PRECISE: Software for prediction of cis-acting regulatory elements
PRECISE: Software for prediction of cis-acting regulatory elements
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DOI：
10.1093/jhered/esi094
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发表时间：
2005-09-01
影响因子：
3.1
通讯作者：
Visser, RGF
中科院分区：
文献类型：
--
作者：
Trindade, LM;van Berloo, R;Visser, RGF
基因表达在转录起始水平的调控是高度复杂的，需要多种转录因子的参与。这些转录因子通常是与所谓的顺式作用元件结合的蛋白质或肽，这些元件存在于启动子区域并在不同物种中保守。为了预测这些顺式作用元件，开发了一个名为PRECISE（预测调节顺式作用元件）的计算机程序。该工具的强大之处在于其用户友好的界面和使用经验基序频率表来过滤许多已发现的基序的可能性。工具来创建经验基序频率表（例如，从一个全基因组序列）包括在包。在第一个案例研究中，拟南芥基因组中所有基因的上游区域被用来创建一个经验基序频率表，并通过PRECISE对已知参与淀粉代谢的64个上游基因序列进行了分析。对选取的20个特异性最高的基序进行了详细分析。在这20个基序中，有15个与已知的顺式作用元件序列具有高度或完全的同源性。这些顺式作用元件受光、生长素和脱落酸的调节，并在叶片和种子等汇器官中具有特异性表达。这些因素都在淀粉的生物合成过程中发挥着重要的作用。在第二个案例研究中，我们利用PRECISE分析了拟南芥中由赤霉素（gibberellins， GA）诱导转录的16个基因的上游区域，并与PLACE数据库中存在的基序进行了比较。在由PRECISE发现的最有希望的基序中，有6个是已知的17个GA基序。这些结果表明了PRECISE软件包在预测调控要素方面的能力。
The regulation of gene expression at the transcription initiation level is highly complex and requires the presence of multiple transcription factors. These transcription factors are often proteins or peptides that bind to the so-called cis-acting elements, which are present in the promoter regions and conserved among different species. In order to predict these cis-acting elements, a computer program called PRECISE (Prediction of REgulatory CIS-acting Elements) was developed. The power of the tool lies in its user-friendly interface and in the possibility of using empirical motif frequency tables to filter through the many discovered motifs. The tools to create the empirical motif frequency table (e.g., from a whole genome sequence) are included in the package. In the first case study, the upstream regions of all the genes in theArabidopsisgenome were used to create an empirical motif frequency table and a set of 64 upstream sequences of genes known to be involved in starch metabolism was subjected to analysis by PRECISE. The 20 motifs with the highest specificity in the selected set were analyzed in more detail. Of these 20 motifs, 15 showed a very high or complete homology to the sequences of known cis-acting elements. These cis-acting elements are regulated by light, auxin, and abscisic acid, and confer specific expression in sink organs such as leaves and seeds. All these factors have been shown to play an important role in starch biosynthesis. In the second case study, the upstream regions of 16 genes whose transcription is induced by gibberellins (GA) inArabidopsiswere analyzed with PRECISE and compared to the motifs present in the PLACE database. Among the most promising motifs found by PRECISE were 6 of the 17 known GA motifs. These results indicate the power of the PRECISE software package in the prediction of regulatory elements.