vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-25-100vavilov-4877Research ArticleКОМПЬЮТЕРНАЯ ГЕНОМИКАMICROBIAL GENETICS AND BIOTECHNOLOGYПрограмма PlantReg 1.1: анализ взаимного расположения сайтов связывания транскрипционных факторов в промоторах генов-мишеней для уточнения молекулярных механизмов их активности в регуляторных сетяхPlantReg 1.1 identifies the mutual arrangement of transcription factor binding sites in the target promoters for the elucidation of molecular mechanisms within regulatory networkshttps://orcid.org/0000-0001-8813-8941ЛаврехаВ. В.LavrekhaV. V.

Новосибирск

Novosibirsk

https://orcid.org/0009-0004-0738-5625ОмельянчукН. А.OmelyanchukN. A.

Новосибирск

Novosibirsk

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

Новосибирск

Novosibirsk

https://orcid.org/0009-0004-9869-8263РябовЮ. А.RyabovY. A.

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Novosibirsk

https://orcid.org/0009-0000-5660-3693МукебеноваП. К.MukebenovaP. K.

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Novosibirsk

https://orcid.org/0009-0005-7316-7690ЗемлянскаяЕ. В.ZemlyanskayaE. V.

Новосибирск

Novosibirsk

ezemlyanskaya@bionet.nsc.ruФедеральный 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 FederationФедеральный 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 Federation202512122025297940951Copyright © Лавреха В.В., Омельянчук Н.А., Богомолов А.Г., Рябов Ю.А., Мукебенова П.К., Землянская Е.В., 20252025Лавреха В.В., Омельянчук Н.А., Богомолов А.Г., Рябов Ю.А., Мукебенова П.К., Землянская Е.В.Lavrekha V.V., Omelyanchuk N.A., Bogomolov A.G., Ryabov Y.A., Mukebenova P.K., Zemlyanskaya E.V.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4877

   Развитие высокопроизводительного секвенирования расширило возможности изучения регуляции экспрессии генов, в том числе для реконструкции генных регуляторных сетей и регуляторных сетей транскрипционных факторов (РСТФ). Актуальной задачей остается выявление молекулярных аспектов регуляции данными сетями биологических процессов. Решение этой задачи для растений позволит существенно продвинуться в понимании механизмов формирования хозяйственно важных признаков. Ранее мы разработали программу PlantReg для реконструкции транскрипционной регуляции биологических процессов у модельного вида Arabidopsis thaliana L. Воспроизводимые этой программой связи между РСТФ и генами, обеспечивающими протекание биологических процессов, охарактеризованы по типу регуляции (активация/подавление). Однако программа не позволяла определять, в каких случаях активация/подавление экспрессии гена-мишени обусловлены кооперативным или конкурентным взаимодействием транскрипционных факторов (ТФ). Мы предложили использовать информацию о взаимном расположении сайтов связывания (СС) ТФ в промоторе гена-мишени, а также данные о типе активности трансактивационных доменов ТФ для выявления кооперативного/конкурентного действия ТФ. Мы усовершенствовали программу, создав версию PlantReg 1.1, где обеспечили возможность точной локализации СС ТФ в протяженных районах связывания ТФ, устанавливаемых на основании полногеномных профилей DAP-seq (https://plamorph.sysbio.ru/fannotf/). Для демонстрации возможностей программы была исследована регуляция генов-мишеней ранее реконструированных нами РСТФ ответа на ауксин и солевой стресс у A. thaliana. В фокусе изучения были гены, кодирующие белки, участвующие в процессах биосинтеза хлорофилла и лигнина, биогенеза рибосом и в передаче сигнала абсцизовой кислоты. В данной работе установлено, что частота случаев конкурентной регуляции под влиянием ауксина и солевого стресса может быть достаточно высока (около 30 %). Показано, что конкуренция ТФ семейства bZIP за общие СС является значимым механизмом подавления транскрипции в ответ на ауксин, и что ауксин и солевой стресс могут задействовать общие механизмы конкурентной регуляции для модуляции экспрессии некоторых генов сигнального пути абсцизовой кислоты.

   The development of high-throughput sequencing has expanded the possibilities for studying the regulation of gene expression, including the reconstruction of gene regulatory networks and transcription factor regulatory networks (TFRNs). Identifying the molecular aspects for regulation of biological processes via these networks remains a challenge. Solving this problem for plants will significantly advance the understanding of the mechanisms shaping agronomically important traits. Previously, we developed the PlantReg program to reconstruct the transcriptional regulation of biological processes in the model species Arabidopsis thaliana L. The links established by this program between TFRNs and the genes regulating biological processes specify the type of regulation (activation/suppression). However, the program does not determine whether activation/suppression of the target gene is due to the cooperative or competitive interaction of transcription factors (TFs). We assumed that using information on the mutual arrangement of TF binding sites (BSs) in the target gene promoter as well as data on the activity type of TF effector domains would help to identify the cooperative/competitive action of TFs. We improved the program and created PlantReg 1.1, which enables precise localization of TF BSs in extended TF binding regions identified from genome-wide DAP-seq profiles (https://plamorph.sysbio.ru/fannotf/). To demonstrate the capabilities of the program, we used it to investigate the regulation of target genes in previously reconstructed TFRNs for auxin response and early reaction to salt stress in A. thaliana. The study focused on genes encoding proteins involved in chlorophyll and lignin biosynthesis, ribosome biogenesis, and abscisic acid (ABA) signaling. We revealed that the frequency of competitive regulation under the influence of auxin or salt stress could be quite high (approximately 30 %). We demonstrated that competition between bZIP family TFs for common BS is a significant mechanism of transcriptional repression in response to auxin, and that auxin and salt stress can engage common competitive regulatory mechanisms to modulate the expression of some genes in the ABA signaling pathway.

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