بررسی نواحی تنظیمی در پروموتور ژن‌های هم بیان تحت شرایط تنش دمای پایین در گوجه‌فرنگی

نوع مقاله: علمی پژوهشی

نویسندگان

1 استادیار گروه زراعت و اصلاح نباتات دانشگاه صنعتی شاهرود، ایران

2 محقق دوره پسا دکترا مؤسسه INET، مونیخ، آلمان

چکیده

روش‌های نسل نوین توالی‌یابی همچون RNA-Seq توانایی ارائه حجم بالایی از اطلاعات در زمینه رونوشت ژن‌ها را دارند. بازسازی شبکه ژن‌های هم‌بیان بر اساس اطلاعات حاصل از داده‌های RNA-seq اطلاعات ارزشمندی جهت درک سیستم پاسخی گیاهان به تغییرات محیطی را ارائه می‌دهد. لذا در این تحقیق پروفایل کامل بیانی ژن‌های گوجه فرنگی تحت تیمار دمای پایین با استفاده از روش شبکه‌های هم بیان وزن‌دار مورد آنالیز قرار گرفت. نتایج کلاسترهای هم بیان نشان داد که 20267ژن‌ نرمال شده در هشت ماژول معنادار قرار می‌گیرند. نتایج آنالیز عبارات GO نشان داد که بین گروه‌های هم بیان عملکردهای متفاوتی بر حسب فرایندهای بیولوژی و عملکرد مولکولی وجود دارد. بر این اساس ماژول اول به پروتئین‌های شوک دمایی (HSPs) اختصاص یافت. پروتئین کینازها و پروتئین‌های درگیر در تغییرات پس از ترجمه به‌ترتیب در ماژول دوم و سوم قرار گرفتند. پروموتور ژن‌های ماژول پنج با توجه به الگوی بیان متفاوت در ژنوتیپ‌ها مورد بررسی قرار گرفت. عناصر سیس ACGTG و TTGACدر پروموتور همه ژن‌ها مشاهده شدند. عوامل رونویسی خانواده AP2/ERF و ZF-HD دارای بیشترین جایگاه اتصال در پروموتور ژن‌های ماژول پنج بودند. نتایج حاصل توانست عناصر تنظیمی کلیدی که در تنظیم بیان یک شبکه ژنی تحت تنش سرما و فرایندهای آنتی‌اکسیدانتی درگیر بودند، را معرفی نماید.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Study of regulatory elements in promoter regions of co-expressed genes in tomato when facing low temperatures

نویسندگان [English]

  • Parviz Heidari 1
  • Thomas Nussbaumer 2
1 Assistant Professor, Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran.
2 Postdoc Researcher, INET Institute, Munchen, Germany.
چکیده [English]

Next-generation sequencing (NGS) techniques such as RNA-Seq can provide expression information per gene and can be used to construct co-expression networks. These networks can produce valuable information to understand plant responses when facing environmental changes. In this study, a complete profile of tomato gene expressions under low temperature treatment was analyzed by “Weighted Gene Co-expression Network Analysis”. The clustering results allowed to group 20,267 genes into eight modules. The results of Gene ontology (GO) term analysis highlighted different functions between co-expression groups in terms of biological process and molecular function. Accordingly, the first module overrepresented to heat shock proteins (HSPs). Protein kinases and proteins involved in post-translational modification were in the second and third modules, respectively. The promoter of genes in fifth module was screened according to the different expression patterns in the tomato genotypes. The cis-elements such as ACGTG and TTGAC were observed in promoter site of all genes. The transcription factor families of AP2 / ERF and ZF-HD have the highest binding status in promoter of genes of the fifth module. The results present the key cis-regulatory elements that effect on co-expressed genes network and involve in anti-oxidant process under cold stress.

کلیدواژه‌ها [English]

  • Cis elements
  • Modules
  • Weighted Gene Co-expression Network
  • Molecular functions
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