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

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Genomics,  bioinformatics  and evolution symposium

Showing: 21 - 28 of 28 RESULTS
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

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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

Genomics,  bioinformatics  and evolution symposiumGenomic analyses of Novymonas esmeraldas and Ca. Pandoraea novymonadis

Genomic analyses of Novymonas esmeraldas and Ca. Pandoraea novymonadis

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/254.pdf”]
Alexandra Zakharova1, Daria Tashyreva2, Jorge Morales3, Eva Nowack4, Julius LukeЕЎ5, Vyacheslav Yurchenko6
1Life Science Research Centre, University of Ostrava, Ostrava, Czech Republic, alexandraz.6946@gmail.com
2Institute of Parasitology, Biological Centre, ДЊeskГ© BudД›jovice, Czech Republic, tashyreva@paru.cas.cz
3Heinrich Heine University, DГјsseldorf, Germany, jjfreites@hotmail.com
4Heinrich Heine University, DГјsseldorf, Germany, E.Nowack@uni-duesseldorf.de
5Institute of Parasitology, Biological Centre, ДЊeskГ© BudД›jovice, Czech Republic, jula@paru.cas.cz
6Life Science Research Centre, University of Ostrava, Ostrava, Czech Republic, Vyacheslav.Yurchenko@osu.cz

Members of the family Trypanosomatidae are intensively studied because some of them are infectious agents of dangerous human ailments, such as Chagas disease, African sleeping sickness and leishmaniasis. It has been recently demonstrated that representatives of 4 trypanosomatid genera of 2 subfamilies [Leishmaniinae (genus Novymonas) and Strigomonadinae (genera Angomonas, Strigomonas and Kentomonas)] harbor bacterial symbionts. The endosymbiont of Novymonas esmeraldas is Ca. Pandoraea novymonadis. This symbiotic system is of particular interest, since none of the participants has close relatives involved in such relationships, indicating its independent and relatively recent origin.

In this work, we have investigated genomes and proteomes of N. esmeraldas and Ca. Pandoraea novymonadis. We found and investigated factors involved in the symbiotic interactions. Biochemical analysis demonstrated that numerous host-encoded proteins were enriched in the bacterial fraction, represented by ОІ-oxidation enzymes, transporters, transmembrane proteins and others. We have found that members of this endosymbiotic system may be a good model to study the establishment and development of symbiosis between bacteria and protists.

Genomics,  bioinformatics  and evolution symposiumGenome and Karyotype Evolution after Whole Genome Duplication in Free-Living Flatworms of the Genus Macrostomum

Genome and Karyotype Evolution after Whole Genome Duplication in Free-Living Flatworms of the Genus Macrostomum

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/221.pdf”]
Kira Zadesenets1, Nikita Ershov2, Dmitry Oshchepkov3, Eugene Berezikov4, Lukas Schärer5, Nikolay B. Rubtsov6
1ICG SB RAS, kira_z@bionet.nsc.ru
2ICG SB RAS, nikotinmail@mail.ru
3ICG SB RAS, diman@bionet.nsc.ru
4ERIBA, Groningen, The Netherlands, e.berezikov@umcg.nl
5Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland, lukas.scharer@unibas.ch
6ICG SB RAS, rubt@bionet.nsc.ru

