Atambayeva et al. BMC Genomics (2017) 18:428 DOI 10.1186/s12864-017-3811-6 RESEARCH ARTICLE Open Access The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes Shara Atambayeva1*, Raigul Niyazova1, Anatoliy Ivashchenko1, Anna Pyrkova1, Ilya Pinsky1, Aigul Akimniyazova1 and Siegfried Labeit2 Abstract Background: Normally, one miRNA interacts with the mRNA of one gene. However, there are miRNAs that can bind to many mRNAs, and one mRNA can be the target of many miRNAs. This significantly complicates the study of the properties of miRNAs and their diagnostic and medical applications. Results: The search of 2,750 human microRNAs (miRNAs) binding sites in 12,175 mRNAs of human genes using the MirTarget program has been completed. For the binding sites of the miR-619-5p the hybridization free energy of the bonds was equal to 100% of the maximum potential free energy. The mRNAs of 201 human genes have complete complementary binding sites of miR-619-5p in the 3’UTR (214 sites), CDS (3 sites), and 5’UTR (4 sites). The mRNAs of CATAD1, ICA1L, GK5, POLH, and PRR11 genes have six miR-619-5p binding sites, and the mRNAs of OPA3 and CYP20A1 genes have eight and ten binding sites, respectively. All of these miR-619-5p binding sites are located in the 3’UTRs. The miR-619-5p binding site in the 5’UTR of mRNA of human USP29 gene is found in the mRNAs of orthologous genes of primates. Binding sites of miR-619-5p in the coding regions of mRNAs of C8H8orf44, C8orf44, and ISY1 genes encode the WLMPVIP oligopeptide, which is present in the orthologous proteins. Binding sites of miR-619-5p in the mRNAs of transcription factor genes ZNF429 and ZNF429 encode the AHACNP oligopeptide in another reading frame. Binding sites of miR-619-5p in the 3’UTRs of all human target genes are also present in the 3’UTRs of orthologous genes of mammals. The completely complementary binding sites for miR-619-5p are conservative in the orthologous mammalian genes. Conclusions: The majority of miR-619-5p binding sites are located in the 3’UTRs but some genes have miRNA binding sites in the 5’UTRs of mRNAs. Several genes have binding sites for miRNAs in the CDSs that are read in different open reading frames. Identical nucleotide sequences of binding sites encode different amino acids in different proteins. The binding sites of miR-619-5p in 3’UTRs, 5’UTRs and CDSs are conservative in the orthologous mammalian genes. Keywords: miR-619-5p, miRNA, mRNA, Gene, Human, Orthologous genes Background and growth and development of plants [6] and animals miRNAs participate in the regulation of the expression [7] have been shown. Connections between miRNA of protein-coding genes at the post-transcriptional stage expression and the development of various diseases have [1]. miRNAs, as a part of the RNA-induced silencing been established. miRNA concentrations change in complex, bind to mRNAs and interfere with translation cancer [8] and cardiovascular diseases [9]. Metabolic or promote mRNA destruction [2]. In the last two perturbations change miRNA concentrations in cells decades, properties of miRNAs and their influences on [10]. The aforementioned roles do not encompass all of the expression of the genes involved in all key cellular the biological processes in which miRNAs participate, processes have been established. The actions of miRNAs which further proves the importance of their biological on the cell cycle [3], apoptosis [4], differentiation [5], functions. Despite the significant success in the study of miRNA properties, there are obstacles in identifying the * Correspondence: [email protected] target genes of miRNAs. Normally, one miRNA interacts 1SRI Of Biology and Biotechnology Problems, Al-Farabi Kazakh National University, Almaty, Kazakhstan with the mRNA of one gene. However, there are Full list of author information is available at the end of the article miRNAs that can bind to many mRNAs, and one mRNA © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Atambayeva et al. BMC Genomics (2017) 18:428 Page 2 of 10 can be the target of many miRNAs, which significantly binding sites in the 5’UTRs, the CDSs and the 3’UTRs complicates the study of the properties of miRNAs and of the mRNAs; b) the free energy of hybridization their diagnostic and medical applications. There are (ΔG, kJ/mole). The ratio ΔG/ΔGm (%) was determined more than 2,500 miRNAs in the human genome, and for each site (ΔGmequalsthefreeenergyofmiRNA they are believed to act on 60% or more genes. There- binding with its perfect complementary nucleotide fore, it is difficult to draw specific conclusions about the