Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences

The binding sites of transcription factors (TFs) in upstream DNA regions are called transcription factor binding sites (TFBSs). TFBSs are important elements for regulating gene expression. To date, there have been few studies on the profiles of TFBSs in plants. In total, 4,873 sequences with 5ʹ upstream regions from 8530 wheat fl-cDNA sequences were used to predict TFBSs. We found 4572 TFBSs for the MADS TF family, which was twice as many as for bHLH (1951), B3 (1951), HB superfamily (1914), ERF (1820), and AP2/ERF (1725) TFs, and was approximately four times higher than the remaining TFBS types. The percentage of TFBSs and TF members showed a distinct distribution in different tissues. Overall, the distribution of TFBSs in the upstream regions of wheat fl-cDNA sequences had significant difference. Meanwhile, high frequencies of some types of TFBSs were found in specific regions in the upstream sequences. Both TFs and fl-cDNA with TFBSs predicted in the same tissues exhibited specific distribution preferences for regulating gene expression. The tissue-specific analysis of TFs and fl-cDNA with TFBSs provides useful information for functional research, and can be used to identify relationships between tissue-specific TFs and fl-cDNA with TFBSs. Moreover, the positional distribution of TFBSs indicates that some types of wheat TFBS have different positional distribution preferences in the upstream regions of genes. Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences

上游DNA区域内的转录因子（Transcription Factors, TFs）结合位点，被定义为转录因子结合位点（Transcription Factor Binding Sites, TFBSs）。TFBSs是调控基因表达的核心功能元件。迄今为止，关于植物TFBSs分布特征的研究仍较为有限。本研究共计从8530条小麦fl-cDNA序列中筛选得到4873条带有5'上游区域的序列，用于TFBSs的预测。本次预测共获得4572个MADS转录因子家族的TFBSs，其数量为bHLH（1951个）、B3（1951个）、HB超家族（1914个）、ERF（1820个）及AP2/ERF（1725个）转录因子的2倍，约为其余TFBS类型总数的4倍。不同组织中TFBSs的占比及对应转录因子成员的分布呈现显著差异。整体而言，小麦fl-cDNA序列上游区域的TFBSs分布存在显著异质性。同时，部分类型的TFBSs在上游序列的特定区域呈现出较高的富集频率。在同一组织中被预测携带TFBSs的转录因子与fl-cDNA，均展现出适配基因表达调控的特异性分布偏好。针对携带TFBSs的转录因子与fl-cDNA的组织特异性分析，可为相关功能研究提供宝贵的参考信息，同时可用于鉴定组织特异性转录因子与携带TFBSs的fl-cDNA之间的潜在关联。此外，TFBSs的位置分布特征表明，部分类型的小麦TFBSs在基因上游区域存在差异化的位置分布偏好。小麦fl-cDNA序列来源基因的转录因子结合位点鉴定及其位置分布分析