MiR-3960 binding sites with mRNA of human genes

Иващенко, А. Т.; Berillo, Olga; Pyrkova, Anna; Niyazova, Raigul; Atambayeva, Shara

doi:10.6026/97320630010423

Cited by 29 publications

(27 citation statements)

References 14 publications

(16 reference statements)

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“…The search for miRNA target genes was carried out in the MirTarget program (Ivashchenko et al, 2014). The program defines the origin of miRNA binding sites with mRNA, the location of sites in the 5′-untranslated region (5′UTR), the protein-coding region (CDS) and the 3′-untranslated region (3′UTR) of mRNA, the free energy of hybridization (∆G, kJ/ mole) and schemes of miRNA nucleotides interaction with mRNA.…”

Section: Methodsmentioning

confidence: 99%

“…Existing programs for detecting miRNA binding sites in the mRNA of target genes, unfortunately, predict many false-positive sites (Peterson et al, 2014). To search for the binding sites, we used the MirTarget program, determining the characteristics of miRNA-mRNA interaction, including the detection of multiple miRNA binding sites (Ivashchenko et al, 2014). To improve the binding sites identification their presence in the mRNA of orthologous genes was verified (Ivashchenko et al, 2013;Atam bayeva et al, 2017).…”

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confidence: 99%

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The Characteristics of Mirna Binding Sites in Mrna of Zfhx3 Gene and Its Orthologs

Kondybaeva¹,

Акимниязова²,

Kamenova³

et al. 2018

Vestn. VOGiS

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Transcription factor gene ZFHX3 is one of the candidate genes involved in stroke development. The ZFHX3 protein contains oligopeptides encoded by trinucleotide repeats (TNRs). TNR variability is considered to be one of the causes of the disease, but their biological function has not yet been established. We assume that TNRs are the binding sites of miRNA to mRNA and are involved in regulation of ZFHX3 gene expression. The characteristics of miRNA–mRNA interaction were determined using MirTarget software. It has been shown that the first TNR in mRNA of the human ZFHX3 gene consists of the seven consecutive miR-12-32603-3p binding encoding polyGlu. The ZFHX3 protein of human polyGlu contains 30 Glu. In the orthologous proteins of 36 animal species the length of polyGlu varied from 27 Glu to 33 Glu. Negatively charged polyGlu of the ZFHX3 transcription factor probably interacted with positive DNA-binding proteins. The following mRNA region of the ZFHX3 gene contained the binding sites for miR-17-39416-3p, miR-5-15733-3p, miR-9-20317-3 encoding polyAla by 15 Ala lengths. In the 33 ZFHX3 orthologous proteins polyAla had the same length. The mRNA region of the human ZFHX3 gene with binding polysite of miR-1322-3p encoded polyGln consisting of 19 Gln. In the 41 orthologs of the ZFHX3 protein the length of polyGln varied from seven Gln to 23 Gln. The binding sites of miR-2-6184-3p, miR-5-14114-5p and miR-19-43437-5p were located with overlapping nucleotides sequences, and encode polyPro. In ZFHX3 human polyPro consisted of 12 Pro. In the orthologs, polyPro contained from 10 Pro to 14 Pro. The binding sites of miR-17-39416-3p, miR-9-20317-3p, miR-1-1819-3p, miR-5-15733-3p, miR-6-17815-3p, miR-18-39953-5p, miR-26862-5p, miR-1260b and miR-X-48174-3p in human ZFHX3 encoded polyGly by 22 Gly length. In the 28 orthologs of ZFHX3 the length of polyGly decreased to 11 Gly. The TNR regions could simultaneously bind several miRNAs, which increased the dependence of gene expression on miRNA. The oligopeptides encoded by the binding polysites of miRNA in mRNA in the orthologous ZFHX3 proteins were flanked by conserved oligopeptides.

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

The Characteristics of Mirna Binding Sites in Mrna of Zfhx3 Gene and Its Orthologs

Kondybaeva¹,

Акимниязова²,

Kamenova³

et al. 2018

Vestn. VOGiS

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“…The miR-1322 binding sites has arranged binding sites were arranged in the CDSs of the orthologous genes MAMLD1, MAML2, and MAML3 genes. These sites encode a polyglutamine oligopeptide ranging from six 6 to 47 amino acids in length [1,10].…”

Section: Results and Their Discussionmentioning

confidence: 99%

“…Numerous microRNAs (miRNAs) that regulate the expression of several hundred genes by binding to their mRNAs have been identified [1][2][3][4]. These miRNAs play key roles in the regulation of many biological processes and changes in their concentrations are observed in various pathologies in humans and other animals [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Features of mir-466-3p binding sites in mRNA genes with different functions

Niyazova

Atambayeva²,

Akimniyazova

et al. 2015

INT J BIOL CHEM

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“…The nucleotide sequences of miRNAs were taken from miRBase v.22 (http://www.mirbase.org/). The miRNAs binding sites in mRNA of several genes were predicted using the MirTarget program [15]. This program defines the following features of miRNA binding to mRNA: a) the start of the initiation of miRNA binding to mRNAs from the first nucleotide of the mRNA's 5'UTR; b) the localization of miRNA binding sites in 5'UTRs, CDSs and 3'UTRs of the mRNAs; c) the free energy of interaction miRNA and the mRNA (∆G, kJ/mole); d) the schemes of nucleotide interactions between miRNAs and mRNAs.…”

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confidence: 99%

CHARACTERISTICS OF miRNA INTERACTION WITH mRNA GENES OF T. AESTIVUM C2H2, ERF, GRAS TRANSCRIPTION FACTORS FAMILIES

Rakhmetullina

Turasheva

Bolshoy

et al. 2020

Series of Biological and Medical

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The molecular mechanisms for increasing plant productivity remain poorly understood. Genes of C2H2, GRAS, ERF transcription factors (TFs) families play a key role in the physiological processes of plants, including wheat. In recent years, the important role of miRNAs in the regulation of the expression of many genes involved in the formation of productivity has been established. Wheat miRNA (mRNA-inhibiting RNA) target genes are involved in the regulation of the development of flowers, seeds, root, shoots, and responses to abiotic and biotic stresses. The miRNAs binding sites in mRNAs of C2H2, ERF, GRAS TFs families were performed using the MirTarget program, which calculates the free energy of miRNA binding with mRNA, the schemes and positions of nucleotide interactions with binding sites. Wheat genes were used as the object of the study, since wheat is one of the main grain crops in Kazakhstan and in many other countries. The presence of miRNA binding sites with high nucleotide complementarity in mRNA of C2H2, ERF, GRAS TF genes of wheat was shown. All binding sites of these miRNAs were located in the CDS of mRNA target genes. Of the 125 miRNAs of T. aestivum, miR319-3p efficiently bound with mRNA of C2H2 family genes with the value of ΔG/ΔGm equal 91 %. miR7757-5p interacted with mRNA of ERF and GRAS family genes with the value of ΔG/ΔGm equal to 92 % and 90 % respectively. miR9778-5p bound with mRNA of C2H2, ERF, GRAS family genes to varying degrees. Each of the miR408-3p, miR9780-3p, and miR9778-5p had four target genes with the value of ΔG/ΔGm equal to 87 % and 89 %. These data indicate the dependency of C2H2, GRAS, ERF TFs families expression on miRNA. The obtained results expand the fundamental ideas about the regulatory mechanisms of miRNA in the process of plant growth and development.

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MiR-3960 binding sites with mRNA of human genes

Cited by 29 publications

References 14 publications

The Characteristics of Mirna Binding Sites in Mrna of Zfhx3 Gene and Its Orthologs

The Characteristics of Mirna Binding Sites in Mrna of Zfhx3 Gene and Its Orthologs

Features of mir-466-3p binding sites in mRNA genes with different functions

CHARACTERISTICS OF miRNA INTERACTION WITH mRNA GENES OF T. AESTIVUM C2H2, ERF, GRAS TRANSCRIPTION FACTORS FAMILIES

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