Genomic cis-regulatory networks in the early Ciona intestinalis embryo
Genomic cis-regulatory networks in the early Ciona intestinalis embryo
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DOI：
10.1242/dev.046789
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发表时间：
2010-05-15
期刊：
影响因子：
4.6
通讯作者：
Satou, Yutaka
中科院分区：
文献类型：
--
作者：
Kubo, Atsushi;Suzuki, Nobuhiro;Satou, Yutaka
在动物发育过程中，精确的时空基因表达是通过基因调控网络来实现的，其中序列特异性转录因子（TF）与靶基因的顺式调控元件结合。虽然许多顺式调控元件已被确定在各种系统中，其全球架构的基因网络，调节动物的发展还没有得到很好的理解。在这里，我们确定的核心网络的结构，在顺式调节水平的脊索玻璃海鞘早期胚胎的染色质免疫沉淀（ChIP）的11个TF。所研究的11个TF基因的调控系统彼此紧密相连。通过将ChIP数据分析与先前对表达谱和调控基因敲除的综合分析结果相结合，我们发现大多数先前确定的相互作用是直接的。我们通过研究网络如何在顺式调节结构水平上指定这些组织，重点关注负责玻璃海鞘中胚层组织的顺式调节网络。我们还发现了许多相互作用，没有被预测的简单的基因敲除实验，我们表明，一个显着的比例TF-DNA相互作用作出重大贡献的调控目标基因的表达。
Precise spatiotemporal gene expression during animal development is achieved through gene regulatory networks, in which sequence-specific transcription factors (TFs) bind to cis-regulatory elements of target genes. Although numerous cis-regulatory elements have been identified in a variety of systems, their global architecture in the gene networks that regulate animal development is not well understood. Here, we determined the structure of the core networks at the cis-regulatory level in early embryos of the chordate Ciona intestinalis by chromatin immunoprecipitation (ChIP) of 11 TFs. The regulatory systems of the 11 TF genes examined were tightly interconnected with one another. By combining analysis of the ChIP data with the results of previous comprehensive analyses of expression profiles and knockdown of regulatory genes, we found that most of the previously determined interactions are direct. We focused on cis-regulatory networks responsible for the Ciona mesodermal tissues by examining how the networks specify these tissues at the level of their cis-regulatory architecture. We also found many interactions that had not been predicted by simple gene knockdown experiments, and we showed that a significant fraction of TF-DNA interactions make major contributions to the regulatory control of target gene expression.