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

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Genomics, transcriptomics, bioinformatics symposium

Showing: 61 - 70 of 71 RESULTS
Genomics, transcriptomics, bioinformatics symposiumConstructing a pipeline for genome variant / gene functioning hybrid prioritization: a case study of type II diabetes

Constructing a pipeline for genome variant / gene functioning hybrid prioritization: a case study of type II diabetes

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Irina Kolesnikova1, Valery Polunovsky2, Konstantin Gunbin3
1LLC NCGI, Novosibirsk, Russia, i.kolesnikova@mygenetics.ru
2LLC NCGI, Novosibirsk, Russia, valeriy.polunovskiy@mygenetics.ru
3ICG SB RAS, Novosibirsk, Russia; NSU, Novosibirsk, Russia, genkvg@bionet.nsc.ru

According to recently proposed “omnigenic model” the genes implicated in complex diseases determination can be divided into core genes and peripheral genes. Mutations in core genes directly affect disease development, while mutations in peripheral genes can only indirectly modulate disease risk. In this study in order to discriminate core genes and their major regulators, we hierarchically combine genome variant prioritization with the prioritization of genes and target tissues.

Genomics, transcriptomics, bioinformatics symposiumTranscription factor Kaiso regulates cell division in the developing mouse brain

Transcription factor Kaiso regulates cell division in the developing mouse brain

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/242.pdf”]
Nina Illarionova1, Maria Borisova2, Ekaterina Bazhenova3, Daria Fursenko4, Daria Zabelina5, Nikita Khotskin6, Alexander Kulikov7
1ICG SB RAS, Novosibirsk, Russia, nina.illarionova@gmail.com
2ICG SB RAS, Novosibirsk, Russia, zolotykh@bionet.nsc.ru
3ICG SB RAS, Novosibirsk, Russia, ekaterina.yu.bazhenova@gmail.com
4Institute of Gene Biology RAS, Moscow, Russia, cenzoored@gmail.com
5NSU, Novosibirsk, Russia, dazabelina@gmail.com
6ICG SB RAS, Novosibirsk, Russia, khotskin@bionet.nsc.ru
7ICG SB RAS, Novosibirsk, Russia, v_kulikov@bionet.nsc.ru

Kaiso is a transcription factor that is known to regulate cell division in different cell types. Kaiso binds kaiso specific binding site and/or methylated CpG islands on the promoter region of different target genes. Kaiso silencing may lead to an increase or a decrease in cell proliferation, which is cell specific and is probably dependent on the methylation status of Kaiso binding sites at the target promoter. In various mammalian cell types Kaiso was shown to regulate cell proliferation via its target genes of cyclins E1 and D1.В Kaiso is widely expressed throughout the brain regions, however its regulation of cell division in brain development was not investigated.В Our preliminary data showed that in the developing hippocampusВ  there was a significant increase in the number of newborn cells in KO mice (17 В± 1) compared with the WT mice (12 В± 1 per 100 Ојm2; p <0,001). The number of newborn cells co-stained with the neuron marker was also significantly greater in KO mice (6 В± 1) compared with the WT mice (4 В± 1 per 100 Ојm2; p <0,05).В In the cortex, striatum, and subventricular zone of the lateral ventricles, there were no significant differences between genotypes in the number of newborn cells.В We have performed expression profiling of genes associated with cell division regulation (c-myc, CCNE1 and CCND1) that were previously noted to be regulated by Kaiso in different cell types. A significant decrease in the expression of the c-myc gene was shown in the hippocampus of KO mice at the age P2 compared to WT (KO: 2,7 В± 0,3; WT: 4,5 В± 0,7; p <0,05). On the mRNA level neither CCNE1 nor CCND1 expression was different between the genotypes in all selected brain regions and corresponding age groups.В Supported by the RFBR (18-04-00869 Рђ)

Genomics, transcriptomics, bioinformatics symposiumLTR-retrotransposon transcripts are ubiqutiously expressed, polyadenylated and underwent splicing in sunflower (Helianthus annuus L.)

LTR-retrotransposon transcripts are ubiqutiously expressed, polyadenylated and underwent splicing in sunflower (Helianthus annuus L.)

