-0002-2414-9518","position":6,"is_corresponding":false},{"id":764445,"name":"Michael T. Wolfinger","orcid":"0000-0003-0925-5205","position":7,"is_corresponding":false},{"id":301766,"name":"Trushar R. Patel","orcid":"0000-0003-0627-2923","position":8,"is_corresponding":false},{"id":818956,"name":"Michael H D’Souza","orcid":"0000-0001-8709-4019","position":0,"is_corresponding":true}],"reference_count":130,"raw_metadata":null,"created_at":"2026-07-19T00:25:25.728895Z","pmid":"35639511","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":[]}