Prediction of miRNA binding sites in mRNA

Иващенко, А. Т.; Pyrkova, Anna; Niyazova, Raigul; Alybayeva, Aigul; Baskakov, Kirill

doi:10.6026/97320630012237

Cited by 20 publications

(19 citation statements)

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“…The nucleotide sequences of the miRNAs were taken from miRBase v.22 (http://www.mirbase.org/). The miRNA binding sites in the mRNAs of several genes were predicted using the MirTarget program (Ivashchenko et al, 2016). This program defines the following features of miRNA binding to mRNA: a) the start of the initiation of the miRNA binding to the mRNAs from the first nucleotide of the mRNA’s; b) the localization of the miRNA binding sites in the 5’-untranslated region (5’UTR), coding domain sequence (CDS) and 3’-untranslated region (3’UTR) of the mRNAs; c) the free energy of the interaction between miRNA and the mRNA (∆G, kJ/mole); and d) the schemes of nucleotide interactions between miRNAs and mRNAs.…”

Section: Methodsmentioning

confidence: 99%

“…ex-miR involvement in the regulation of recipient gene expression may affect disease (Chin, Fong & Somlo, 2016; Gopinath, 2019; Hou et al, 2018; Jones et al, 2016). The program for searching binding sites in target genes can reliably identify pl-miR and an-miR binding sites regardless of the origin of miRNAs (Ivashchenko et al, 2016), which makes it possible to predict the interaction of pl-miR with hsa-mRNA. We studied the possible interactions of pl-miRs with hsa-mRNA genes after pl-miRs have entered the human body.…”

Section: Introductionmentioning

confidence: 99%

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Human Genes AreIn SilicoPotential Targets For Rice miRNA

Rakhmetullina

Pyrkova

Aisina

et al. 2020

Preprint

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16Exogenous miRNAs enter the human body through food, and their effects on metabolic 17 processes can be considerable. It is important to determine which miRNAs from plants 18 affect the expression of human genes and the extent of their influence. The binding sites of 19 738 osa-miRNAs that interact with 17508 mRNAs of human genes were determined using 20 the MirTarget program. The characteristics of the binding of 46 single osa-miRNAs to 86 21 mRNAs of human genes with a value of free energy (ΔG) interaction equal 94% to 100% 22 from maximum ΔG were established. The findings showed that osa-miR2102-5p, osa-23 miR5075-3p, osa-miR2097-5p, osa-miR2919 targeted the largest number of genes at 38, 36, 24 23, 19 sites, respectively. mRNAs of 86 human genes were identified as targets for 93 osa-25 miRNAs of all family osa-miRNAs with ΔG values equal 94% to 98% from maximum ΔG. 26Each miRNA of the osa-miR156-5p, osa-miR164-5p, osa-miR168-5p, osa-miR395-3p, osa-27 miR396-3p, osa-miR396-5p, osa-miR444-3p, osa-miR529-3p, osa-miR1846-3p, osa-28 miR2907-3p families had binding sites in mRNAs of several human target genes. The 29 binding sites of osa-miRNAs in mRNAs of the target genes for each family of osa-miRNAs 30 were conserved when compared to flanking nucleotide sequences. mRNA human genes of 31 osa-miRNAs are candidate genes of cancer, cardiovascular and neurodegenerative diseases.32 33 104genes. Each of the 35 miRNAs could bind to mRNAs of one target gene, six miRNAs had targets 105 with two genes, and four miRNAs had three target genes with a value ΔG/ΔGm equal to 94-106 98%. miR2102-5p had 11 target genes with a value ΔG/ΔGm of 94-100%, and the free energy of 107 the interaction of the miRNAs with the mRNAs of these genes varied from -115 kJ/mole to -121 108 4 kJ/mole. The miR2102-5p binding sites were located mainly in the 5'UTR, which suggests that 109 they have a role in the early inhibition of the translation process. However, this property of 110 miR2102-5p indicates the need to control its plant food-derived concentration in the human 111 body. 19 target genes were associated with miR2919. miR5075-3p could bind to three mRNAs at 112 binding sites located in the coding domain sequence and the 5'-untranslated region. The high-113 affinity binding sites were located in the 5'UTR and CDS of the mRNAs with the ΔG/ΔGm value 114 was 94-98%. 17 miRNA binding sites were located in 5'UTR, 39 in CDS and 33 in 3'-115 untranslated region. Therefore, monitoring the concentrations of miR2102-5p, miR2919 and 116 miR5075-3p in human biological fluids is also necessary. 117 118 122 development of cancer of various types: ENAH, MAPT, PRKCE, PRRT2, RBMS2, RHOBTB2, 123 RPS6KA5 and ZFHX3 -breast cancer (Aisina et al., 2019); ADAMTS5, PRAPRGG1A, PVR, 124 SPRY4 -colorectal cancer; CHSY1 -colorectal cancer and hepatocellular carcinoma; PPM1F, 125 FXYD6, DUT, FAM83H -hepatocellular carcinoma; HK2 -gallbladder cancer and leukaemia; 126 C19orf6 -ovarian carcinoma; AFAP1 -oesophageal adenocarcinoma; IOGAP1 -pancreatic 127 6 ductal adenoca...

