Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli.
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli.
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DOI：
10.1186/s12864-018-4469-4
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发表时间：
2018-05-09
期刊：
影响因子：
4.4
通讯作者：
Chang WC
中科院分区：
文献类型：
--
作者：
Chow CN;Chiang-Hsieh YF;Chien CH;Zheng HQ;Lee TY;Wu NY;Tseng KC;Hou PF;Chang WC
转录因子（TF）在植物发育和应对环境胁迫过程中发挥着重要作用。然而，在内源和外源刺激下转录因子、顺式作用元件和靶基因表达之间的关系尚未得到系统的表征。在这里，我们开发了一系列生物信息学分析方法，通过使用来自非生物胁迫和激素治疗的大量基因表达数据来推断转录调控。过滤TF编码基因的表达谱后，获得291个条件特异性转录因子（CsTF）。然后根据每个 CsTF 将差异表达的基因分为各种共表达基因组。在热应激和 ABA 治疗的案例研究中，根据我们的生物信息学方法，发现了几种已知的和新颖的顺式作用元件。值得注意的是，热响应元件的回文序列被识别，并且还从热休克蛋白-DNA复合物的3D蛋白结构中获得。值得注意的是，富集的 8 聚体基序中过多的 3 聚体和 4 聚体基序可能是 CsTF 的核心顺式元件。此外，结果表明，根据不同的条件，相同的 CsTF 的 DNA 结合偏好是不同的。总体结果表明，这项研究可能有助于识别条件特异性顺式和反式调节元件，并有助于我们理解转录因子、顺式作用元件和靶基因表达之间的关系。本文的在线版本 (10.1186/s12864-018-4469-4) 包含补充材料，可供授权用户使用。
Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. Here, we developed a series of bioinformatics analysis methods to infer transcriptional regulation by using numerous gene expression data from abiotic stresses and hormones treatments. After filtering the expression profiles of TF-encoding genes, 291 condition specific transcription factors (CsTFs) were obtained. Differentially expressed genes were then classified into various co-expressed gene groups based on each CsTFs. In the case studies of heat stress and ABA treatment, several known and novel cis-acting elements were identified following our bioinformatics approach. Significantly, a palindromic sequence of heat-responsive elements is recognized, and also obtained from a 3D protein structure of heat-shock protein-DNA complex. Notably, overrepresented 3- and 4-mer motifs in an enriched 8-mer motif could be a core cis-element for a CsTF. In addition, the results suggest DNA binding preferences of the same CsTFs are different according to various conditions. The overall results illustrate this study may be useful in identifying condition specific cis- and trans- regulatory elements and facilitate our understanding of the relationships among TFs, cis-acting elements and target gene expression. The online version of this article (10.1186/s12864-018-4469-4) contains supplementary material, which is available to authorized users.
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影响因子：
14.9
作者：
Goujon M;McWilliam H;Li W;Valentin F;Squizzato S;Paern J;Lopez R
通讯作者：
Lopez R
DOI：
10.1093/dnares/dsr040
发表时间：
2012
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Maruyama K;Todaka D;Mizoi J;Yoshida T;Kidokoro S;Matsukura S;Takasaki H;Sakurai T;Yamamoto YY;Yoshiwara K;Kojima M;Sakakibara H;Shinozaki K;Yamaguchi-Shinozaki K
通讯作者：
Yamaguchi-Shinozaki K
DOI：
10.1073/pnas.1316278111
发表时间：
2014-02-11
影响因子：
11.1
作者：
Franco-Zorrilla, Jose M.;Lopez-Vidriero, Irene;Solano, Roberto
通讯作者：
Solano, Roberto
影响因子：
7.4
作者：
Ikeda, Miho;Mitsuda, Nobutaka;Ohme-Takagi, Masaru
通讯作者：
Ohme-Takagi, Masaru
拟南芥中NAC转录因子的DNA结合位置景观和调节网络分析。
影响因子：
14.9
作者：
Lindemose S;Jensen MK;Van de Velde J;O'Shea C;Heyndrickx KS;Workman CT;Vandepoele K;Skriver K;De Masi F
通讯作者：
De Masi F