Genomic architecture of selected schizophrenia-associated regions: co-location of non-coding and protein-coding genes

Abstract Background Non-coding RNAs (ncRNAs) are increasingly recognized as important factors in the progression of schizophrenia (SZ); however, their involvement in disease etiology remains incompletely understood. This study aimed to characterize the genomic architecture of selected SZ-associated regions by examining the co-location of ncRNA and protein-coding genes and to explore sequence variants within these regions for potential associations with clinical outcomes. Methods Genomic regions containing co-located protein-coding and ncRNA genes, specifically those with overlapping exonic sequences, were identified. Functional annotations of the selected SNPs were obtained from Ensembl, including predicted functional effects (SIFT, PolyPhen, CADD) and regulatory features. Association analyses were performed in SZ patients and controls, testing associations with disease occurrence, treatment response and psychopathological symptoms assessed by the Brief Psychiatric Rating Scale (BPRS). Results Among 21 selected SZ-associated protein-coding genes (SZGs), seven showed genomic co-location with ncRNA genes. Exonic co-location was identified in four regions: BDNF/BDNF-AS, DDC/DDC-AS1, GNAS/GNAS-AS1 and HTR5A/HTR5A-AS1. Four SNPs within these co-located regions were selected for analysis: rs1800900 (GNAS/GNAS-AS1) and rs6265, rs11030101 and rs28722151 (BDNF/BDNF-AS). None of these associations reached statistical significance after multiple comparison adjustment. Functional annotations indicated that some variants are located in constrained elements, overlap regulatory features or have predicted deleterious effects, suggesting functional relevance. Conclusions This exploratory study provides insights into the genomic architecture of SZ-associated regions, particularly the co-location between protein-coding SZGs and ncRNAs. It highlights the complexity of the SZ-associated genomic architecture and provides a framework for SNP prioritization and future genomic and functional studies in SZ and related disorders.