{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:06:52Z","timestamp":1792789612273,"version":"4.5.0"},"reference-count":27,"publisher":"MDPI AG","issue":"19","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan","award":["AP26102055"],"award-info":[{"award-number":["AP26102055"]}],"id":[{"id":"https:\/\/ror.org\/05tyne317","id-type":"ROR","asserted-by":"crossref"}]},{"award":["AP26102055"],"award-info":[{"award-number":["AP26102055"]}],"id":[{"id":"https:\/\/ror.org\/05dwvd537","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>More than three decades have passed since the discovery of miRNAs in human cells, yet many of their biological properties remain poorly understood. The aim of this study was to investigate whether miRNAs can interact with target gene mRNAs through fully complementary base pairing. Using the MirTarget program, we demonstrated that all nucleotides of miRNAs can form fully complementary interactions with nucleotides of target gene mRNAs. A total of 1036 miRNAs, which were identified by Backes et al. and we designated as BmiRNAs and mRNAs from 17,508 human genes, were analyzed, revealing several important characteristics. The vast majority of BmiRNAs were found to bind fully complementarily to the 3\u2032-untranslated regions (3\u2032UTRs) of target gene mRNAs. Many mRNAs contained binding sites (BSs) for multiple BmiRNAs, forming binding site clusters in which BmiRNAs may compete for interaction with the same mRNA. We also identified identical groups of up to four BmiRNAs capable of binding to the mRNAs of different genes. In addition, genes whose mRNAs contained up to eight BmiRNA binding sites were identified. These findings broaden our understanding of the mechanisms by which BmiRNAs regulate human gene expression at the mRNA translation stage and provide new insights into their potential role in post-transcriptional gene regulation.<\/jats:p>","DOI":"10.3390\/ijms27198773","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:19:37Z","timestamp":1790777977000},"page":"8773","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Features of Complementary Interactions of BmiRNAs with mRNAs of Human Genes"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7969-2016","authenticated-orcid":false,"given":"Anatoliy","family":"Ivashchenko","sequence":"first","affiliation":[{"name":"Department of Biotechnology, Farabi University, Almaty 050040, Kazakhstan"},{"name":"Center for Bioinformatics and Nanomedicine, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8483-451X","authenticated-orcid":false,"given":"Anna","family":"Pyrkova","sequence":"additional","affiliation":[{"name":"Department of Computer Sciences, Farabi University, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4380-2460","authenticated-orcid":false,"given":"Saltanat","family":"Orazova","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Farabi University, Almaty 050040, Kazakhstan"},{"name":"Center for Bioinformatics and Nanomedicine, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7946-1189","authenticated-orcid":false,"given":"Raigul","family":"Niyazova","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Farabi University, Almaty 050040, Kazakhstan"},{"name":"Center for Bioinformatics and Nanomedicine, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/0092-8674(93)90529-Y","article-title":"The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14","volume":"75","author":"Lee","year":"1993","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"W110-6","DOI":"10.1093\/nar\/gkw345","article-title":"miEAA: microRNA enrichment analysis and annotation","volume":"44","author":"Backes","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Ludwig, N., Werner, T.V., Backes, C., Trampert, P., Gessler, M., Keller, A., Lenhof, H.P., Graf, N., and Meese, E. (2016). Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes. Int. J. Mol. Sci., 17.","DOI":"10.3390\/ijms17040475"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Keller, A., Ludwig, N., Fehlmann, T., Kahraman, M., Backes, C., Kern, F., Vogelmeier, C.F., Diener, C., Fischer, U., and Biertz, F. (2019). Low miR-150-5p and miR-320b Expression Predicts Reduced Survival of COPD Patients. Cells, 8.","DOI":"10.3390\/cells8101162"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Kern, F., Ludwig, N., Backes, C., Maldener, E., Fehlmann, T., Suleymanov, A., Meese, E., Hecksteden, A., Keller, A., and Meyer, T. (2019). Systematic Assessment of Blood-Borne MicroRNAs Highlights Molecular Profiles of Endurance Sport and Carbohydrate Uptake. Cells, 8.","DOI":"10.1101\/721928"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1007\/s40291-016-0221-4","article-title":"Specific miRNA disease biomarkers in blood, serum and plasma: Challenges and prospects","volume":"20","author":"Backes","year":"2016","journal-title":"Mol. Diagn. Ther."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.cell.2004.12.035","article-title":"Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets","volume":"120","author":"Lewis","year":"2005","journal-title":"Cell"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Ragan, C., Zuker, M., and Ragan, M.A. (2011). Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations. PLoS Comput. Biol., 7.","DOI":"10.1371\/journal.pcbi.1001090"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1186\/s13046-021-01910-0","article-title":"ChrXq27.3 miRNA cluster functions in cancer development","volume":"40","author":"Yoshida","year":"2021","journal-title":"J. Exp. Clin. Cancer Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"117417","DOI":"10.1016\/j.bcp.2025.117417","article-title":"Multi-oncogene targeting in cancer therapy: A miRNA-driven pharmacological approach","volume":"242","author":"Salunkhe","year":"2025","journal-title":"Biochem. Pharmacol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.canlet.2020.12.025","article-title":"Dissecting miRNA signature in colorectal cancer progression and metastasis","volume":"501","author":"Huang","year":"2021","journal-title":"Cancer Lett."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Coradduzza, D., Cruciani, S., Arru, C., Garroni, G., Pashchenko, A., Jedea, M., Zappavigna, S., Caraglia, M., Amler, E., and Carru, C. (2022). Role of miRNA-145, 148, and 185 and Stem Cells in Prostate Cancer. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23031626"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4025","DOI":"10.1007\/s12033-024-01312-5","article-title":"Shedding Light on the Molecular Diversities of miRNA in Cancer- an Exquisite Mini Review","volume":"67","author":"Venkatesh","year":"2025","journal-title":"Mol. Biotechnol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Konishi, H., Sato, H., Takahashi, K., and Fujiya, M. (2021). Tumor-Progressive Mechanisms Mediating miRNA-Protein Interaction. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222212303"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1080\/14712598.2026.2648644","article-title":"Extracellular RNAs in pancreatic cancer: From pathogenesis to precision medicine","volume":"26","author":"Rezazadeh","year":"2026","journal-title":"Expert. Opin. Biol. Ther."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"117639","DOI":"10.1016\/j.bios.2025.117639","article-title":"Development of a multimiRNA detection platform for enhanced diagnostics of colorectal cancer","volume":"287","author":"Zhou","year":"2025","journal-title":"Biosens. Bioelectron."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Ilieva, M., Panella, R., and Uchida, S. (2022). MicroRNAs in Cancer and Cardiovascular Disease. Cells, 11.","DOI":"10.3390\/cells11223551"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1016\/j.cub.2005.02.060","article-title":"RNAi-mediated allelic trans-interaction at the imprinted Rtl1\/Peg11 locus","volume":"15","author":"Davis","year":"2005","journal-title":"Curr. Biol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1134\/S0026893319040174","article-title":"The interaction of miR-5p and miR-3p with the mRNAs of orthologous genes","volume":"53","author":"Yurikova","year":"2019","journal-title":"Mol. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Ivashchenko, A., Pyrkova, A., Niyazova, R., and Orazova, S. (2026). Fully complementary interactions between LmiRNA and mRNA of human genes. Curr. Issues Mol. Biol., 48.","DOI":"10.20944\/preprints202603.1354.v2"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"423","DOI":"10.6026\/97320630010423","article-title":"MiR-3960 binding sites with mRNA of human genes","volume":"10","author":"Ivashchenko","year":"2014","journal-title":"Bioinformation"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev.biophys.30.1.1","article-title":"Hydrogen bonding, base stacking, and steric effects in DNA replication","volume":"30","author":"Kool","year":"2001","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3497","DOI":"10.1093\/nar\/gkf481","article-title":"The non-watson-crick base pairs and their associated isostericity matrices","volume":"30","author":"Leontis","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1038\/35888","article-title":"Potent and specific genetic interference by double-s9randed RNA in Caenorhabditis elegans","volume":"391","author":"Fire","year":"1998","journal-title":"Nature"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Belkozhayev, A., Niyazova, R., Wilson, C., Jainakbayev, N., Pyrkova, A., Ashirbekov, Y., Akimniyazova, A., Sharipov, K., and Ivashchenko, A. (2022). Bioinformatics analysis of the interaction of miRNAs and piRNAs with human mRNA genes having di-and trinucleotide repeats. Genes, 13.","DOI":"10.3390\/genes13050800"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Pyrkova, A., Akhmetova, K., Zhanuzakov, M., Tauassarova, M., Rakhmetulina, A., Niyazova, R., Orazova, S., Zielenkiewicz, P., and Ivashchenko, A. (2026). Regulatory Potential of piRNA target Klotho and other genes. Genes, 17.","DOI":"10.3390\/genes17020241"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Kamenova, S., Sharapkhanova, A., Akimniyazova, A., Kuzhybayeva, K., Kondybayeva, A., Rakhmetullina, A., Pyrkova, A., and Ivashchenko, A. (2022). piRNA and miRNA Can Suppress the Expression of Multiple Sclerosis Candidate Genes. Nanomaterials, 13.","DOI":"10.3390\/nano13010022"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/19\/8773\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:19:52Z","timestamp":1790777992000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/19\/8773"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,30]]},"references-count":27,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2026,10]]}},"alternative-id":["ijms27198773"],"URL":"https:\/\/doi.org\/10.3390\/ijms27198773","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,30]]}}}