Prediction of characteristics of interactions of miRNA with mRNA of GRAS, ERF, C2H2 genes of A. thaliana, O. sativa and Z. mays

Modern methods of increasing plant productivity are based on knowledge of the molecular basis of plant growth and development. The key regulators of these processes are transcription factors (TF) that control the expression of the genome at all stages of ontogenesis. The expression of significant part of the TF genes depends on miRNAs, therefore, it is necessary to find out which miRNAs and to what extent they can affect TFs. In the present work, using the MirTarget program, we identified miRNAs capable of affecting the expression of GRAS (gibberellic-acid insensitive, repressor of gai and scarecrow), ERF (ethylene responsive factor), C2H2 (cysteine and histidine residues in their secondary structures) TF genes of A. thaliana, O. sativa, and Z. mays. The obtained characteristics of the interaction of miRNA with mRNA TF genes revealed effective associations of miRNA and TF of GRAS, ERF, and C2H2 families. During the interaction of 428 ath-miRNAs with mRNAs of 37 GRAS family genes of A. thaliana, only 11 target genes were found for eight ath-miRNAs. Of the 60 genes of the GRAS family of O. sativa, 18 genes were targets only for 16 osa-miRNAs out of 738 osa-miRNAs. Of 325 zma-miRNAs and 86 genes of the GRAS family of Z. mays, only 14 genes were targets for eight zma-miRNAs. Of 428 ath-miRNAs of A. thaliana with 123 mRNA genes of the ERF family, 25 target genes were identified for eight ath-miRNAs. Out of 738 osa-miRNAs only 13 osa-miRNAs efficiently bind to mRNA of 16 ERF genes. Of 325 zma-miRNAs with mRNAs of 186 genes of the ERF family of Z. mays, only two genes were targets for two zma-miRNAs. Of 428 ath-miRNAs and 87 genes of C2H2 family of A. thaliana, only 17 genes were targets of nine ath-miRNAs. Ten osa-miRNAs could interact with mRNA of 17 genes of the C2H2 family of O. sativa. An important role of osa-miRNA in the regulation of rice growth and development is suggested by influencing the C2H2 family TF genes of O. sativa. The ath-miR5021–5p, ath-miR5658–5p, osa-miR2102–5p, and osa-miR5075–3p interacted with several TF target genes of the C2H2, ERF, and GRAS families and had conserved binding sites that encode conserved oligopeptides.