Molecular mechanisms of cell fate specification

神经源性动物板区基因调控网络指导性规范(55%)。 利用生物信息学以及基于微阵列和原位杂交的筛选，我们已经鉴定了在动物平板中选择性表达的大多数调控蛋白(50)。我们将通过监测单个基因功能丧失对其他基因表达的数量水平和空间模式的影响来确定基因在网络中的位置。其中最有趣的基因之一是FoxQ2，这是已知的最早的apd特异性基因，我们今年展示了它对于apd中三种已知细胞类型的分化是必要的。出乎意料的是，FoxQ2还抑制了节点的表达，节点编码了启动胚胎次级轴图案形成的关键信号分子。FoxQ2从结节反应的动物半球中被依赖于植物卵裂球中典型的Wnt信号的信号消除。我们认为，FoxQ2提供了一个连接Wnt和Node信号的检查点，它协调胚胎主轴和次轴的发育。这是一种新的机制，对于建立胚胎的主要组织类型至关重要，已经提交了一份手稿供发表(Yaguchi，S.，Yaguchi，J.，Angerer，R.C.和Angerer，L.M.(2007)Wnt-FoxQ2节点路径连接了海胆胚胎的主轴和次轴规范。戴夫。单元格，正在审核中。) 早期内胚层规范的机制。(25%) 我们已经发现，通过Alk4/5/7受体的ActivinB信号是在裂解阶段从微粒及其后代发出的经典信号，这是内胚层发育和适时原肠形成所必需的。这一早期信号被认为是海胆胚胎内胚层发育中依赖于b-连环素的第一步。ActivinB或Alk4/5/7功能的丧失类似于微粒的丧失，异位的ActivinB信号可以由异位的微粒诱导。我们已经确定了内胚层基因调控网络中对ActivinB信号做出反应的特定基因子集。由于这些结果改变了海胆内胚层基因调控网络的现状，一个主要的目标是确定ActivinB信号如何适应内胚层规范的机制。一份手稿正在准备中(Sethi，A.，Angerer，R.C.和Angerer，L.M.(2007)ActivinB/Alk4/5/7信号是海胆胚胎早期内胚层指定所需的早期微米依赖信号)。 生物信息学(20%) 我们继续改进公开可用的海胆基因序列分析的计算方法，将所有海胆基因预测与GO类别、时间表达和转录组数据联系起来。这些方法对于建立控制不同细胞类型发育的全面基因网络至关重要。

The gene regulatory network guiding specification of the neurogenic animal plate domain (APD)(55%). Using bioinformatics as well as microarray-based and in situ hybridization screens, we have identified most of the regulatory proteins (50) expressed selectively in the animal plate. We will determine positions of genes with the network by monitoring effects of loss of individual gene functions on quantitative levels and spatial patterns of expression of the others. One of the most interesting genes is FoxQ2, the earliest known APD-specific gene, which we showed this year to be necessary for differentiation of the three known cell types in the APD. Unexpectedly, FoxQ2 also inhibits expression of nodal, which encodes the key signaling molecule that initiates patterning along the secondary axis of the embryo. FoxQ2 is eliminated from the nodal-responsive animal hemisphere by signals dependent on canonical Wnt signaling from underlying vegetal blastomeres. We propose that FoxQ2 provides a checkpoint linking Wnt and nodal signals, which coordinates development long the primary and secondary axes of the embryo. This is a new mechanism that is critical for establishing the major tissue types of the embryo and a manuscript has been submitted for publicatin (Yaguchi, S., Yaguchi, J., Angerer, R.C. and Angerer, L.M. (2007) A Wnt-FoxQ2-nodal pathway links primary and secondary axis specification in sea urchin embryos. Dev. Cell, in review.) The mechanisms of early endoderm specification.(25%) We have discovered that ActivinB signaling through the Alk4/5/7 receptor is the classic signal sent during cleavage stages from micromeres and their progeny, which is required for endoderm development and timely gastrulation. This early signal is thought to be the first nuclear b-catenin-dependent step in sea urchin embryo endoderm development. Loss of either ActivinB or Alk4/5/7 function mimics loss of micromeres and ectopic ActivinB signaling can be induced by ectopic micromeres. We have identified a specific subset of genes in the endoderm gene regulatory network that respond to ActivinB signaling. Because these results alter the current status of the sea urchin endomesoderm gene regulatory network, a major goal is to determine how ActivinB signaling fits into the mechanism underlying endoderm specification. A manuscript is in preparatino (Sethi, A., Angerer, R.C. and Angerer, L.M. (2007) ActivinB/Alk4/5/7 signaling is an early micromere-dependent signal required for early endoderm specification in sea urchin embryos). Bioinformatics.(20%) We continued to improve publicly available computational methods for sequence analysis of sea urchin genes by linking all of the sea urchin gene predictions to GO categories, to temporal expression and transcriptome data. These methods are essential for building the comprehensive networks of genes that control development of different cell types.