Computational analysis of 3′UTR region of CASP3 with respect to miRSNPs and SNPs in targetting miRNAs

Ergün, Sercan; Öztuzcu, Serdar

doi:10.1016/j.compbiolchem.2014.10.004

Cited by 5 publications

(2 citation statements)

References 61 publications

(62 reference statements)

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“…Ten unique online databases including DIANA Tools, miRTarBase, Miranda, TargetScan, miRDB, miRecords, miRcode, miRO, miRWalk, and MiCosm were used for the detection of miRNA targeting the 3′UTR of the APOL1 gene, and then we followed several algorithms and calculations below methodologies provided (Ergun and Oztuzcu 2014;Safdar et al 2020). Accordingly, the scanning of all miRNA targets can be performed without missing any of them using the multiple databases below.…”

Section: Screening Of Mirna Targeting 3′utr Of Apol1 Genementioning

confidence: 99%

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SNPs at 3′UTR of APOL1 and miR-6741-3p target sites associated with kidney diseases more susceptible to SARS-COV-2 infection: in silco and in vitro studies

et al. 2021

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Acute Kidney Injury (AKI) is a common manifestation of COVID-19 and several cases have been reported in the setting of the high-risk APOL1 genotype (common genetic variants). This increases the likelihood that African American people with the high-risk genotype APOL1 are at increased risk for kidney disease in the COVID-19 environment. Single-nucleotide polymorphisms (SNPs) are found in various microRNAs (miRNAs) and target genes change the miRNA activity that leads to different diseases. Evidence has shown that SNPs increase/decrease the effectiveness of the interaction between miRNAs and disease-related target genes. The aim of this study is not only to identify miRSNPs on the APOL1 gene and SNPs in miRNA genes targeting 3′UTR but also to evaluate the effect of these gene variations in kidney patients and their association with SARS-COV-2 infection. In 3′UTR of the APOL1 gene, we detected 96 miRNA binding sites and 35 different SNPs with 10 different online software in the binding sites of the miRNA (in silico). Also we studied gene expression of patients and control samples by using qRT-PCR (in vitro). In silico study, the binding site of miR-6741-3p on APOL1 has two SNPs (rs1288875001, G > C; rs1452517383, A > C) on APOL1 3′UTR, and its genomic sequence is the same nucleotide as rs1288875001. Similarly, two other SNPs (rs1142591, T > A; rs376326225, G > A) were identified in the binding sites of miR-6741-3p at the first position. Here, the miRSNP (rs1288875001) in APOL1 3′UTR and SNP (rs376326225) in the miR-6741-3p genomic sequence are cross-matched in the same binding region. In vitro study, the relative expression levels were calculated by the 2 −ΔΔCt method & Mann-Whitney U test. The expression of APOL1 gene was different in chronic kidney patients along with COVID-19. By these results, APOL1 expression was found lower in patients than healthy (p < 0.05) in kidney patients along with COVID-19. In addition, miR-6741-3p targets many APOL1-related genes (TLR7,

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Section: Screening Of Mirna Targeting 3′utr Of Apol1 Genementioning

confidence: 99%

“…SNPs in the genes of miRNAs and miRSNPs in the 3′UTR of APOL1 were matched (Table 2). Cross-match SNPs were searched as done by Ergun and Oztuzcu (2014); Safdar et al (2020). Matched and unmatched SNPs are shown and interpreted for APOL1 activity with kidney diseases that has susceptibility to COVID-19.…”

Section: Screening Of Mirsnpsmentioning

confidence: 99%