vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-25-101vavilov-4878Research ArticleКОМПЬЮТЕРНАЯ ГЕНОМИКАMICROBIAL GENETICS AND BIOTECHNOLOGYБаза знаний FlyDEGdb по дифференциально экспрессирующимся генам Drosophila melanogaster – модельного объекта биомедициныFlyDEGdb knowledge base on differentially expressed genes of Drosophila melanogaster, a model object in biomedicinehttps://orcid.org/0000-0003-3247-0114ПодколоднаяО. А.PodkolodnayaO. A.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-5233-1755ДерюженкоМ. А.DeryuzhenkoM. A.

Новосибирск

Novosibirsk

ТвердохлебН. Н.TverdokhlebN. N.

Новосибирск

Novosibirsk

https://orcid.org/0009-0006-3933-208XЗолотареваК. А.ZolotarevaK. A.

Новосибирск

Novosibirsk

https://orcid.org/0009-0000-4441-6188МаковкаЮ. В.MakovkaYu. V.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-9132-7997ПодколодныйН. Л.PodkolodnyN. L.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-1940-9389СусловВ. В.SuslovV. V.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-2724-5441ЧадаеваИ. В.ChadaevaI. V.

Новосибирск

Novosibirsk

https://orcid.org/0009-0009-8397-9771ФедосееваЛ. А.FedoseevaL. A.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-8807-2580СеряпинаА. А.SeryapinaA. A.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-6097-5155ОщепковД. Ю.OshchepkovD. Yu.

Новосибирск

Novosibirsk

https://orcid.org/0000-0003-4359-6089БогомоловА. Г.BogomolovA. G.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-8672-7216КондратюкЕ. Ю.KondratyukE. Yu.

Новосибирск; Новосибирская область; Краснообск

Novosibirsk; Novosibirsk region; Krasnoobsk

https://orcid.org/0000-0003-0942-8460РединаО. Е.RedinaO. E.

Новосибирск

Novosibirsk

https://orcid.org/0000-0002-1550-1647МаркельА. Л.MarkelA. L.

Новосибирск

Novosibirsk

https://orcid.org/0000-0003-3272-1518ГрунтенкоН. Е.GruntenkoN. E.

Новосибирск

Novosibirsk

https://orcid.org/0000-0003-1663-318XПономаренкоМ. П.PonomarenkoM. P.

Новосибирск

Novosibirsk

pon@bionet.nsc.ruФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Институт вычислительной математики и математической геофизики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Institute of Computational Mathematics and Mathematical Geophysics of the Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Сибирский федеральный научный центр агробиотехнологий Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университетРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityRussian Federation202512122025297952962Copyright © Подколодная О.А., Дерюженко М.А., Твердохлеб Н.Н., Золотарева К.А., Маковка Ю.В., Подколодный Н.Л., Суслов В.В., Чадаева И.В., Федосеева Л.А., Серяпина А.А., Ощепков Д.Ю., Богомолов А.Г., Кондратюк Е.Ю., Редина О.Е., Маркель А.Л., Грунтенко Н.Е., Пономаренко М.П., 20252025Подколодная О.А., Дерюженко М.А., Твердохлеб Н.Н., Золотарева К.А., Маковка Ю.В., Подколодный Н.Л., Суслов В.В., Чадаева И.В., Федосеева Л.А., Серяпина А.А., Ощепков Д.Ю., Богомолов А.Г., Кондратюк Е.Ю., Редина О.Е., Маркель А.Л., Грунтенко Н.Е., Пономаренко М.П.Podkolodnaya O.A., Deryuzhenko M.A., Tverdokhleb N.N., Zolotareva K.A., Makovka Y.V., Podkolodny N.L., Suslov V.V., Chadaeva I.V., Fedoseeva L.A., Seryapina A.A., Oshchepkov D.Y., Bogomolov A.G., Kondratyuk E.Y., Redina O.E., Markel A.L., Gruntenko N.E., Ponomarenko M.P.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4878

