A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo
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DOI：
10.1006/dbio.2002.0635
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发表时间：
2002-06-01
影响因子：
2.7
通讯作者：
Bolouri, H
中科院分区：
文献类型：
--
作者：
Davidson, EH;Rast, JP;Bolouri, H
我们提出了目前形式的一个临时的DNA序列为基础的调控基因网络，在大纲中解释如何在海胆胚胎内中胚层规范控制。随着新基因的加入和新的实验结果的出现，网络的模型处于不断修正和增长的过程中;最新版本见http://www.its.caltech.edu/similar tomirsky/endomeso.htm（End-mes基因网络更新）。该网络目前包含40多个基因，其中许多是在这项工作中新发现的，并且大多数编码DNA结合转录调控因子。网络的体系结构最初是通过构建一个逻辑模型来实现的，该模型集成了目前可用于内中胚层规范的大量实验证据。网络中基因之间的内部联系已被确定功能，通过测量调控扰动的影响，在网络中的所有相关基因的表达。已经应用了五种扰动：（1）使用靶向网络中许多关键调控基因的吗啉代反义寡核苷酸;（2）通过构建Engrailed阻遏物结构域融合物将其他调控因子转化为显性阻遏物;（3）给定调控因子从遗传表达构建体和从注射的mRNA异位表达;（4）通过引入编码钙粘蛋白胞内结构域的mRNA阻断β-连环蛋白/Tcf途径;和（5）通过引入编码Notch受体胞外域的mRNA阻断Notch信号传导途径。网络模型预测了将每个基因连接到网络中的顺式调节输入。因此，其结构是可测试的顺式调控分析。已对包含网络中大量基因的红球海胆和杂色绿绒螯蟹基因组BAC重组体进行了测序和注释。该模型的顺式调控预测的测试是非常方便的种间计算序列比较，它提供了一个快速识别可能的顺式调控元件的实验分析之前。该网络指定了早期卵裂和原肠胚阶段之间的基因组编码调控过程。这些控制着微节谱系和初始veg（2）内中胚层结构域的特化;中央veg（2）中胚层结构域的囊胚期分离（即，次级间充质祖细胞区域）;这些区域内特化状态的稳定;以及一些下游分化基因的激活。每个时空阶段的规范表示在一个子元素的网络模型，在特定阶段的相关胚胎细胞核内的监管事件。(C)2002 Elsevier Science（美国）。
We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/similar tomirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of the model are greatly facilitated by interspecific computational sequence comparison, which affords a rapid identification of likely cis-regulatory elements in advance of experimental analysis. The network specifies genomically encoded regulatory processes between early cleavage and gastrula stages. These control the specification of the micromere lineage and of the initial veg(2) endomesodermal domain; the blastula-stage separation of the central veg(2) mesodermal domain (i.e., the secondary mesenchyme progenitor field) from the peripheral veg(2) endodermal domain; the stabilization of specification state within these domains; and activation of some downstream differentiation genes. Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages. (C) 2002 Elsevier Science (USA).