International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

Tag

gene

7 RESULTS
Bioinformatics and systems biology of plants symposiumThe characteristics of interaction of miRNA with mRNA of C2H2, ERF and GRAS transcription factors of arabidopsis, rice and maize

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

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Rakhmetullina Aizhan1, Turasheva Svetlana2, Pyrkova Anna3
1SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, zhanullina1994@gmail.com
2SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, svetlana.turasheva@kaznu.kz
3SRI 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.  

Systems Biology and Biomedicine symposiumCluster organization of miRNA binding sites in mRNA of atherosclerosis candidate genes

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

No Comment on Cluster organization of miRNA binding sites in mRNA of atherosclerosis candidate genes

Mukushkina Dina1, Aisina Dana2, Ivashchenko Anatoliy3
1SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, dina.mukushkina@gmail.com
2SRI of biology and biotechnology problems Al-Farabi Kazakh National University Almaty, Kazakhstan, dana.aisina03@gmail.com
3SRI 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.

Genomics, transcriptomics, bioinformatics symposiumDisruptive natural selection by male reproductive potential prevents underexpression of the genes encoding proteins on the human Y chromosome as a self-domestication syndrome

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

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/98.pdf”]
Mikhail Ponomarenko1, Irina Chadaeva2, Dmitry Oshchepkov3, Dmitry Rasskazov4, Alexander Osadchuk5, Ludmila Osadchuk6
1Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, pon@bionen.nsc.ru
2Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, ichadaeva@bionet.nsc.ru
3Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, diman@bionet.nsc.ru
4Systems Biology Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, rassk@bionen.nsc.ru
5Animal Genetics Department Institute of Cytology and Genetics, ICG SB RAS Novosibirsk, Russia, osadchuk@bionet.nsc.ru
6Animal 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.

Bioinformatics and systems biology of plants symposiumMolecular genetic analysis of alloplasmic recombinant lines (Triticum dicoccum) -Triticum aestivum

Molecular genetic analysis of alloplasmic recombinant lines (Triticum dicoccum) -Triticum aestivum

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/133.pdf”]
Shcherban A.B.1, Perfil’ev R.N2, Salina E.A.3
1Institute of Cytology and Genetics SB RAS, atos@bionet.nsc.ru
2Novosibirsk State Agrarian University, pervf.1999@gmail.com
3Institute of Cytology and Genetics SB RAS, sunday01@mail.ru

Molecular markers were used to analyze the mitochondrial genome of the alloplasmic lines of wheat containing the nuclear genome of the hexaploid wheat T. aestivum against the background of the cytoplasm of tetraploid wheat T.dicoccum. Eight lines showed patterns of PCR and CAPS markers corresponding to the species T. aestivum, indicating the substitution of the mitochondrial genome of T. dicoccum during backcrossing with hexaploid wheat. In the D-N-05 line, the rps19 and orf256 gene markers corresponded to the parental species T.dicoccum. This line is promising in terms of studying the mechanisms of fertility restoration in hybrids with CMS. Also, using molecular marker, the nuclear gene Dreb-1, which is a regulator of drought tolerance, was analyzed and it was shown that В line D-41-05 had an introgression of this gene from the B genome of T. dicoccum, which may lead to the previously established increased drought tolerance of this line.

Genomics,  bioinformatics  and evolution symposiumCandidate 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

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

No Comment on 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)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/283.pdf”]
Dmitry Rasskazov1, Irina Chadaeva2, Mikhail Ponomarenko3, Ekaterina Sharypova4, Irina Drachkova5, Maria Nazarenko6
1Systems Biology Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, rassk@bionen.nsc.ru
2Systems Biology Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, ichadaeva@bionet.nsc.ru
3Systems Biology Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, pon@bionen.nsc.ru
4Molecular Genetics Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, sharypova@bionet.nsc.ru
5Molecular Genetics Department, Institute of Cytology and Genetics (ICG SB RAS), Novosibirsk, Russia, drachkova@bionet.nsc.ru
6Population 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

Animal Genetics and genomics symposiumEffect of overexpression of the 5-HT7 receptor gene on behavior and brain serotonin system in ASC mice with predisposition to depressive-like behavior

Effect of overexpression of the 5-HT7 receptor gene on behavior and brain serotonin system in ASC mice with predisposition to depressive-like behavior

No Comment on Effect of overexpression of the 5-HT7 receptor gene on behavior and brain serotonin system in ASC mice with predisposition to depressive-like behavior

Baraboshkina I.A.1, Bazovkina D.V.2, Ilchibaeva T.V.3, Antonov E.V.4, Kulikova E.A.5, Naumenko V.S.6
1ICG SB RAS, irina.10.24@yandex.ru
2ICG SB RAS, daryabazovkina@gmail.com
3ICG SB RAS, rbicehok@mail.ru
4ICG SB RAS, a.yegor.v@gmail.com
5ICG SB RAS, kulikova.elisa@gmail.com
6ICG SB RAS, naumenko2002@gmail.com

Abstract The serotonin (5-HT) system of the brain plays an important role in controlling various behaviors due to the wide variety of serotonin receptors. The 5-HT7 receptor is of great interest because it is involved in the pathogenesis of depressive disorders. Mice of ASC (Antidepressant Sensitive Catalepsy) line with genetic predisposition to depressive-like behavior were obtained in the Laboratory of Behavioral Neurogenomics of ICG SB RAS (Novosibirsk). In this work, the effect of adenoassociated virus (AAV)-mediated overexpression of the 5-HT7 receptor gene in the midbrain on the behavior and brain serotonin system in ASC mice was comprehensively studied. The ASC mice with overexpression of 5-HT7 receptor gene showed the decrease in depressive-like behavior in the forced swim test compared to control group. The introduction of a vector construct with the 5-HT7 receptor gene affected the expression of the gene encoding the 5-HT7 receptor itself, only in the midbrain. The overexpression of 5-HT7 receptor gene in midbrain led to an increase in the serotonin metabolism index in the cortex, hippocampus, and midbrain of mice, without affecting serotonin levels. The results indicate the effect of overexpression of the 5-HT7 receptor gene on the behavior and serotonin system of the brain in ASC mice with a genetic predisposition to depressive-like behavior.

Systems computational biology: analysis, mathematical modeling and information technologies symposiumCandidate 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

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

No Comment on 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)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/435.pdf”]
Natalya Klimova1, Dmitry Oshchepkov2, Irina Chadaeva3, Mikhail Ponomarenko4, Evgeniya Oshchepkova5, academician Vladimir Kozlov6
1Molecular Genetics Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, klimova@bionet.nsc.ru
2Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, diman@bionet.nsc.ru
3Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, ichadaeva@bionet.nsc.ru
4Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, pon@bionen.nsc.ru
5Systems Biology Department, Institute of Cytology and Genetics, ICG SB RAS, Novosibirsk, Russia, nzhenia@bionet.nsc.ru
6Research 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).