Brachyury-downstream gene networks in the notochord

描述（由申请人提供）：脊索在所有脊索动物胚胎中起着支持和塑造发育体计划的基本作用。转录因子Brachyury是脊索形成所必需的，已知它可以激活脊索动物胚胎（如海鞘和人类）中许多脊索基因的转录。Brachyury编码区的突变与椎体畸形和脊柱裂的风险增加有关。此外，最近的研究表明，人类Brachyury基因座的重复与家族性脊索瘤（一种恶性脊索源性肿瘤）之间存在直接关联。Brachyury-下游基因级联的知识，特别是Brachyury下游或与Brachyury协同作用的转录因子的身份仍然是不完整的。我们使用基础脊索动物Ciona ninteinalis（海鞘），一种简单但信息丰富的脊椎动物亲戚，作为一种可接近的，快速发展的模型系统，用于鉴定进化保守的转录激活因子，并阐明它们与Ciona Brachyury （Ci-Bra）的等级关系。通过对脊索顺式调控模块（CRMs）的结构和功能的比较分析，以及对从脊椎动物进化保守的脊索转录因子的具体搜索，我们获得了初步数据，这些数据使我们假设：1)Ci-Bra通过转录中介间接控制部分靶点；2)Ci-Bra通过与其他转录因子协同作用来控制部分靶点。我们建议表征迟发性脊索转录因子最近确定在我们的实验室。我们的主要目标是阐明这些因素在脊索发育中所起的作用，并阐明它们在Ci-Bra基因调控网络中的等级地位。我们的具体目标是：1)分析一个新发现的转录因子的发育作用和靶点，以及它与Ci-Bra的关系；2)鉴定本实验室鉴定的脊索CRMs的激活因子，研究其在脊索发育中的作用；3)通过分析Ci-Bra的一个潜在转录介质Ci-XBP-1及其下游靶点，表征Ci-Bra在脊索晚期分化中的作用。本研究的广泛范围是利用Ciona的实验优势，快速获得脊索发育和进化过程中基因表达控制机制的基本见解。从更广泛的角度来看，本研究旨在阐明Brachyury控制其靶基因的分子机制，这些基因在受损时负责脊索畸形和脊索衍生的肿瘤发生。鉴于在所有被分析的脊索动物中Brachyury在脊索形成中的普遍作用，这些发现很可能适用于包括人类在内的脊椎动物。

DESCRIPTION (provided by applicant): The notochord plays a fundamental role in supporting and patterning the developing body plan in all chordate embryos. The transcription factor Brachyury is required for notochord formation and it is known to activate the transcription of numerous notochord genes in chordate embryos as different as sea squirts and humans. Mutations in the Brachyury coding region have been associated with vertebral malformations and increased risk of spina bifida. In addition, recent studies have indicated a direct association between the duplication of the human Brachyury locus and familial chordoma, a malignant notochord-derived tumor. The knowledge of the Brachyury-downstream gene cascade and, in particular, the identities of the transcription factors that act downstream of or in concert with Brachyury is still fragmentary. We use the basal chordate Ciona intestinalis (sea squirt), a simple yet informative vertebrate relative, as an accessible, fast-developing model system for identifying evolutionarily conserved transcriptional activators and for elucidating their hierarchical relationship with Ciona Brachyury (Ci-Bra). Our preliminary data, gathered from the comparative analysis of the structure and function of notochord cis-regulatory modules (CRMs) and from specific searches for notochord transcription factors evolutionarily conserved from Ciona to vertebrates, lead us to hypothesize that: 1) Ci-Bra controls part of its targets indirectly, via transcriptional intermediaries and 2) Ci-Bra controls part of its targets by acting synergistically with other transcription factors. We propose to characterize late-onset notochord transcription factors recently identified in our lab. Our main goals are to elucidate the role played by these factors in notochord development and to shed light on their hierarchical position within the Ci-Bra gene regulatory network. Our specific aims are: 1) Analyze the developmental role and targets of a newly identified transcription factor, and its relationship with Ci-Bra; 2) Identify the activators controlling the notochord CRMs identified in our lab and study their function in notochord development; 3) Characterize the role of Ci-Bra in late notochord differentiation through the analysis of one of its potential transcriptional intermediaries, Ci-XBP-1, and of its downstream targets. The broad scope of the proposed research is to exploit the experimental advantages of Ciona to rapidly gain basic insights into the mechanisms controlling gene expression in the notochord during development and evolution. In a wider perspective, this research aims to shed light on the molecular mechanisms employed by Brachyury to control its target genes, which, when compromised, are responsible for notochord malformations and notochord-derived tumorigenesis. Given the pervasive role of Brachyury in notochord formation in all chordates analyzed, it is likely that these findings will be applicable to vertebrates, including humans. PUBLIC HEALTH RELEVANCE: Brachyury is a transcription factor required for the formation of the notochord, a structure that supports and patterns the body of all chordates, including humans. In addition to its developmental role, Brachyury is also a specific marker, immunotherapeutic target and causative agent of chordomas, malignant notochord-derived tumors. The proposed studies use the Ciona embryo to rapidly shed light on Brachyury- downstream transcription factors, the way they are controlled by Brachyury, their function, and their target genes.