   С 1909 г. благодаря исследованиям нобелевского лауреата Моргана дрозофила Drosophila melanogaster стала одним из самых популярных модельных животных в генетике. Фундаментальные исследования с дрозофилой в качестве модельного объекта неоднократно были отмечены Нобелевской премией: в 1946 г. (Мёллер, мутагенез при рентгеновском излучении), в 1995 (Льюис, Нюссляйн-Фольхард, Вишаус, генетический контроль эмбриогенеза), в 2004 (Эксел и Бак, обонятельная система), в 2011 (Стайнман, дендритные клетки в адаптивном иммунитете; Бётлер и Офман, активация врожденного иммунитета) и в 2017 г. (Холл, Росбаш и Янг, молекулярный механизм циркадного ритма). Столь яркая роль дрозофилы в генетике обусловлена рядом ее ключевых признаков: кратким жизненным циклом, частой сменой поколений, легкостью в содержании, высокой плодовитостью, малым размером, прозрачностью эмбриона, простым строением личинки, возможностью визуальных наблюдений хромосомных перестроек за счет наличия политенных хромосом, доступностью для молекулярно-генетических манипуляций. Кроме того, благодаря высокой консервативности ряда сигнальных путей и генных сетей дрозофилы и их сходству с таковыми у млекопитающих и человека в совокупности с техническим развитием геномного секвенирования стало возможно использование D. melanogaster как модельного объекта в биомедицинских исследованиях в области фармакологии, токсикологии, кардиологии, онкологии, иммунологии, геронтологии и радиобиологии для поиска генетической и эпигенетической основ патогенеза болезней человека. В настоящей статье описана созданная нами курируемая база знаний FlyDEGdb (https://www.sysbio.ru/FlyDEGdb), в которой представлена информация о дифференциально экспрессирующихся генах (ДЭГ) дрозофилы, экстрагированная из 50 научных статей с экспериментальными данными об изменении экспрессии 20 058 генов (80 %) из числа всех 25 079 генов дрозофилы согласно базе данных NCBI Gene под действием 52 стрессовых факторов, включая высокую и низкую температуры, обезвоживание, тяжелые металлы, радиацию, голод, яды, бытовую химию, лекарства, удобрения, инсектициды, пестициды и гербициды. Содержание базы знаний FlyDEGdb проиллюстрировано на примере гена dysf (dysfusion) дрозофилы, который был идентифицирован в качестве ДЭГ при множестве стрессовых воздействий: холодовом шоке и в испытаниях на токсичность гербицида параквата, растворителя толуола, лекарственного препарата менадиона, пищевой добавки Е923. В FlyDEGdb представлена информация об изменениях экспрессии гена dysf и его гомологов Clk, cyc, per у дрозофилы и генов NPAS4, CLOCK, BMAL1, PER1 и PER2 человека, а также информация о биологических процессах, в которые вовлечены эти гены: созревание ооцитов (оогенез), регуляция стресс-ответа и циркадного ритма, канцерогенез, старение и др. Поэтому FlyDEGdb, содержащая информацию о таком модельном организме, как дрозофила, может быть полезна для исследователей, работающих в области молекулярной биологии и генетики человека и животных, физиологии, трансляционной медицины, фармакологии, диетологии, агрохимии, радиобиологии, токсикологии и биоинформатики.

   Since the work of Nobel Prize winner Thomas Morgan in 1909, the fruit fly Drosophila melanogaster has been one of the most popular model animals in genetics. Research using this fly was honored with the Nobel Prize many times: in 1946 (Muller, X-ray mutagenesis), in 1995 (Lewis, Nüsslein-Volhard, Wieschaus, genetic control of embryogenesis), in 2004 (Axel and Buck, the olfactory system), in 2011 (Steinman, dendritic cells in adaptive immunity; Beutler and Hoffman, activation of innate immunity), and in 2017 (Hall, Rosbash and Young, the molecular mechanism of the circadian rhythm). The prominent role of Drosophila in genetics is due to its key features: short life cycle, frequent generational turnover, ease of maintenance, high fertility, small size, transparent embryos, simple larval structure, the possibility to observe visually chromosomal rearrangements due to the presence of polytene chromosomes, and accessibility to molecular genetic manipulation. Furthermore, the highly conserved nature of several signaling pathways and gene networks in Drosophila and their similarity to those of mammals and humans, taken together with the development of high-throughput genomic sequencing, motivated the use of D. melanogaster as a model organism in biomedical fields of inquiry: pharmacology, toxicology, cardiology, oncology, immunology, gerontology, and radiobiology. These studies add to the understanding of the genetic and epigenetic basis of the pathogenesis of human diseases. This paper describes our curated knowledge base, FlyDEGdb (https://www.sysbio.ru/FlyDEGdb), which stores information on differentially expressed genes (DEGs) in Drosophila. This information was extracted from 50 scientific articles containing experimental data on changes in the expression of 20,058 genes (80 %) out of the 25,079 Drosophila genes stored in the NCBI Gene database. The changes were induced by 52 stress factors, including heat and cold exposure, dehydration, heavy metals, radiation, starvation, household chemicals, drugs, fertilizers, insecticides, pesticides, herbicides, and other toxicants. The FlyDEGdb knowledge base is illustrated using the example of the dysf (dysfusion) Drosophila gene, which had been identified as a DEG under cold shock and in toxicity tests of the herbicide paraquat, the solvent toluene, the drug menadione, and the food additive E923. FlyDEGdb stores information on changes in the expression of the dysf gene and its homologues: (a) the Clk, cyc, and per genes in Drosophila, and (b) the NPAS4, CLOCK, BMAL1, PER1, and PER2 genes in humans. These data are supplemented with information on the biological processes in which these genes are involved: oocyte maturation (oogenesis), regulation of stress response and circadian rhythm, carcinogenesis, aging, etc. Therefore, FlyDEGdb, containing information on the widely used model organism, Drosophila, can be helpful for researchers working in the molecular biology and genetics of humans and animals, physiology, translational medicine, pharmacology, dietetics, agricultural chemistry, radiobiology, toxicology, and bioinformatics.

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The authors declare that there are no conflicts of interest present.