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

MicroRNA
Saverio SabinaMaria Grazia Andreassi

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 ...Continue Reading

Citations

Apr 22, 2015·Environment International·Somnath Paul, Ashok K Giri
Apr 28, 2016·Revista Española De Cardiología·Silvia PulignaniMaria Grazia Andreassi
May 16, 2017·Clinica Chimica Acta; International Journal of Clinical Chemistry·Sellamuthu KarthiBalasubramaniem Ashokkumar
Aug 23, 2020·International Journal of Molecular Sciences·Ombretta MelaiuDoriana Fruci
Jan 17, 2019·Journal of Clinical Medicine·Alessandro TonacciSebastiano Gangemi
Oct 31, 2020·Personalized Medicine·Cecilia VecoliMaria Grazia Andreassi

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