Dataset Information

Circular RNAs are depleted of polymorphisms at microRNA binding sites.

ABSTRACT:

Motivation

Circular RNAs (circRNAs) are an abundant class of highly stable RNAs that can affect gene regulation by binding and preventing microRNAs (miRNAs) from regulating their messenger RNA (mRNA) targets. Mammals have thousands of circRNAs with predicted miRNA binding sites, but only two circRNAs have been verified as being actual miRNA sponges. As it is unclear whether these thousands of predicted miRNA binding sites are functional, we investigated whether miRNA seed sites within human circRNAs are under selective pressure.

Results

Using SNP data from the 1000 Genomes Project, we found a significant decrease in SNP density at miRNA seed sites compared with flanking sequences and random sites. This decrease was similar to that of miRNA seed sites in 3' untranslated regions, suggesting that many of the predicted miRNA binding sites in circRNAs are functional and under similar selective pressure as miRNA binding sites in mRNAs.

SUBMITTER: Thomas LF

PROVIDER: S-EPMC4207428 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Circular RNAs are depleted of polymorphisms at microRNA binding sites.

Thomas Laurent F LF Sætrom Pål P

Bioinformatics (Oxford, England) 20140424 16

<h4>Motivation</h4>Circular RNAs (circRNAs) are an abundant class of highly stable RNAs that can affect gene regulation by binding and preventing microRNAs (miRNAs) from regulating their messenger RNA (mRNA) targets. Mammals have thousands of circRNAs with predicted miRNA binding sites, but only two circRNAs have been verified as being actual miRNA sponges. As it is unclear whether these thousands of predicted miRNA binding sites are functional, we investigated whether miRNA seed sites within hu ...[more]

PMID: 24764460

Similar Datasets

Project description:BACKGROUND: MicroRNA dysregulation is a common event in leukemia. Polymorphisms in microRNA-binding sites (miRSNPs) in target genes may alter the strength of microRNA interaction with target transcripts thereby affecting protein levels. In this study we aimed at identifying miRSNPs associated with leukemia risk and assessing impact of these miRSNPs on miRNA binding to target transcripts. METHODS: We analyzed with specialized algorithms the 3' untranslated regions of 137 leukemia-associated genes and identified 111 putative miRSNPs, of which 10 were chosen for further investigation. We genotyped patients with acute myeloid leukemia (AML, n?=?87), chronic myeloid leukemia (CML, n?=?140), childhood acute lymphoblastic leukemia (ALL, n?=?101) and healthy controls (n?=?471). Association between SNPs and leukemia risk was calculated by estimating odds ratios in the multivariate logistic regression analysis. For miRSNPs that were associated with leukemia risk we performed luciferase reporter assays to examine whether they influence miRNA binding. RESULTS: Here we show that variant alleles of TLX1_rs2742038 and ETV6_rs1573613 were associated with increased risk of childhood ALL (OR (95% CI)?=?3.97 (1.43-11.02) and 1.9 (1.16-3.11), respectively), while PML_rs9479 was associated with decreased ALL risk (OR?=?0.55 (0.36-0.86). In adult myeloid leukemias we found significant associations between the variant allele of PML_rs9479 and decreased AML risk (OR?=?0.61 (0.38-0.97), and between variant alleles of IRF8_ rs10514611 and ARHGAP26_rs187729 and increased CML risk (OR?=?2.4 (1.12-5.15) and 1.63 (1.07-2.47), respectively). Moreover, we observed a significant trend for an increasing ALL and CML risk with the growing number of risk genotypes with OR?=?13.91 (4.38-44.11) for carriers of ?3 risk genotypes in ALL and OR?=?4.9 (1.27-18.85) for carriers of 2 risk genotypes in CML. Luciferase reporter assays revealed that the C allele of ARHGAP26_rs187729 creates an illegitimate binding site for miR-18a-3p, while the A allele of PML_rs9479 enhances binding of miR-510-5p and the C allele of ETV6_rs1573613 weakens binding of miR-34c-5p and miR-449b-5p. CONCLUSIONS: Our study implicates that microRNA-binding site polymorphisms modulate leukemia risk by interfering with the miRNA-mediated regulation. Our findings underscore the significance of variability in 3' untranslated regions in leukemia.

Dataset Information

Circular RNAs are depleted of polymorphisms at microRNA binding sites.

Motivation

Results

Publications

Circular RNAs are depleted of polymorphisms at microRNA binding sites.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets