Properties of mirna binding sites with mrna of tcp plant transcription factors

Transcription factors of the ТСР family are involved in many processes of plant development and growth. Expression ofTCPfamily genes depends on miRNAs, the effect of which on the translation of their mRNAs is poorly understood[1]. We have created the MirTarget program, which allows to determine the quantitative characteristics of binding of the entire miRNA nucleotide sequence to mRNA. This program defines the following features of binding: a) the origin of the miRNA binding to mRNA; b) the localization of miRNA binding sites in 5'UTR, CDS and 3'UTR of mRNA; c) the free energy of interaction (∆G, kJ/mole); and d) the scheme of nucleotide interaction miRNA with mRNA. In the present work, using the bioinformatics approach, the interaction of miRNAs with mRNAs of TCP genes of different plant species were investigated [2].

The quantitative characteristics of 429 miRNAs binding to mRNAs of 27 TCP family genes of the Arabidopsis thaliana were established. Only nine genes are targets for miRNAs. Their mRNAsbind with miR319- 3p, miR4228-5p, miR4228-3p, miR5021-5p, miR5658-5p and miR8181-5p. The mRNA of AT1G53230,

AT2G31070 genes have binding sites for miR319c-3p, miR5021-5p and miR5658-5p, and mRNA of AT3G15030gene has binding sites for miR319a-3p and miR4228-3p. By two miRNAs bind to mRNA ofAT1G69690, AT3G02150 and AT3G47620genes. By one miRNA bindto mRNA ofAT1G30210, AT4G18390 and AT5G08330 genes. miRNAs binding sites are located in 5'UTR, CDS and 3'UTR mRNAТСР family genes of A.thaliana.

As a result of studying the binding of 126 miRNAsto mRNAs of 28 ТСР family genes of Triticumaestivum family it was revealed that only ten genes were targets for miRNAs. miR319-3p, miR444a-3p, miR5086-5p, miR9666a-3p, miR9780-3p, miR10516-5p and miR10518-5p bind with mRNAs of these genes. Each mRNA of Traes_6AL_DA27ABCA61 and Traes_6DL_136DE13FB genes binds with miR10516-5p and miR10518-5p. Two miRNAs bindto the mRNA ofTraes_2BL_36A3AB3A2.1gene. By one miRNA bindto mRNA of other genes. The miRNAs binding sites in mRNA ofTCPfamily genes of T.aestivumare located only in the CDS.

The binding of 738 miRNAsto mRNAs of 22 TCPfamily genes of Orysa sativa was studied. Only eight genes are targets for miRNAs. miR1861d-5p, miR2102-5p, miR5075-3p and miR5819-5p interact with the mRNA of these genes. The binding sites for miR2102-5p and miR5819-5p were found in LOC_Os01g11550 gene. By one miRNA bindto mRNA of other genes. The miRNA binding sites in mRNA of TCPfamily genes of O.sativaare located in 5'UTR and CDS.

As a result of studying the binding of 325 miRNAsto mRNAsof 46 TCP family genes of Zea mays, it was found only 11 targets for miRNAs. miR164g-3p, miR164h-5p, miR166a-5p, miR168a-5p, miR171d-5p, miR399d- 3p and miR408a-3p bindto the mRNA of these target genes. The mRNA of GRMZM2G031905_P01, GRMZM2G055024_P01, GRMZM2G062711_P01 and GRMZM2G170232_P01 genes bind with zma-miR166a-5p. The mRNAs ofAC213524.3_FGP003, AC233950.1_FGP002, GRMZM2G034638_P01 genes bind each with two miRNAs. By one miRNA bindto the mRNA of GRMZM2G035944_P01, AC190734.2_FGP003 and

AC205574.3_FGP006 genes. The miRNA binding sites are located in 5'UTR and CDS of mRNATCP family genes of Z.mays.

Polyserine, polyhistidinewere detected in proteinsof TCP genes family, encoded respectively by the binding sites of miR-5021-5p, miR-5658-5p. The miRNA binding sites in the mRNA of orthologous TCP genes of many plant species encode conservative oligopeptides, which indicates the early emergence of functional relationship between miRNAs and target genes and confirms the existence of the found miRNAs binding sites. This relationship persists for tens and hundreds of millions of years[3].miR444a-3p has binding sites in mRNAs of three T.aestivum genes, two O.sativa genes, and three Z. mays genes encoding STSETS oligopeptides.miR168a-5p has binding sites in mRNAs of one T. aestivum genes, one O. sativa genes, three Z. mays genes and oneA. thaliana gene encoding PALCAAR oligopeptide.miR10518-5p has binding sites in the mRNA of two T. aestivum genes, two O. sativa genes, three Z. mays genes and two A.thalianagenes encoding the conservative TSLNIS oligopeptide. miR319-3p has conserved binding sites in the mRNA of TRAES3BF014900010CFD_t1T. aestivum gene, LOC_Os01g11550.1O. sativa gene, AC205574.3_FGP006 and GRMZM2G015037_P01Z. mays genes and AT3A11615A.thaliana gene, encoding the RGPLQSoligopeptide.

The results of the following research are: a) the target genes from TCPfamily of A. thaliana, T. aestivum, O. sativa and Z. mays for miRNAs have been identified; b) the binding sites of these miRNAs are conserved among target genes of orthologues; c) specific miRNAs for different plant species have been detected; d) miR319- 3p has conserved binding sites in the mRNA of TCP family genes of the studied plant species.


  1. LiS (2015). The Arabidopsis thaliana TCP Transcription Factors: A Broadening Horizon Beyond Development. Plant Signaling & Behavior journal,
  2. Ivashchenko A, Pyrkova A, Niyazova R, Alybayeva A, Baskakov K (2016).Prediction of miRNA binding sites in mRNA.Bioinformation journal, vol. 12(4). pp. 237-240.
  3. Ding J, Zhou S, Guan J (2012).Finding MicroRNA Targets in Plants: Current Status and Perspectives, Genomics Proteomics Bioinformatics journal, vol. 10. pp. 264–275.
Year: 2018
City: Shymkent
Category: Medicine