vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-24-102vavilov-4416Research ArticleСИСТЕМНАЯ КОМПЬЮТЕРНАЯ БИОЛОГИЯSYSTEMS COMPUTATIONAL BIOLOGYPlantReg: реконструкция связей между регуляторными сетями транскрипционных факторов и контролируемыми ими признакамиPlantReg: the reconstruction of links between transcription factor regulatory networks and biological processes under their controlhttps://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/0009-0005-7316-7690ЗемлянскаяЕ. 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 Federation202426012025288950959Copyright © Лавреха В.В., Омельянчук Н.А., Богомолов А.Г., Землянская Е.В., 20252025Лавреха В.В., Омельянчук Н.А., Богомолов А.Г., Землянская Е.В.Lavrekha V.V., Omelyanchuk N.A., Bogomolov A.G., Zemlyanskaya E.V.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4416

Описание пути от гена к признаку как основная задача многих отраслей биологии в настоящее время оснащается новыми методами не только в технике экспериментов, но и в системном анализе их результатов. Плейотропный эффект гена осуществляется за счет его участия во многих биологических процессах, вовлеченных в разные признаки. Широкое распространение полногеномного секвенирования транскриптов и районов связывания транскрипционных факторов (ТФ) сделало актуальными задачи установления плейотропных эффектов ТФ за счет знаний о функциях их мишеней, составление списков ТФ, регулирующих интересующие исследователя биологические процессы, описание путей их действия (первичные и вторичные мишени, мишени следующих порядков, взаимодействие между ТФ в исследуемом процессе). Ранее мы разработали метод реконструкции регуляторных сетей ТФ и предложили подход, позволяющий выявлять, какие биологические процессы и каким образом эти сети регулируют. В данной работе мы реализовали этот подход в виде программы PlantReg, доступной пользователям через веб-интерфейс. В статье описан принцип работы программы. На вход подаются список генов и список ТФ – известных или предполагаемых регуляторов транскрипции этих генов. На выходе программа выдает список биологических процессов, которые обогащены в этих генах, а также информацию о том, какими ТФ и через какие гены эти процессы регулируются. Работа PlantReg проиллюстрирована на примере исследования регуляции процессов, инициируемых на начальных этапах ответа на солевой стресс у Arabidopsis thaliana L. С помощью программы PlantReg нами выявлены биологические процессы, стимулируемые в раннем ответе на солевой стресс, и специфический набор ТФ, активирующих каждый из этих процессов. На примере одного из таких процессов – ответа на фитогормон абсцизовую кислоту – мы показали, что солевой стресс активирует в основном сигнальный путь этого гормона, и выделили ключевые ТФ в этой регуляции. Таким образом, программа PlantReg – удобный инструмент для создания гипотез о молекулярных механизмах регуляции признаков растений.

The description of the path from a gene to a trait, as the main task of many areas in biology, is currently being equipped with new methods affecting not only experimental techniques, but also analysis of the results. The pleiotropic effect of a gene is due to its participation in numerous biological processes involved in different traits. A widespread use of genome-wide sequencing of transcripts and transcription factor (TF) binding regions has made the following tasks relevant: unveiling pleiotropic effects of TFs based on the functions of their target genes; compiling the lists of TFs that regulate biological processes of interest; and describing the ways of TF functioning (their primary and secondary targets, higher order targets, TF interactions in the process under study). We have previously developed a method for the reconstruction of TF regulatory networks and proposed an approach that allows identifying which biological processes are controlled by these networks and how this control is exerted. In this paper, we have implemented the approach as PlantReg, a program available as a web service. The paper describes how the program works. The input consists of a list of genes and a list of TFs – known or putative transcriptional regulators of these genes. As an output, the program provides a list of biological processes enriched for these genes, as well as information about by which TFs and through which genes these processes are controlled. We illustrated the use of PlantReg deciphering transcriptional regulation of processes initiated at the early salt stress response in Arabidopsis thaliana L. With PlantReg, we identified biological processes stimulated by the stress, and specific sets of TFs that activate each process. With one of these processes (response to abscisic acid) as an example, we showed that salt stress mainly affects abscisic acid signaling and identified key TFs in this regulation. Thus, PlantReg is a convenient tool for generating hypotheses about the molecular mechanisms that control plant traits.

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