sequence). participation of miRNAs in specific biological processes, and until then the connections between the majority of Results miRNAs and their target genes will remain unknown. The search of 2,750 human microRNAs (miRNAs) bind- Recently, a set of unique miRNAs (umiRNA) were iden- ing sites in 12,175 mRNAs of human genes using the tified that have hundreds of target genes and bind to MirTarget program has been completed. The mRNAs mRNAs with high affinity [11–14]. The binding sites of have different miRNA binding site origins, lengths, these umiRNAs are located in the 3’UTRs, CDSs, and quantities, and properties. The list of miR-619-5p target 5’UTRs of mRNAs. Among these umiRNAs, miR-619-5p genes and the positions of binding sites are outlined in interacts with the largest number of target genes that Table 1. miR-619-5p is 22 nucleotides in length and is have the greatest number of binding sites with complete coded by an intron of the slingshot protein phosphatase complementarity of miR-619-5p and mRNAs. It is 1(SSH1) gene, which is located on chromosome 12 necessary to identify many miRNA binding sites in the [17, 18]. mRNAs of 201 genes have complete comple- mRNAs of these genes for the control of gene expression. mentary binding sites for miR-619-5p (ΔG/ΔGm = 100%). Furthermore, it is important to control the expression of Therefore, the energy of interaction of miR-619-5p with the corresponding gene complexes that are functionally mRNA of all the genes listed in the table is the same and associated with miRNAs. Therefore, we have studied a equal to ΔG=−121 kJ/mole. unique miR-619-5p that binds to the mRNAs of several The mRNAs of 201 human genes have complete com- hundred human and orthologous genes. plementary binding sites of miR-619-5p in the 3’UTR (214 sites), CDS (3 sites), and 5’UTR (4 sites). The Methods mRNAs of 27 genes have four binding sites, seven genes The nucleotide sequences of mRNAs of human genes have five binding sites, and CATAD1, ICA1L, GK5, (Homo sapience – Hsa) and orthologous genes (Bos mutus POLH, and PRR11 genes have six miR-619-5p binding - The wild yak (Bmu), Callithrix jacchus – The common sites. The mRNAs of OPA3 and CYP20A1 genes have marmoset (Cja), Camelus dromedarius – Arabian camel eight and ten binding sites, respectively. All of these sites (Cdr), Camelus ferus – The wild Bactrian camel (Cfe), are located in the 3’UTRs of mRNAs. Chlorocebus sabaeus – The green monkey (Csa), Colobus The target genes of the miR-619-5p carry out one or angolensis palliatus – The Angola colobus (Can), Equus more different functions and are involved in the devel- caballus - The horse (Eca), Gorilla gorilla - The western opment of various diseases (Table 1). gorilla (Ggo), Macaca fascicularis – The crab-eating The mRNAs of the C17orf75, C8orf44, CIAO1, CPM, macaque (Mfa), Macaca mulatta – The rhesus macaque CYP20A1, DCAF10, FKBP14, RAB3IP, SYNJ2BP, VHL (Mmu), Macaca nemestrina - Pig-tailed macaque (Mne), genes have two complete complementary binding sites for Mandrillus leucophaeus – The drill (Mle), Nomascus miR-619-5p, and the mRNA of the CACNG8 gene has leucogenys - The northern white-cheeked gibbon (Nle), three such binding sites. This indicates a stronger depend- Ovis aries – The sheep (Oar), Pan paniscus - Bonobos ence of the expression of these genes on miR-619-5p. (Ppa), Pan troglodytes – The common chimpanzee (Ptr), One of the methods to establish the credibility of the Papio anubis – The olive baboon (Pan), Pongo abelii - The presence of miRNA binding site in the mRNA is to Sumatran orangutan (Pab), Rhinopithecus roxellana – The verify this site in the mRNAs of orthologous genes. In golden snub-nosed monkey (Rro))weredownloadedfrom finding the miRNA binding sites raises the question of NCBI GenBank (http://www.ncbi.nlm.nih.gov) [15] in the level of reliability of the found sites. One effective FASTA format using Lextractor002 script [11]. Nucleotide way to establish the credibility of the binding sites is to sequences of human mature miR-619-5p (GCUGGGA establish binding sites in the orthologous genes and the UUACAGGCAUGAGCC) were downloaded from the identification of orthologous miRNA. Location of bind- miRBase database (http://mirbase.org) [16]. The miR-619- ing site in the protein coding region facilitates its con- 5p binding sites in the 5’-untranslated regions (5’UTRs), servation in evolution, especially if the corresponding the coding domain sequences (CDSs) and the 3’-untrans- oligopeptide plays an important role in the function of lated regions (3’UTRs) of several genes were predicted the protein.