Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and binding sites

• Published in: BMC cancer 2024-09, Vol.24 (1), p.1147-12, Article 1147
• Main Authors: Mustafa, Aneela, Shabbir, Maria, Badshah, Yasmin, Khan, Khushbukhat, Abid, Fizzah, Trembley, Janeen H, Afsar, Tayyaba, Almajwal, Ali, Razak, Suhail
• Format: Article
• Language: English
• Subjects: 3' Untranslated regions; 3' Untranslated Regions - genetics; 5' Untranslated Regions; 5' Untranslated Regions - genetics; Analysis; Binding Sites; Cancer; Colorectal cancer; Data collection; Diabetes; Diagnosis; Disease; DNA methylation; Gene expression; Gene polymorphism; Genetic aspects; Genetic diversity; Genetic polymorphisms; Genomes; Genomic analysis; Homeostasis; Humans; In-silico tools; Kinases; Medical prognosis; MicroRNAs; MicroRNAs - genetics; miRNA; mRNA stability; Mutation; Neurological diseases; Non-coding SNPs; Nucleic Acid Conformation; Oncological disorders; Phenotypes; Phenotypic variations; Polymorphism, Single Nucleotide; PRKCZ; Prostate cancer; Protein kinase C; Protein Kinase C - genetics; Protein Kinase C - metabolism; Protein kinases; Protein structure; Protein-serine/threonine kinase; Proteins; Risk factors; RNA Stability - genetics; RNA, Messenger - genetics; RNA, Messenger - metabolism; Secondary structure; Therapeutic targets; Transcription factors; Untranslated Regions - genetics; UTR
• ISSN: 1471-2407; 1471-2407
• DOI: 10.1186/s12885-024-12900-8

Variations in untranslated regions (UTR) alter regulatory pathways impacting phenotype, disease onset, and course of disease. Protein kinase C Zeta (PRKCZ), a serine-threonine kinase, is implicated in cardiovascular, neurological and oncological disorders. Due to limited research on PRKCZ, this study aimed to investigate the impact of UTR genetic variants' on binding sites for transcription factors and miRNA. RNA secondary structure, eQTLs, and variation tolerance analysis were also part of the study. The data related to PRKCZ gene variants was downloaded from the Ensembl genome browser, COSMIC and gnomAD. The RegulomeDB database was used to assess the functional impact of 5' UTR and 3'UTR variants. The analysis of the transcription binding sites (TFBS) was done through the Alibaba tool, and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) was employed to identify pathways associated with PRKCZ. To predict the effect of variants on microRNA binding sites, PolymiRTS was utilized for 3' UTR variants, and the SNPinfo tool was used for 5' UTR variants. The results obtained indicated that a total of 24 variants present in the 3' UTR and 25 variants present in the 5' UTR were most detrimental. TFBS analysis revealed that 5' UTR variants added YY1, repressor, and Oct1, whereas 3' UTR variants added AP-2alpha, AhR, Da, GR, and USF binding sites. The study predicted TFs that influenced PRKCZ expression. RNA secondary structure analysis showed that eight 5' UTR and six 3' UTR altered the RNA structure by either removal or addition of the stem-loop. The microRNA binding site analysis highlighted that seven 3' UTR and one 5' UTR variant altered the conserved site and also created new binding sites. eQTLs analysis showed that one variant was associated with PRKCZ expression in the lung and thyroid. The variation tolerance analysis revealed that PRKCZ was an intolerant gene. This study laid the groundwork for future studies aimed at targeting PRKCZ as a therapeutic target.