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Pavel Merkulov, Murad Omarov, Ilya Kirov1
1All-Russian Research Institute of Agricultural Biotechnology RAS, paulmerkulov97@gmail.com

LTR-retrotransposons are mobile genetic elements widespread in plant genomes. Dispite the fact of significant part of genome engaged by retrotransposons (up to 80 percent), their activity is suppressed by multiple posttranscriptional and epigenetic mechanisms in normal conditions. Retrotransposon escape from silencing and subsequent expression are, in turn, purely described for plants.

Genomics, transcriptomics, bioinformatics symposiumStatistical problems of clusters of transcription factor binding sites in plant genomes

Statistical problems of clusters of transcription factor binding sites in plant genomes

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Artur Dergilev1
1Institute of Cytology and Genetics SB RAS, arturd1993@yandex.ru

AbstractВ В В В 

This work presents the results of using computer scripts to analyze ChIP-seq data, calculate clusters, and visualize them in the form of heat maps. In the work, ChIP-seq peaks were used to study the stem cell niche of three plants, among which the well-known Talus (Arabidopsis Thailana), Physcomitrella patens, Chlamydomonas reinhardti. What about the tendency of co-localization of transcription factors in plant genomes? What are the features of this co-localization?

Genomics, transcriptomics, bioinformatics symposiumDifferentially expressed microRNAs in carotid paraganglioma

Differentially expressed microRNAs in carotid paraganglioma

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Anastasiya Snezhkina1, Elena Pudova2, Vladislav Pavlov3, Maria Fedorova4, George Krasnov5, Anna Kudryavtseva6
1EIMB RAS, Moscow, Russia, leftger@rambler.ru
2EIMB RAS, Moscow, Russia, pudova_elena@inbox.ru
3EIMB RAS, Moscow, Russia, vladislav1pavlov@gmail.com
4EIMB RAS, Moscow, Russia, fedorowams@yandex.ru
5EIMB RAS, Moscow, Russia, gskrasnov@mail.ru
6EIMB RAS, Moscow, Russia, rhizamoeba@mail.ru

Molecular mechanisms underlying the formation of rare tumors are insufficiently known. It the work, we performed the analysis of microRNA profiles in a rare neuroendocrine tumor of the head and neck, carotid paraganglioma (CPGL). We found four microRNAs (miR-1185-1/2-3p, miR-431-5p, miR-504-5p, and miR-200c-3p) that are differentially expressed among CPGL samples studied. This is the first study of microRNA expression in CPGL. Obtained results allow a better understanding of molecular changes associated with the development of the tumor.

Genomics, transcriptomics, bioinformatics symposiumIdentification and description of the genes with a high mutation frequency in vagal paragangliomas

Identification and description of the genes with a high mutation frequency in vagal paragangliomas

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Vladislav Pavlov1, Anastasiya Snezhkina2, George Krasnov3, Dmitry Kalinin4, Alexander Golovyuk5, Anna Kudryavtseva6
1EIMB RAS, vladislav1pavlov@gmail.com
2EIMB RAS, leftger@rambler.ru
3EIMB RAS, gskrasnov@mail.ru
4A.V. Vishnevsky National Medical Research Center of Surgery, dmitry.v.kalinin@gmail.com
5A.V. Vishnevsky National Medical Research Center of Surgery, algolovyuk@inbox.ru
6EIMB RAS, rhizamoeba@mail.ru

Vagal paragangliomas (VPGLs) are rare neuroendocrine tumors of the head and neck. Germline and somatic mutations in a number of genes are associated with the development of VPGLs. The MutSigCV algorithm was implemented in a search for genes characterized by a high mutation frequency in VPGLs. For this purpose, we used the previously obtained results of the exome sequencing of 8 VPGL samples. Ten genes have been identified (ZNF717, MUC16, PKD1L2, TTN, MUC3A, MUC5AC, HYDIN, SSPO, FLG, OBSCN), that can potentially be involved in the development and progression of VPGLs. The involvement of these genes in the VPGL pathogenesis is shown for the first time.

