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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  • June 29, 2020
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Disruptive natural selection by male reproductive potential prevents underexpression of the genes encoding proteins on the human Y chromosome as a self-domestication syndrome

Poster (download) Mikhail Ponomarenko1, Irina Chadaeva2, Dmitry Oshchepkov3, Dmitry Rasskazov4, Alexander Osadchuk5, Ludmila Osadchuk61Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, pon@bionen.nsc.ru2Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, ichadaeva@bionet.nsc.ru3Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, diman@bionet.nsc.ru4Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, rassk@bionen.nsc.ru5Animal Genetics Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, osadchuk@bionet.nsc.ru6Animal Genetics Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, losadch@bionet.nsc.ru We performed an in silico genome-wide analysis of all SNPs located within 70 bp proximal promoters in front of the all experimentally knowns starts of protein-coding transcripts from human Y chromosome within the framework of the current release #151 of the dbSNP database and GRCh38/hg38 assembly of the human reference genome, which are publicly available using the UCSC Genome Browser. As a result, we first found disruptive natural selection by male reproductive potential preventing underexpression of the Y-linked proteins under this study as if self-domestication would have happened during the human origing and evolution that could cause male fertility disorders as self-domestication syndrome.

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Candidate SNP markers of atherosclerosis reliably altering the affinity of TATA-binding protein for human gene promoters point to stabilizing natural selection as sum of neutral drift spuring atherogenesis and directional natural selection preventing it

Poster (download) Dmitry Rasskazov1, Irina Chadaeva2, Mikhail Ponomarenko3, Ekaterina Sharypova4, Irina Drachkova5, Maria Nazarenko61Systems Biology Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, rassk@bionen.nsc.ru2Systems Biology Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, ichadaeva@bionet.nsc.ru3Systems Biology Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, pon@bionen.nsc.ru4Molecular Genetics Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, sharypova@bionet.nsc.ru5Molecular Genetics Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, drachkova@bionet.nsc.ru6Population Genetics Laboratory, Institute of Medical Genetics (IMG TNRMC RAS), Tomsk, Russia, maria.nazarenko@medgenetics.ru In this work we carried out a computer-based whole-genome search for all variants of single-nucleotide polymorphism (SNP) within 70 bp regions upstream the all experimentally proven transcription start sites of the human genes associated with atherogenesis according to the current release #151 of the dbSNP database and GRCh38/hg38 assembly of the human reference genome, both of which are publicly available due to the UCSC Genome Browser. In the end, we first found atherosclerosis-related candidate SNP markers signoficantly changing the affinity of TATA-binding protein for promoters of these human gene, frequencies of which differes from the commonly accepted genome-wide norm as if they were under pressure of stabilizing natural selection, which summing up neutral drift accelerating atherogenesis and directional natural selection slowing it down

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MicroRNA content of horse and human milk exosomes

Sergey Sedykh1, Kuleshova Anna2, Georgy Nevinsky31SB RAS ICBFM, NSU, sedyh@niboch.nsc.ru2SB RAS ICBFM, aekuleshova25@gmail.com3SB RAS ICBFM, NSU, nevinsky@niboch.nsc.ru Exosomes are 40-100 nm diameter natural vesicles, containing CD9, CD63 and CD81 tetraspanins on the surface. It was shown that milk obtained from different sources contain exosomes: human, horse, bovine, rat. Horse milk is a unique source of exosomes since is less allergenic than bovine and not prion prone. Also, horse milk can be obtained in larger amounts than human milk. According to the results, published by the other research groups, milk exosomes contain hundreds and thousands of proteins, mRNA and microRNA molecules. Our recent results show that these numbers may be significantly overestimated.В Isolation of exosomes from sediments obtained after ultracentrifugation with an additional step of gel-filtration allows decreasing the number of proteins, that co-isolate with vesicles. Many microRNAs are described in exosomes, obtained from human and bovine milk. Here we show the content of more than two dozens major microRNA molecules, isolated fromВ human and horse milk exosomes on different stages of centrifugations, ultracentrifugations, before and after gel-filtration. According to these data, several microRNAs may be used as indicators of milk exosomes\’ purity. The study was funded by the Russian Scientific Foundation (research project 187410055 to S. Sedykh) and by the Program of Fundamental Research of Government Academia (РђРђРђРђ-Рђ17-117020210023-1 to Prof. G. Nevinsky).

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Candidate SNP markers of rheumatoid arthritis changing the affinity of TATA-binding protein for the human gene promoters expo disruptive selection of immunoactivative and immunosuppressive genenets that provoke and prevent this disorder, respectively, as if it could be a self-domestication syndrome

Poster (download) Natalya Klimova1, Dmitry Oshchepkov2, Irina Chadaeva3, Mikhail Ponomarenko4, Evgeniya Oshchepkova5, academician Vladimir Kozlov61Molecular Genetics Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, klimova@bionet.nsc.ru2Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, diman@bionet.nsc.ru3Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, ichadaeva@bionet.nsc.ru4Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, pon@bionen.nsc.ru5Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, nzhenia@bionet.nsc.ru6Research Institute of Fundamental and Clinical Immunology, RIFCI SB RAS, Novosibirsk, Russia, niiki01@online.nsk.su Here we conducted a computational genome-wide study of the all known single-nucleotide polymorphism (SNP) of 70 bp proximal promoters of 67 human rheumatoid arthritis (RA)-related genes that displayed disruptive natural selections of immunoactivative or immunosuppressive genes raising or reducing risks of RA, respectively, as if it maybe a domestication syndrome. That is why, we confirmed it in vivo using the genome-wide transcriptome profiling (RNA-seq assay) of the differentially expressed genes (DEGs) within hypothalamus of adult male rats (Rattus norvegicus) of two unique outbred lines bred in aggressiveness and tameness as an animal model of human diseases (statistical significance padj < 0.025 at Pearson\’s П‡2 criterion with Bonferroni\’s correction).

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