Wheat and maize miRNAs are potential regulators of human genes expression

Rakhmetullina Aizhan1, Ivashchenko Anatoliy2, Pyrkova Anna31SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, zhanullina1994@gmail.com2SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, a.iavashchenko@gmail.com3SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, anna.pyrkova@kaznu.kz With food, a huge variety of biological material gets into the human digestive tract, which the body uses for life support. The variety of food material entering the gastrointestinal tract, especially at the molecular level, cannot be distinguished from endogenous metabolites and these exogenous compounds can significantly alter the body\’s metabolism. Such compounds include plant miRNAs, which are indistinguishable from endogenous human miRNAs in physicochemical properties. It is necessary to clarify the degree of influence of exogenous plant miRNAs on the expression of human genes, since it is not known in advance what consequences can occur when plant miRNAs enters the human body. A huge amount of research does not allow experiments with all human genes and all plant miRNAs, so we have studied the effect of wheat and maize miRNAs on human genes using computer methods. As a result of studying the binding of 125 tae-miRNAs and 325 zma-miRNAs to mRNAs of 17508 human genes it was revealed that 158 genes were targets for 52 tae-miRNAs and 51 genes for 11 zma-miRNAs. Binding sites in the mRNA of human genes were located in 5\’UTR, CDS, 3\’UTR.

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The characteristics of interaction of miRNA with mRNA of C2H2, ERF and GRAS transcription factors of arabidopsis, rice and maize

Rakhmetullina Aizhan1, Turasheva Svetlana2, Pyrkova Anna31SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, zhanullina1994@gmail.com2SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, svetlana.turasheva@kaznu.kz3SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, anna.pyrkova@kaznu.kz The miRNA binding sites with mRNA of genes encoding C2H2, ERF, GRAS transcription factors (TFs) were identified for Arabidopsis thaliana, Oryza sativa and Zea mays. The free energy (ΔG) of interaction of miRNA with mRNA target genes, the maximum of free energy (ΔGm), the ratio ΔG/ΔGm, and location of the potential binding sites were calculated using MirTarget program. In mRNA of C2H2, ERF, GRAS genes of all studied plants, miRNA binding sites were located in the protein-coding part (CDS) and 5’-untranslated region (5’UTR). The ath-miR5658-5p, ath-miR5021-5p, osa-miR2102-5p, osa-miR5075-3p had binding sites in mRNA of three studied families, with the value of ΔG/ΔGm from 91% to 98%. The miR171a-3p had binding sites in mRNA GRAS transcription factors family of all studied plants, with the value of ΔG/ΔGm equal 100%. The nucleotide sequences of ath-miR171a-3p, osa-miR171a-3p, and zma-miR171a-3p were similar, and their quantitative characteristics of interaction with mRNA of LOC_Os02g44360.1, GRMZM2G037792_P01, and AT2G45160.1 genes, were also similar. The obtained results indicate the dependence of expression TF of C2H2, ERF, GRAS families on miRNA.  

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Cluster organization of miRNA binding sites in mRNA of atherosclerosis candidate genes

Mukushkina Dina1, Aisina Dana2, Ivashchenko Anatoliy31SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, dina.mukushkina@gmail.com2SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, dana.aisina03@gmail.com3SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, a.iavashchenko@gmail.com Many candidate genes are involved in the development of atherosclerosis, which are manifested in a variety of metabolic processes, disturbances of which are observed in this disease. Many publications describe the involvement of miRNAs in the development of atherosclerosis. Therefore, it is necessary to establish which miRNAs can affect the expression of candidate genes. Quantitative characteristics of the interaction of miRNAs with mRNAs candidate genes were determined using the MirTarget program, which detects localization of miRNA binding sites in 3\’UTR, 5\’UTR and CDS; free energy interaction miRNA with mRNA; schemes of nucleotide interaction between miRNA and mRNA. In the mRNA of atherosclerosis genes, the binding sites of two or more miRNAs located in 3\’UTR, 5\’UTR and CDS are established. The organization of miRNAs binding sites with overlapping nucleotide sequences forming clusters was revealed. Such an organization of miRNAs binding sites leads to their compaction several times and causes competition among miRNAs for binding to mRNA. The features of the interaction of miRNAs with mRNA of candidate genes depending on their expression are established. Associations of miRNAs and candidate atherosclerosis genes are proposed for the early diagnosis of this disease.

