Methods for evolutionary analysis of eukaryotic transcriptional regulation

描述(申请人提供：狐狸转录因子基因家族在哺乳动物中已扩展到40多个成员，并参与各种关键的发育过程和人类疾病。然而，关于它们的进化扩展、功能细化、转录调控和选择等几个关键问题还没有完全了解。基因复制是进化创新的主要驱动力，因为它允许有机体通过专门化或多样化来阐述现有的生物功能，同时潜在地避免负面适应效应。新的或特定的基因功能的阐述至少涉及两条不同的途径：(1)改变基因的空间和时间表达模式；(2)改变相互作用伙伴，包括DNA和蛋白质。表达模式的改变可能涉及上游顺式调控元件的进化分化，而相互作用伙伴的改变可能涉及蛋白质功能结构域的序列变化。以前的比较和进化研究主要集中在基因序列、结构和网络的保守方面。研究分歧的部分挑战在于，很难区分功能上相关的分歧和中性漂移。我们建议开发以进化差异的相关模式为关键的计算算法和统计分析方法，以识别新的调控元件，并帮助阐明基因家族成员的进化及其与疾病表型的关系。在具体目标1中，我们将开发一种新的方法-基因组内系统发生足迹-通过利用调控序列和同源基因表达中相关的差异模式来识别顺式元件。在特定的目标2中，我们将研究基因旁路在功能上多样化的其他途径，并描述这些途径之间的关系。在具体目标3中，我们将开发方法来量化人类顺式调节多态之间的选择压力和上位性相互作用。这些方法将广泛应用于多物种的基因家族。对特定基因家族的应用将为其功能扩展提供洞察力。选定的预测将得到实验验证。除了提供对人类种群中基因家族扩大、转录调控和种内变异的更广泛的进化理解外，拟议研究的具体应用将具有直接的生物医学意义。与公共卫生相关：狐狸转录因子基因家族在哺乳动物中已扩大到40多个成员，并参与各种关键的发育过程和人类疾病。然而，关于它们的进化扩展、功能细化、转录调控和选择等几个关键问题还没有完全了解。我们建议开发计算算法和统计分析方法来解决其中一些关于基因家族进化和转录调控的问题。

DESCRIPTION (provided by applicant: FOX family of transcription factor genes have expanded to over 40 members in mammals, and are involved in a variety of key developmental processes and human diseases. However, several key question concerning their evolutionary expansion, functional elaboration, transcriptional regulation, and selection are not completely understood. Gene duplication is a major driver of evolutionary innovation, as it allows an organism to elaborate existing biological function with specialization or diversification, while at the same time potentially avoiding negative fitness effects. Elaboration of new or specialized gene functions can involve at least two distinct pathways: (1) alteration of the spatial and temporal expression pattern of the gene, (2) alteration of the interaction partners, both DNA and protein. Alteration of expression patterns is likely to involve evolutionary divergence of the upstream cis regulatory elements while the alteration of interaction partners may involve sequence changes in functional domains of the protein. Previous comparative and evolutionary studies have focused on conserved aspects of gene sequence, structure and networks. Part of the challenge in studying divergence is that it is difficult to distinguish functionally relevant divergence from neutral drift. We propose to develop computational algorithms and statistical analysis methods that key in on correlated patterns of evolutionary divergence to identify novel regulatory elements and help elucidate the evolution of gene family members and their relation to disease phenotypes. In specific aim 1 we will develop a novel method - Intra-genomic Phylogenetic Footprinting - to identify cis elements by exploiting correlated patterns of divergence in the regulatory-sequence and the expression of paralogs. In specific aim 2, we will investigate additional pathways by which gene paralogs diversify in function and characterize the relationships between these pathways. In specific aim 3, we will develop methods to quantify selective pressure and epistatic interactions among human cis regulatory polymorphisms. The methods will be comprehensively applied to gene families in multiple species. Application to specific gene families will provide insights into their functional expansion. Selected predictions will be experimentally validated. Besides providing a broader evolutionary understanding of gene family expansion, transcriptional regulation, and intraspecific variability in human populations, specific applications of the proposed research will be of direct biomedical relevance. PUBLIC HEALTH RELEVANCE: FOX family of transcription factor genes have expanded to over 40 members in mammals, and are involved in a variety of key developmental processes and human diseases. However, several key question concerning their evolutionary expansion, functional elaboration, transcriptional regulation, and selection are not completely understood. We proposed to develop computational algorithms and statistical analysis methods to address some of these questions concerning the evolution of gene families and transcriptional regulation.