{"doi":"10.1101/2022.12.02.518772","title":"Disease-Associated Non-Coding Variants Alter NKX2-5 DNA-Binding Affinity","abstract":"1. Abstract Genome-wide association studies (GWAS) have mapped over 90% of disease- or trait-associated variants within the non-coding genome, like cis -regulatory elements (CREs). Non-coding single nucleotide polymorphisms (SNPs) are genomic variants that can change how DNA-binding regulatory proteins, like transcription factors (TFs), interact with the genome and regulate gene expression. NKX2-5 is a TF essential for proper heart development, and mutations affecting its function have been associated with congenital heart diseases (CHDs). However, establishing a causal mechanism between non-coding genomic variants and human disease remains challenging. To address this challenge, we identified 8,475 SNPs predicted to alter NKX2-5 DNA- binding using a position weight matrix (PWM)-based predictive model. Five variants were prioritized for in vitro validation; four of them are associated with traits and diseases that impact cardiovascular health. The impact of these variants on NKX2-5 binding was evaluated with electrophoretic mobility shift assay (EMSA) using recombinantly expressed and purified human NKX2-5 homeodomain. Binding curves were constructed to determine changes in binding between variant and reference alleles. Variants rs7350789, rs7719885, rs747334, and rs3892630 increased binding affinity, whereas rs61216514 decreased binding by NKX2-5 when compared to the reference genome. Our findings suggest that differential TF-DNA binding affinity can be key in establishing a causal mechanism of pathogenic variants. Abstract Figure","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":313552,"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":0.9444,"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":1011781,"name":"Alejandro Rivera-Madera","orcid":"0000-0003-0037-4822","position":1,"is_corresponding":false},{"id":1002385,"name":"Diego A. Pomales‐Matos","orcid":"0000-0002-4129-7678","position":2,"is_corresponding":false},{"id":1011782,"name":"Leandro Sanabria-Alberto","orcid":"0009-0004-8203-4139","position":3,"is_corresponding":false},{"id":1012315,"name":"Brittany M. Rosario-Cañuelas","orcid":null,"position":4,"is_corresponding":false},{"id":826964,"name":"Jessica M. Rodríguez-Ríos","orcid":"0000-0001-9845-9642","position":5,"is_corresponding":false},{"id":828125,"name":"Emmanuel A. Carrasquillo‐Dones","orcid":null,"position":6,"is_corresponding":false},{"id":826965,"name":"José A. Rodríguez‐Martínez","orcid":"0000-0002-1191-2887","position":7,"is_corresponding":false},{"id":1011780,"name":"Edwin G. Peña-Martínez","orcid":"0000-0002-9076-528X","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":null,"created_at":"2026-07-19T00:33:44.454239Z","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":[]}