Defining nucleosome features regulating the function of chromatin modifiers and remodelers

与遗传物质的表达和维持相关的所有过程都与染色质的动态结构密切相关。细胞已经形成了一个复杂的因子网络，不仅可以调节染色质结构，还可以将其标记为具有不同翻译后修饰的信号平台。染色质修饰剂和重塑剂是大多数基于DNA的过程的关键调节剂，事实上控制细胞周期进程和细胞命运。这些酶进行非常精确的修饰和结构改变，这反过来又被不同的效应模块/蛋白质识别。这被认为是表观遗传现象的核心，其中染色质的信号标记不同的基因组位点，并被效应器读取以翻译生物反应并在分裂/发育期间建立细胞记忆。这些表观遗传标记的准确写入和阅读导致基因组内以靶向方式的染色质动态变化。我们的工作特点的结构和功能的几个多蛋白复合物，控制染色质的修改，重塑和组成。过去的十年强调了使用生物化学来充分剖析起作用的分子机制的必要性。此外，我们已经反复表明需要使用天然样分子组装来重建染色质修饰/重塑酶的准确特异性。我们仍然缺乏对每个复合物的特定作用/作用机制的完整结构和功能理解，以及与基因调控和基因组维持中涉及的其他因子/修饰的必要交叉对话。我们的研究计划旨在通过使用各种不同类型的染色质底物来填补这一知识空白，以生物化学表征调节几种重要染色质重塑和修饰复合物功能的特征。我们大量的染色质底物包括具有不同接头/间距和翻译后修饰的单核/双核体，在特定区域突变或含有非标准组蛋白变体。这些特征中的每一个都可以对不同染色质修饰或重塑复合物的结合和功能产生影响。在短期内，我们将筛选四种重塑剂和三种修饰剂的结合和活性。通过这些酶/底物的组合，我们将获得重要的新的信息，染色质的具体功能，差异调节这些复合物的功能。从长远来看，通过这种生物化学方法发现的新的有趣的概念将在体内结构研究和功能测定中进行测试。总的来说，这项研究将提供大量新的分子信息，这将大大提高我们对控制基因组表达和维持的关键调控过程的理解。

All processes associated with the expression and maintenance of the genetic material are intimately linked to the dynamic structure of chromatin. The cell has developed an intricate network of factors not only to modulate chromatin structure but also to mark it as a signaling platform with different post-translational modifications. Chromatin modifiers and remodelers are critical regulators of most DNA-based processes, de facto controlling cell cycle progression and cell fate. These enzymes perform very precise modifications and structural alterations, which in turn are recognized by different effector modules/proteins. This is thought to be at the heart of the epigenetic phenomena, in which signals to chromatin mark different genomic loci and are read by effectors to translate a biological response and establish cellular memory during division/development. Accurate writing and reading of these epigenetic marks lead to changes in chromatin dynamics, in a targeted manner within the genome. Our work has characterized the structure and function of several multiprotein complexes that control chromatin modifications, remodeling and composition. The past decade has highlighted the need to use biochemistry to fully dissect the molecular mechanisms at play. Furthermore, we have repeatedly shown the need to use native-like molecular assemblies to recreate accurate specificity of the chromatin modifying/remodeling enzymes. We still lack complete structural and functional understanding of each complex' specific role/mechanism of action, as well as essential cross-talks with other factors/modifications implicated in gene regulation and genome maintenance. Our research program aims at filling this knowledge gap by using a wide array of different types of chromatin substrates to biochemically characterize the features that regulate the function of several important chromatin remodeling and modifying complexes. Our large collection of chromatin substrates includes mono-/di-nucleosomes with different linkers/spacings and post-translational modifications, mutated on specific regions or containing non-canonic histone variants. Each one of these features can have an impact on the binding and function of different chromatin modifying or remodeling complexes. In the short term, we will screen the binding and activities of four remodelers and three modifiers. Through these enzyme/substrate combinations we will obtain crucial new information on the specific features of chromatin that differentially regulate the function of these complexes. In the longer term, new interesting concepts uncovered through this biochemical approach will be tested in structural studies and functional assays in vivo. Overall, this research will provide a large amount of new molecular information that will greatly improve our understanding of key regulatory processes controlling expression and maintenance of the genome.