Analysis of miRNAs Targeting 3'UTR of H2AFX Gene: a General in Silico Approach.
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.
Saverio
S
Sabina
CNR Istituto di Fisiologia Clinica, Via Moruzzi, 1 - 56124 Pisa, Italy. vecoli@ifc.cnr.it.
Cecilia
C
Vecoli
Andrea
A
Borghini
Roberto
R
Guarino
Maria G
MG
Andreassi
D020413:3' Untranslated Regions; D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D030541:Databases, Genetic; D006657:Histones / Q000235:genetics*; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide
D020413:3' Untranslated Regions; C468783:H2AX protein, human; D006657:Histones; D035683:MicroRNAs