Whole genome duplication (WGD) is a large-scale evolutionary transformation that took place in genome evolution in many taxa of existing animal species. However, the mechanisms underlying the early stages of genome evolution after a WGD event in animals has remained unclear. The study of genome organization of neopolyploid species may shed light on the processes of genome reorganization leading to its re-diploidization after a recent round of WGD. Earlier we uncovered a group of free-living flatworms in which genomes have likely undergone a recent WGD. We found out that karyotype instability was linked to hidden polyploidy in both species M. lignano (2n = 8) and its sibling species M. janickei (2n = 10). Additional studies of other species of the genus Macrostomum revealed a new species (further called M. mirumnovem) with a highly unstable karyotype. The detailed cytogenetic analyses using a set of different DNA probes (microdissected region- and chromosome specific DNA probes, DNA repeats, unique DNA fragments) revealed the peculiarities of karyotype and genome organization in three Macrostomum species with unstable karyotypes. Similar to M. lignano and M. janickei, our findings suggest that M. mirumnovem arose via whole genome duplication (WGD) followed by considerable reshuffling of its chromosomes. The combined approach allowed us to explore the peculiarity of the M. lignano genome organization, the strategy included bioinformatics analysis of the existed genome assemblies of M. lignano and NGS data for its separate chromosomes. Based on the obtained results, we suggest possible evolutionary scenarios for the emergence and reorganization of the karyotypes and genomes of the post-WGD Macrostomum species.

Genomics,  bioinformatics  and evolution symposiumMethylation and expression profiles in Apoe vicinity point to specific neighboring interaction of Apoe and TOMM40 genes: implication for The Alzheimer disease.

Methylation and expression profiles in Apoe vicinity point to specific neighboring interaction of Apoe and TOMM40 genes: implication for The Alzheimer disease.

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Vladimir Babenko1
1Institute of Cytology and Genetics SB_RAS, bob@bionet.nsc.ru

We assessed the dynamics of 8 genes including TOMM40, Apoe and other adjacent ones for overall chromatin marks landscape, including methylation profiles across ENCODE brain cell lines, and histone and ctcf marks. We revealed the region manifests Hi-C topology dynamics in a cell-specific manner. Additionally, based on methylation and histone marks profiles we underscore competitive manner of genes expression implying disrupted locus wide genes expression balance in Alzheimer patients due to Apoe extended locus methylation profile alteration.

Genomics,  bioinformatics  and evolution symposiumDistribution of Bax protein in the rat hippocampus

Distribution of Bax protein in the rat hippocampus

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/155.pdf”]
Pavel D. Lisachev1, Anna L. Proskura2
1Institute of Computational Technologies SB RAS, lisachev@ngs.ru
2Institute of Computational Technologies SB RAS, annleop@mail.ru

AbstractBcl-2 family protein Bax is involved in mechanisms of synaptic plasticity. The induction of long term potentiation in hippocampal slices leads to increased Bax expression, but the localization of these changes remains unclear. Bax immunoreactivity is visually detected mainly in the layer of pyramidal neurons and is rarely detected in S100B-positive glial cells. However, a quantitative assessment of Bax colocalization with glial and neuronal markers (S100B and NeuN, respectively) showed that although the Bax content in S100B-positive glial cells is really low, the Bax neuronal somatic pool is not the main source of Bax protein in the hippocampus.

Genomics,  bioinformatics  and evolution symposiumCircular RNA host gene and orthologue prediction using the self-designed CircParser pipeline

Circular RNA host gene and orthologue prediction using the self-designed CircParser pipeline

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Artem Nedoluzhko1, Fedor Sharko2, Golam Rbanni3, Anton Teslyuk4, Ioannis Konstantinidis5, Jorge M.O. Fernandes6
1Nord University, artem.nedoluzhko@nord.no
2NRC \”Kurchatov Institute\”, fedosic@gmail.com
3Nord University, golam.rbbani@nord.no
4NRC \”Kurchatov Institute\”, anthony.teslyuk@gmail.com
5Nord University, ioannis.konstantinidis@nord.no
6Nord University, jorge.m.fernandes@nord.no

Circular RNAs (circRNAs) are long noncoding RNAs that play a significant role in various biological processes, including embryonic development and stress responses. A number of circRNA de novo and host gene prediction tools are available to date, but their ability to accurately predict circRNA host genes is limited in the case of low-quality genome assemblies or annotations.

Here we describe CircParser, a novel, easy to use and Unix/Linux pipeline for circular RNAs host gene and orthologue prediction using the blastn program and the freely available bedtools software. CircParser is most useful for circRNA host gene prediction analysis in whole transcriptomic datasets for low-quality assembled as well as poorly annotated genomes.

