Analysis of miRNAs Targeting 3’UTR of H2AFX Gene: a General in Silico Approach

Author(s): Saverio Sabina, Cecilia Vecoli, Andrea Borghini, Roberto Guarino, Maria G. Andreassi

Journal Name: MicroRNA

Volume 4 , Issue 1 , 2015

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Graphical Abstract:


MiRNAs are gene (post-transcriptional) regulators that bind the 3’UTR of target genes. Single-nucleotide polymorphisms (SNPs) located within a miRNA binding site can impact miRNAdependent gene regulation by weakening or reinforcing the microRNA:mRNA bond. We present a general in silico approach enabling researchers to “predict” which of the several SNPs of 3’UTR of H2AFX gene can mainly affect its regulation. H2AFX gene encodes a member of the H2A histone family which is central in the detection of and response to DNA double-strand breaks. All the 17 common SNPs located within the 3’UTR of H2AFX gene were analyzed for putative miRNA-binding sites by using different databases (such as dbSNP and miRBase) and pre-existing algorithms (such as MicroSNiPer and RNAcofold) in order to calculate the minimum free energies of hybridization of the microRNA:mRNA duplex, for both the wild-type and mutant alleles. The difference in these energies was also calculated. Since in each tissue one target sequence can bind only one miRNA at a time, the sum of all the difference of energies can be considered a relevant parameter for predicting the importance of a SNP with respect to miRNA regulation. We used tertiles to classify the SNPs and provide a priority list based on their theoretically strongest impact on miRNA binding. By using the described approach, we provided the basis for a reasoned, user-friendly algorithm-driven selection of SNPs impacting miRNA biology. The proposed method is helpful for selecting SNPs having a more powerful (putative) biological function, minimizing workflow and costs for experimental and clinical investigations.

Keywords: 3’UTR, H2AFX, miRNA, prioritization, single-nucleotide polymorphism, SNP.

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Article Details

Year: 2015
Published on: 27 February, 2015
Page: [41 - 49]
Pages: 9
DOI: 10.2174/2211536604666150227232003

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