A universal algorithm for genome-wide in silicio identification of biologically significant gene promoter putative cis-regulatory-elements;: identification of new elements for reactive oxygen species and sucrose signaling in Arabidopsis
A universal algorithm for genome-wide in silicio identification of biologically significant gene promoter putative cis-regulatory-elements;: identification of new elements for reactive oxygen species and sucrose signaling in Arabidopsis
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DOI：
10.1111/j.1365-313x.2005.02634.x
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发表时间：
2006-02-01
期刊：
影响因子：
7.2
通讯作者：
Karpinski, S
中科院分区：
文献类型：
--
作者：
Geisler, M;Kleczkowski, LA;Karpinski, S
许多顺式调控元件（cre）的短基序可以在大多数拟南芥基因的启动子中找到，这就提出了它们的存在如何赋予特定调控的问题。我们开发了一种通用算法来测试CRE的生物学意义，首先鉴定每个具有CRE的拟南芥基因，然后在多个DNA微阵列上将该元件的存在或缺失与基因表达谱进行统计相关。该算法在拟南芥中成功验证了先前表征的脱落酸、乙烯、蔗糖和干旱响应cre，表明这些元素的存在确实与处理特异性基因诱导相关。随后，我们使用标准基序采样方法鉴定了128个由过量光照、活性氧和蔗糖诱导的推测基序。我们的算法能够从128个新的cre中筛选出20个，这些cre与热、活性氧和/或蔗糖的基因诱导显著相关。通过分析自然序列变异基因的表达，在硅氧烷中检测cre的位置、取向和序列特异性。在三种新的cre中，正向取向与蔗糖诱导相关，反向取向与蔗糖抑制相关。用短启动子片段转化的拟南芥细胞悬浮培养或与GUS报告基因融合的人工启动子，实验证实了预测的新型cre的功能。我们的全基因组分析为新发现的cre的生物学意义的有机验证开辟了新的可能性，并允许后续选择这些cre进行实验研究。
Short motifs of many cis-regulatory elements ( CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment-specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell-suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome-wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.