We demonstrate the prediction capacity of CircParser on a recently published transcriptomic data set from the wild and domesticated females of Nile tilapia (Oreochromis niloticus) fast muscle using the five most popular circRNAs in silico prediction tools – CIRI, CIRI2, CircExplorer2, find_circ, and circFinder (Fig. 1).

The Perl implementation of CircParser is available at https://github.com/SharkoTools/CircParser

Genomics,  bioinformatics  and evolution symposiumComparative genomics of heat shock proteins system in extremophile nonbiting midges

Comparative genomics of heat shock proteins system in extremophile nonbiting midges

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[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/128.pdf”]
Olga Kozlova1, Guzel Gazizova2, Elena Shagimardanova3, Oleg Gusev4
1Kazan Federal University, olga-sphinx@yandex.ru
2Kazan Federal University, grgazizova@gmail.com
3Kazan Federal University, rjuka@mail.ru
4Kazan Federal University, gaijin.ru@gmail.com

Here we compare the number and expression profiles of HSP-coding genes in larvae of Chironomidae family (Diptera), who are known for their ability to successfully combat abiotic stresses using wide range of behavioral, morphological and biochemical features. In order to perform comparative studies we sequenced and assembled genomes of 4 chironomids from different habitats and also sequenced whole-genome RNA of their larvae in control and stressed conditions. It was shown that compact genome sizes (up to 200 Mb) are typical for Chironomidae, while changes in size of a genome are mediated by elongation and shortening of introns length, as well as by changes in quantity and content of dispersed repeats. For all extremophile species under consideration species-specific gene expansion accompanied by formation of compact clusters in a genome was detected. The most amplitudinous reaction towards abiotic stress (desiccation) was shown by anhydrobiotic species Polypedilum vanderplanki (Africa). As for HSP-coding genes, it was noticed that genes of HSP20 and HSP70 show the most dramatic and universal up-regulation of expression in response to abiotic stress, while genes of chaperonins (HSP60) tend to be up-regulated in response to desiccation, but not to heat shock. But the most surprising notion was linked to acid-tolerant species Polipedilum cf. tamanigrum (Japan), because none of HSP-coding genes in this species showed statistically significant up-regulation, what may be explained by absence of special regulatory sequence – heat shock element (HSE) in their promotor regions.

Genomics,  bioinformatics  and evolution symposiumThe phenotypic manifestation of Wolbachia genetic diversity in host fitness

The phenotypic manifestation of Wolbachia genetic diversity in host fitness

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/84.pdf”]
Elena Burdina1, Nataly Gruntenko2, Petr Menshanov3, Roman Bykov4, Yury Ilinsky5, Inga Rauschenbach6
1Institute of Cytology and Genetics SB RAS, bella79@list.ru
2Institute of Cytology and Genetics SB RAS, nataly@bionet.nsc.ru
3Institute of Cytology and Genetics SB RAS, eternity@bionet.nsc.ru
4Institute of Cytology and Genetics SB RAS, bykovra@bionet.nsc.ru
5Institute of Cytology and Genetics SB RAS, paulee@bionet.nsc.ru
6Institute of Cytology and Genetics SB RAS, iraushen@bionet.nsc.ru

The maternally inherited bacterial endosymbiont of arthropods Wolbachia is deeply integrated into the biology of its host and can be regarded as a component of the host cell. There is evidence that Wolbachia contributes to the fitness of the host species, including the increase in heat stress resistance and resistance to viral infections. However, the exact mechanisms of this contribution, as well as Wolbachia-host interactions in total, remain largely unclear. In order to study these mechanisms we composed several Drosophila melanogaster lineages with the same nuclear background (wild type Bi90 line) and different Wolbachia genotypes in cytoplasm. Here we showed that the symbiont did not effect on host insect heat stress resistance and fertility with the exception of two unique Wolbachia strains: the well-known pathogenic wMelPop strain and first discovered here wMelPlus.