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Competition and collaboration in the miRNA science field

Artemiy Firsov1, Igor Titov21Institute of Informatics Systems, a.firsov@g.nsu.ru2Institute of Cytology and Genetics, titov@bionet.nsc.ru In this work we present the analysis of the characteristics of institutions interactions in the miRNA science field using the data from PubMed digital library. We identified the leaders of the field – China, USA -, characterized the interactions and described the country level features of co-authorship. We observed that the USA were leading in the publication activity until China took the lead 4 years ago. However, the USA are the main co-authorship driver in this field. We have also identified the pioneers and show, that they are the leaders of co-authorship activity. We compare the publications activity patterns on the organization level, identifying leaders. We compare the organization interaction graph with the authors interaction graph, and provide additional insights of miRNA science field evolution.

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Computational prediction of miRNA binding sites in mRNA of colorectal cancer candidate genes

Aigul Akimniyazova11SRI of Biology and Biotechnology problems, al-Farabi Kazakh National University, akimniyazova@gmail.com The identification of causative miRNAs in colorectal cancer is unclear due to a lack of understanding of how specific miRNAs affect biological pathways and consequences of disease development. The miRNA is a class of nano-sized non-coding RNAs that regulate many mRNAs, and mRNA can be related to many miRNAs, which make them suitable for diagnosis purposes. Therefore it is required to identify candidate genes of colorectal cancer and to what extent they can interact with miRNA. To determine the important miRNAs biding sites in genes, involved in the development of colorectal cancer, there were used the MirTarget program. The paper presents the results of studying the characteristics of the interaction of miRNAs with mRNAs of 135 candidate genes involved in the development of colorectal cancer. The binding sites of 446 miRNAs have in 113 mRNA of genes at 5\’UTR, CDS, and 3\’UTR. Found miRNA binding sites with overlapped nucleotide sequences (clusters). The research results are useful for the development of methods for early diagnosis of this disease.

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MIRNA EXPRESSION PROFILE IN ABNORMALLY INVASIVE PLACENTA: ACCRETA, INCRETA AND PERCRETA CASES

Poster (download) Angelika Timofeeva1, Oksana Vasilchenko2, Mariya Pirogova3, Ivan Fedorov4, Vitaliy Chagovets5, Larisa Ezhova6, Roman Shmakov7, Gennadiy Sukhikh81FSBI В«National Medical Research Center For Obstetrics, Gynecology And Perinatology Named After Academician V.I.KulakovВ» Ministry of Healthcare of the Russian Federation, Moscow, Russia, avtimofeeva28@gmail.com2FSBI В«National Medical Research Center For Obstetrics, Gynecology And Perinatology Named After Academician V.I.KulakovВ» Ministry of Healthcare of the Russian Federation, Moscow, Russia, vasilchenko-on@mail.ru3FSBI В«National Medical Research Center For Obstetrics, Gynecology And Perinatology Named After Academician V.I.KulakovВ» Ministry of Healthcare of the Russian Federation, Moscow, Russia, pirogovamariya@gmail.com4FSBI В«National Medical Research Center For Obstetrics, Gynecology And Perinatology Named After Academician V.I.KulakovВ» Ministry of Healthcare of the Russian Federation, Moscow, Russia, i_fedorov@oparina4.ru5FSBI В«National Medical Research Center For Obstetrics, Gynecology And Perinatology Named After Academician V.I.KulakovВ» Ministry of Healthcare of the Russian Federation, Moscow, Russia, vvchagovets@gmail.com6FSBI В«National Medical Research Center For Obstetrics, Gynecology And Perinatology Named After Academician V.I.KulakovВ» Ministry of Healthcare of the Russian Federation, Moscow, Russia, l_ezhova@oparina4.ru7FSBI В«National Medical Research Center For Obstetrics, Gynecology And Perinatology Named After Academician V.I.KulakovВ» Ministry of Healthcare of the Russian Federation, Moscow, Russia, r_shmakov@oparina4.ru8FSBI В«National Medical Research Center For Obstetrics, Gynecology And Perinatology Named After Academician V.I.KulakovВ» Ministry of Healthcare of the Russian Federation, Moscow, Russia, g_sukhikh@oparina4.ru It is well-known that abnormal placental invasion is a condition characterized by pathological invasion of chorionic villi into the the basal layer of the uterus that is complicated by massive obstetric hemorrhage, blood transfusions, a need for hysterectomy and even mortality. The altered miRNA expression profiles were found by deep sequencing not only directly in the area of pathological invasion, but also in the outside distant placenta areas with more pronounced changes in the former case. An increase in the level of miR-21-5p, miR-25-3p, miR-92a-3p, miR-320a in maternal plasma may indicate abnormally invasiveВ placenta and potentially be used in the early diagnosis and management of this condition.

