PlantReg: реконструкция связей между регуляторными сетями транскрипционных факторов и контролируемыми ими признаками

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.

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