DNA-binding specificities of plant transcription factors and their potential to define target genes
DNA-binding specificities of plant transcription factors and their potential to define target genes
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DOI：
10.1073/pnas.1316278111
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发表时间：
2014-02-11
影响因子：
11.1
通讯作者：
Solano, Roberto
中科院分区：
文献类型：
--
作者：
Franco-Zorrilla, Jose M.;Lopez-Vidriero, Irene;Solano, Roberto
转录因子（TFS）通过与其靶基因启动子中的顺式调节特定序列结合来调节基因表达。与遗传密码相反，转录调节代码远非被解密，并且由TF的序列特异性，TFS和染色质能力之间的组合合作确定。在这里，我们使用蛋白质结合微阵列表征了代表25个家族的63个植物TF的目标序列特异性来解决这些决定因素之一。值得注意的是，这些TF中几乎一半识别出二级基序，在某些情况下，这些基序与主要元素完全无关。对TFS突变体的核心基因和转录组数据的分析显示，所有已鉴定序列的80％以上的功能意义和每个TF的至少一个目标序列的功能意义。此外，将目标序列信息与共表达分析相结合，我们可以通过特定的DNA序列预测TF作为激活剂或阻遏物的功能。我们的数据支持顺式调节元件与使用蛋白质结合微阵列在体外确定的序列之间的相关性，并提供了探索植物中调节网络的框架。
Transcription factors (TFs) regulate gene expression through binding to cis-regulatory specific sequences in the promoters of their target genes. In contrast to the genetic code, the transcriptional regulatory code is far from being deciphered and is determined by sequence specificity of TFs, combinatorial cooperation between TFs and chromatin competence. Here we addressed one of these determinants by characterizing the target sequence specificity of 63 plant TFs representing 25 families, using protein-binding microarrays. Remarkably, almost half of these TFs recognized secondary motifs, which in some cases were completely unrelated to the primary element. Analyses of coregulated genes and transcriptomic data from TFs mutants showed the functional significance of over 80% of all identified sequences and of at least one target sequence per TF. Moreover, combining the target sequence information with coexpression analysis we could predict the function of a TF as activator or repressor through a particular DNA sequence. Our data support the correlation between cis-regulatory elements and the sequence determined in vitro using the protein-binding microarray and provides a framework to explore regulatory networks in plants.