In vivo validation of a computationally predicted conserved Ath5 target gene set
In vivo validation of a computationally predicted conserved Ath5 target gene set
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DOI：
10.1371/journal.pgen.0030159
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发表时间：
2007-09-01
期刊：
影响因子：
4.5
通讯作者：
Wittbrodt, Joachim
中科院分区：
文献类型：
--
作者：
Del Bene, Filippo;Ettwiller, Laurence;Wittbrodt, Joachim
到目前为止，脊椎动物基因组的复杂性阻碍了转录因子结合位点的计算鉴定。在这里，我们提出了一种利用转录因子的结合位点来预测复杂基因组中转录因子的目标位点的电子计算机程序。在第一步序列中，对密切相关的基因组进行比较，确定保守顺式调节区中的结合位点(系统发育足迹)。随后，更多的远程基因组被引入到比较中，以确定高度保守的因此可能具有功能的结合位点(系统发育筛选)。当应用于无性同系物5(Ath5或ATOH7)的结合位点时，该程序有效地从脊椎动物基因组中的300,000多个实例中过滤出进化上保守的结合位点。我们通过显示与Ath5的共表达和转录调节来验证所连接的目标基因的选择。最后，染色质免疫沉淀证实了靶基因启动子被Ath5占据。因此，我们的程序，应用于整个基因组，是一个快速和预测的工具，以电子筛选给定的转录因子的目标基因与明确的结合位点。
So far, the computational identification of transcription factor binding sites is hampered by the complexity of vertebrate genomes. Here we present an in silico procedure to predict target sites of a transcription factor in complex genomes using its binding site. In a first step sequence, comparison of closely related genomes identifies the binding sites in conserved cis-regulatory regions (phylogenetic footprinting). Subsequently, more remote genomes are introduced into the comparison to identify highly conserved and therefore putatively functional binding sites ( phylogenetic filtering). When applied to the binding site of atonal homolog 5 (Ath5 or ATOH7), this procedure efficiently filters evolutionarily conserved binding sites out of more than 300,000 instances in a vertebrate genome. We validate a selection of the linked target genes by showing coexpression with and transcriptional regulation by Ath5. Finally, chromatin immunoprecipitation demonstrates the occupancy of the target gene promoters by Ath5. Thus, our procedure, applied to whole genomes, is a fast and predictive tool to in silico filter the target genes of a given transcription factor with defined binding site.