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How miRNAs can protect humans from coronaviruses COVID-19, SARS-CoV, and MERS-CoV

Anatoliy Ivashchenko1, Aizhan Rakhmetullina2, Aigul Akimniyazova3, Dana Aisina41Al-Farabi Kazakh National University, a.iavashchenko@gmail.com2Al-Farabi Kazakh National University, zhanullina1994@gmail.com3Al-Farabi Kazakh National University, akimniyazova@gmail.com4Al-Farabi Kazakh National University, dana.aisina03@gmail.com Viral diseases cause significant harm to human health and often cause high mortality. In the past twenty years, humanity has undergone infection by SARS-CoV (severe acute respiratory syndrome), MERS-CoV (Middle East respiratory syndrome) and COVID-19 coronaviruses, which spread from animals to humans and from person to person. These diseases have led to large economic losses. To fight coronaviruses and other viruses, it is proposed to use miRNAs, which regulate protein synthesis at the translational level. Out of 2565 miRNAs, miR-4778-3p, miR-6864-5p and miR-5197-3p were identified as the most effectively interacting with the gRNA of SARS-CoV, MERS-CoV and COVID-19, respectively. Based on the miR-4778-3p, miR-6864-5p and miR-5197-3p sequences, complete complementary miRNA (cc-miR) binding sites in the gRNA coronaviruses were created. Detected binding sites of these cc-miRs did not form intramolecular complexes in the 2D structure of the gRNA of SARS-CoV, MERS-CoV, and COVID-19 with a value of more than 85%. Therefore, cc-miRs will bind gRNA at these sites without competition. The cc-miRs for SARS-CoV, MERS-CoV, and COVID-19 did not have target genes among the 17508 human coding genes with a О”G/О”Gm of more than 85%, which implies the absence of side effects of cc-miRs on the translation of human mRNAs. cc-miRs can be used as therapeutic agents by incorporating them into exosomes or other vesicles and introducing them into the blood or lung by inhalation. The introduction of cc-miR into the blood will suppress the reproduction of the virus in the blood and in all organs into which it can enter.

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Errors in miRNA Recognition

Pavel Vorozheykin1, Igor Titov21NSU, pavel.vorozheykin@gmail.com2ICG SB RAS, titov@bionet.nsc.ru Selecting and using the key miRNA features are crucial for the identification of miRNA sequences. These criteria may help us to take out junk data from the miRNA databases and to improve the prediction of miRNA ends in order to obtain more accurate forecasting of the seed-related functions. We consider different processes of the miRNA identification to determine their role and influence on the prediction quality.

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