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Human Genes AreIn SilicoPotential Targets For Rice miRNA

Rakhmetullina

Pyrkova

Aisina

et al. 2020

Preprint

Self Cite

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“…The miRNA nucleotide sequences were borrowed from miRBase (http://www.mirbase.org/). The free energy (ΔG) of miRNA binding, the position and schemes of potential binding sites were calculated using the MirTarget program (Ivashchenko et al, 2016). ΔGm for miRNA was defined as the free energy of miRNA binding with its fully complementary nucleotide sequence.…”

Section: Methodsmentioning

confidence: 99%

Features of the interaction of miRNAs with genes of the rice MYB family under stress

2019

Plant Genetic Resources for Breeding and Producing Functional Nutraceutical Food

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Data on the involvement of miRNA in the plant response to stress factors are considered. The MYB family of transcription factors plays a great role in the plant development, metabolism and responses to biotic and abiotic stress. The free energy of miRNA binding, the value of free energy of interaction, the position and schemes of potential binding sites were calculated using the MirTarget program. To identify miRNAs whose targets are genes in the MYB family, a search for binding sites of 738 miRNAs in mRNAs of 124 MYB family genes of Oryza sativa was performed. 16 genes were identified as targets for 11 miRNAs. The results show that miRNA can regulate the expression of most MYB genes and thus affect productivity and sustainability.

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“…The n�cleoti�e seq�ences of mRNAs of 102 h�man genes were ta�en from the GenBan� �atabase (http://www.ncbi.nlm.nih.gov), an� 2567 miRNAs were ta�en from miRBase (http://mirbase.org). The search for target genes for miRNA was performe� �sing the MirTarget program [18]. This program �efines the feat�res of bin�ing: a) the localization of miRNA bin�ing sites in the 5'UTRs, the CDSs an� the 3'UTRs of the mRNAs; b) the free energy of hybri�ization (∆G, �J/mole).…”

Section: Methodsmentioning

confidence: 99%

The prediction of miRNAs binding sites in CDS mRNA genes having trinucleotide repeats

Belkozhayev¹,

Niyazova²,

Иващенко³

2019

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In human diseases and physiology, the function of miRNAs is expanding; however, especially nucleotide repeats disorder the majority of miRNA-driven regulatory structure is remaining uncertain. The aim of this work is to reveal which candidate genes of nucleotide repeat diseases and in which degrees can interact with miRNA. We present results on the interaction of 2567 miRNAs with mRNA 102 candidate genes of having nucleotide repeats using the MirTarget program. miRNAs binding sites in the CDS mRNAs of 36 genes from 102 candidate genes with nucleotide repeats have been shown. Among miRNAs that bind with high energy to mRNA genes with nucleotide repeats, we choose five miRNAs that have binding sites for two or more genes: miR-3656 (ARX, EP400, HTT, NCOR2); miR-3960 (ARX, CACNA1I, HTT); miR-1322 (ATN, EP400, GIGYF2, HTT, NCOR2); miR-1281 (CACNA1I, HRC, HTT); miR-4279 (CACNA1I, NCOR2). It was determined that considering miRNAs binding sites are located mainly in regions with CAG, GCG, GAG repeats. Neurological disorders are known to be caused by an increased number of CAG, GCG, GAG repeats, typically in coding regions of otherwise unrelated proteins. Better understanding of interaction specificity of miRNAs and genes promises to offer further in sights into the pathogenic pathways of trinucleotide repeats expansion disorders.

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Prediction of miRNA binding sites in mRNA

Cited by 20 publications

References 5 publications

Human Genes AreIn SilicoPotential Targets For Rice miRNA

Human Genes AreIn SilicoPotential Targets For Rice miRNA

Features of the interaction of miRNAs with genes of the rice MYB family under stress

The prediction of miRNAs binding sites in CDS mRNA genes having trinucleotide repeats

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