Function and evolution of zinc finger transcription factors

与大多数转录因子（TF）不同，大C2 H2锌指家族在后生动物中表现出广泛的重复和多样化选择。大多数C2 H2蛋白质的特征很差，因此它们的功能作用以及驱动它们进化轨迹的因素仍然未知。然而，在一种情况下，四足特异性KRAB-C2 H2蛋白，其代表了所有人类C2 H2蛋白的大约一半，最近的证据表明，该家族通过招募KAP 1辅阻遏物来进化以沉默逆转录元件。* 我的实验室最近表明，C2 H2蛋白的基因组结合位点是高度多样的，并且每个人KRAB-C2 H2蛋白结合特定类别的内源性逆转录因子（ERE）。奇怪的是，大多数结合的ERE都是古老的，长期以来一直没有活性，这表明结合它们的蛋白质和/或ERE本身承担了额外的角色。我们还发现，C2 H2蛋白，包括KRAB-C2 H2s，往往具有独特的蛋白质-蛋白质相互作用（PPI）的配置文件，这表明新的主机功能可以通过改变效应功能在相对较短的进化时间尺度。这些观察结果表明，一个基因组特异性的调控网络模型，不同于保守的监管模式普遍存在于进化发展的文献，以及不同的力量，驱动基因扩增。* 在这里，我们提出了两条主要的实验路线，以探索四足动物和非四足动物脊椎动物中的C2 H2蛋白，以获得更广泛和更详细的功能和进化。* （1）我们将绘制基因组结合位点图，以确定哺乳动物中正向KRAB-C2 H2蛋白的DNA结合位点变化率，以及鱼类中最近进化的C2 H2蛋白是否完全结合ERE。* （2）我们将探索C2 H2蛋白的PPI的机制和进化。我们预计有三种不同的进化“模式”，我们将详细探讨每一种模式：（a）结构化蛋白结合模块的多样化，（B）使用非结构化或非结构域多肽作为新PPI的模板，或（c）利用C2 H2（或其他结构域）用于PPI，这将代表“兼职”的一个例子。* 整个项目将对脊椎动物进化的研究以及我们对调控网络和元素的理解做出重大贡献。这是一份为期一年的发现补助金的续期申请。 在此期间，我的小组已经发表了两篇先前被描述为初步数据的论文，并提交了第三篇（见附录）。 我很感谢这笔资金，它允许生成新的初步数据，并期待在此广泛修订（和更名）应用程序的基础上获得更长的资助间隔。

Unlike most transcription factors (TFs), the large C2H2 zinc finger family displays widespread duplication and diversifying selection in metazoans. Most C2H2 proteins are poorly characterized, and therefore it remains unknown what are their functional roles and what drives their evolutionary trajectories. In one case, however that of the tetrapod-specific KRAB-C2H2 proteins, which represent roughly half of all human C2H2 proteins recent evidence indicates that the family evolves to silence retroelements by recruiting the KAP1 corepressor. *** My lab recently showed that the genomic binding sites of C2H2 proteins are highly diverse and that each human KRAB-C2H2 protein binds a specific class of endogenous retroelements (EREs). Curiously, most of the EREs bound are ancient and have long been inactive, suggesting that the proteins that bind them, and/or the EREs themselves, have taken on additional roles. We have also found that C2H2 proteins, including KRAB-C2H2s, often have unique protein-protein interaction (PPI) profiles, suggesting that new host functions can be acquired by changing the effector function over relatively short evolutionary timescales. These observations suggest a genome-specific regulatory network model, distinct from the conserved regulatory models prevalent in the evolutionary development literature, as well as different forces that drive the gene expansions. *** Here, we propose two major lines of experimentation to explore C2H2 proteins in both tetrapod and non-tetrapod vertebrates, in order to gain a broader and more detailed view of their function and evolution. *** (1) We will map genomic binding sites to determine the rate at which DNA binding sites change for orthologous KRAB-C2H2 proteins across mammals, and whether EREs are bound at all by recently evolved C2H2 proteins in fish. *** (2) We will explore the mechanisms and evolution of PPIs with C2H2 proteins. We anticipate three different evolutionary “modes”, each of which we will explore in detail: (a) Diversification in structured protein-binding modules, (b) use of unstructured or non-domain polypeptide as a template for new PPIs, or (c) utilization of C2H2 (or other domains) for PPIs, which would represent an example of “moonlighting”. *** The project overall will make a major contribution to the study of vertebrate evolution, and to our understanding of regulatory networks and elements.*****This is a renewal application for a Discovery Grant that was funded for one year. In the interim, my group has published two papers previously described as preliminary data, and submitted a third (see Appendices). I am grateful for the funding, which allowed generation of new preliminary data, and look forward to a longer funding interval on the basis of this extensively revised (and retitled) application.****