Genomics, transcriptomics, bioinformatics symposiumWebMCOT web-service for prediction of co-occurred DNA motifs in ChIP-seq data

WebMCOT web-service for prediction of co-occurred DNA motifs in ChIP-seq data

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/217.pdf”]
Aleksey Mukhin1, Victor Levitsky2, Dmitriy Y. Oschepkov3, Sergey A. Lashin4
1Institute Cytology and Genetics SB RAS Novosibirsk, Russia, mukhin@bionet.nsc.ru
2Institute Cytology and Genetics SB RAS, levitsky@bionet.nsc.ru
3Institute Cytology and Genetics SB RAS, diman@bionet.nsc.ru
4Institute Cytology and Genetics SB RAS, lashin@bionet.nsc.ru

Regulation of eukaryotic gene expression is controlled by specific regulatory proteins transcription factors. Binding sites of transcription factors are called motifs. Conventionally, genome-wide annotation of motifs performed with chromatin immunoprecipitation followed by massive sequencing (ChIP-seq) approach. The term composite element (CE) implied two closely located and frequently occurred in genomic DNA motifs. CEs contain two overlapping or spacing motifs. Earlier we proposed Motif Co-Occurrence Tool (MCOT) package that is capable of (a) predicting CEs with both overlapping and spacing of motifs in a single ChIP-seq dataset; (b) all predicted CEs were classified by conservation of both participant motifs. This work presents a web interface WebMCOT for MCOT package

Genomics, transcriptomics, bioinformatics symposiumFunctional Roles of the E3 Ubiquitin Ligase HYD in Drosophila Tissues

Functional Roles of the E3 Ubiquitin Ligase HYD in Drosophila Tissues

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/215.pdf”]
Iuliia Galimova1, Natalia Vladimirovna Dorogova2, Svetlana Fedorova3
1IMCB SB RAS, Novosibirsk, Russia, galimova@mcb.nsc.ru
2ICG SB RAS, Novosibirsk, Russia, dorogova@bionet.nsc.ru
3ICG SB RAS, Novosibirsk, Russia, fsveta@bionet.nsc.ru

Drosophila tumor suppressor HYD is required for the regulation of cell proliferation, growth and differentiation. HYD is involved in cell processes at different levels: it can regulate gene expression by binding to its promoters, it binds to some RNA for gene silencing and it participates in protein degradation due to its ubiquitin-ligase activity. Analysis of Drosophila hyd mutants revealed that HYD functions depend on tissue and stage of development: misexpression in larval somatic tissues causes over-proliferation, defects of meiosis and spermatid differentiation in spermatogenesis, and massive cell death with occasional germline overproliferation during oogenesis.

Genomics, transcriptomics, bioinformatics symposiumEvolution and diversity of uORFs in mammals

Evolution and diversity of uORFs in mammals

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Alla Fedorova1, Pasha Baranov2
1University College Cork, School of Biochemistry and Cell Biology, fedorovaad1995@yandex.ru
2University College Cork, School of Biochemistry and Cell Biology, P.Baranov@ucc.ie

5’ regions which are located upstream of CDS (coding sequence) in transcripts have been thought to be untranslated for a long time and therefore have been referred as 5’UTRs (untranslated regions). However, some of them may contain translated parts which are known as uORFs (upstream open reading frames). Some uORFs can participate in regulatory mechanisms of downstream translation and there are known mechanisms of such regulation. However, there are still plenty of uORFs with unknown function or still undiscovered and mis-annotated. In this work we investigated diversity and evolution of uORFs at a genome-wide level using the advent of Ribo-seq method (robosome profiling) and different databases and software. 

Genomics, transcriptomics, bioinformatics symposiumDifferentially methylation of ANKRD53 and GATA3 genes in human miscarriages with trisomy 16

Differentially methylation of ANKRD53 and GATA3 genes in human miscarriages with trisomy 16

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/209.pdf”]
E. N. Tolmacheva1, S.A.Vasilyev2, O.Yu. Vasilyeva3, T.V. Nikitina4, E.A.Sazhenova5, A.V.Markov6, E.S. Serdyukova7, D.I. Zhigalina8, I.N.Lebedev9
1Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, katetolmacheva35@gmail.com
2Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, stas.vasilyev@gmail.com
3Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, vasilyeva.o.yu@gmail.com
4Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, t.nikitina@medgenetics.ru
5Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, elena.sazhenova@mail.ru
6Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, anton.markov@medgenetics.ru
7National Research Tomsk State University, Tomsk, katya.serdyukova.1997@mail.ru
8Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, dasha_150291@mail.ru
9Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, igor.lebedev@medgenetics.ru

An excess dosage of the genes at the whole chromosome can lead to a disturbance of the epigenetic background of the entire genome. We analyzed the DNA methylation of several genes that are important for normal embryogenesis in miscarriages with aneuploidy and normal karyotype.