Suzuki Masaharu, Ketterling Matthew G, McCarty Donald R
Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, 32611, USA.
Plant Physiol. 2005 Sep;139(1):437-47. doi: 10.1104/pp.104.058412. Epub 2005 Aug 19.
We have developed a simple quantitative computational approach for objective analysis of cis-regulatory sequences in promoters of coregulated genes. The program, designated MotifFinder, identifies oligo sequences that are overrepresented in promoters of coregulated genes. We used this approach to analyze promoter sequences of Viviparous1 (VP1)/abscisic acid (ABA)-regulated genes and cold-regulated genes, respectively, of Arabidopsis (Arabidopsis thaliana). We detected significantly enriched sequences in up-regulated genes but not in down-regulated genes. This result suggests that gene activation but not repression is mediated by specific and common sequence elements in promoters. The enriched motifs include several known cis-regulatory sequences as well as previously unidentified motifs. With respect to known cis-elements, we dissected the flanking nucleotides of the core sequences of Sph element, ABA response elements (ABREs), and the C repeat/dehydration-responsive element. This analysis identified the motif variants that may correlate with qualitative and quantitative differences in gene expression. While both VP1 and cold responses are mediated in part by ABA signaling via ABREs, these responses correlate with unique ABRE variants distinguished by nucleotides flanking the ACGT core. ABRE and Sph motifs are tightly associated uniquely in the coregulated set of genes showing a strict dependence on VP1 and ABA signaling. Finally, analysis of distribution of the enriched sequences revealed a striking concentration of enriched motifs in a proximal 200-base region of VP1/ABA and cold-regulated promoters. Overall, each class of coregulated genes possesses a discrete set of the enriched motifs with unique distributions in their promoters that may account for the specificity of gene regulation.
我们开发了一种简单的定量计算方法，用于对共调控基因启动子中的顺式调控序列进行客观分析。该程序名为MotifFinder，可识别在共调控基因启动子中过度富集的寡核苷酸序列。我们分别使用这种方法分析了拟南芥（Arabidopsis thaliana）中与胎萌1（VP1）/脱落酸（ABA）调控基因和冷调控基因的启动子序列。我们在上调基因中检测到了显著富集的序列，而在下调基因中未检测到。这一结果表明，基因激活而非抑制是由启动子中的特定和共同序列元件介导的。富集的基序包括几个已知的顺式调控序列以及以前未鉴定的基序。关于已知的顺式元件，我们剖析了Sph元件、ABA响应元件（ABREs）和C重复/脱水响应元件核心序列的侧翼核苷酸。这项分析确定了可能与基因表达的定性和定量差异相关的基序变体。虽然VP1和冷响应都部分由ABA通过ABREs信号传导介导，但这些响应与由ACGT核心侧翼的核苷酸区分的独特ABRE变体相关。ABRE和Sph基序在共调控基因集中紧密且独特地关联，显示出对VP1和ABA信号传导的严格依赖性。最后，对富集序列分布的分析揭示了在VP1/ABA和冷调控启动子近端200碱基区域中富集基序的显著集中。总体而言，每类共调控基因在其启动子中都拥有一组离散的富集基序，具有独特的分布，这可能解释了基因调控的特异性。
