Genomic Regulation at the Nuclear Periphery

描述(由申请人提供)： 一百多年来，科学家们一直在观察细胞核内染色体组织的空间偏好。虽然我们现在已经破译了从酵母到人类的真核物种的整个基因组序列，但这些基因组是如何物理组织以支持基因组功能的仍然是一个悬而未决的问题。在过去的几年里，在酵母和哺乳动物模型中的几项研究表明，基因与核外围的联系，可能与内核膜蛋白，起到调节转录的作用。这些研究的重要性得到了突显，因为发现几种人类疾病与包括Emerin在内的完整内核膜蛋白的突变有关，这会导致Emery-Dreifuss肌营养不良症(EDMD)。然而，治疗策略的设计具有极大的挑战性，因为对于核外围如何影响转录的两个关键问题仍然存在很大的困惑：1)在酵母中，与核外围的关联似乎激活了一些基因，而抑制了其他基因；2)将报告基因异源驱动到外围是否足以诱导哺乳动物细胞的转录抑制仍然存在争议。在这项建议中，我们的策略是在两个酵母模型，酿酒酵母和庞贝酵母(目标1)中得出染色质-内核膜相互作用的全基因组图谱。这些生物显示出80%的蛋白质编码基因的一致性，但缺乏显著的联结；我们可以利用这些特性来识别具有保守的内核膜结合位点的基因(以及它们所贡献的调控途径)，我们预测这将反映功能重要性。在目标2中，我们将研究调控刺激如何改变基因与核外周的联系，评估在调控这些基因中对特定内核膜蛋白的需求，并测试工程和可逆系链在核外周重述基因调控的能力。我们的长期目标是了解我们如何改善内核膜蛋白突变导致的转录组变化，并建立范例，使我们能够设计策略来应对包括EDMD在内的越来越多的遗传病，这些疾病统称为“核包膜病”。

DESCRIPTION (provided by applicant): For over one hundred years, scientists have observed spatial preferences for the organization of the chromosomes within the nucleus. While we have now deciphered the entire genome sequences of eukaryotic species from yeasts to humans, how those genomes are physically organized to support genomic functions remains an open question. Within the last few years, several studies in yeast and mammalian models have suggested that association of genes with the nuclear periphery, likely with inner nuclear membrane proteins, acts to regulate transcription. The importance of these studies is underscored by the discovery that several human diseases are associated with mutations within integral inner nuclear membrane proteins including emerin, which causes Emery-Dreifuss Muscular Dystrophy (EDMD). Treatment strategies are extremely challenging to devise, however, since there remains substantial confusion over two key issues of how the nuclear periphery influences transcription: 1) in yeast, association with the nuclear periphery appears to activate some genes while repressing others, and 2) it remains controversial whether heterologously driving a reporter gene to the periphery is sufficient to induce transcriptional repression in mammalian cells. In this proposal, our strategy is to derive genome-wide maps of chromatin-inner nuclear membrane interactions in two yeast models, S. cerevisiae and S. pombe (Aim 1). These organisms display correspondence of 80% of their protein coding genes while lacking significant synteny; we can leverage these properties to identify genes (and the regulatory pathways they contribute to) with conserved sites for inner nuclear membrane association, which we predict will reflect functional importance. In Aim 2, we will examine how regulatory stimuli alter the association of genes with the nuclear periphery, assess the requirement for specific inner nuclear membrane proteins in the regulation of these genes, and test the ability of engineered and reversible tethers to recapitulate gene regulation at the nuclear periphery. Our long-term goal is to understand how we might ameliorate the changes in the transcriptome that result from mutations in inner nuclear membrane proteins, and establish paradigms to allow us to devise strategies to tackle a growing number of genetic diseases including EDMD, which are collectively called "nuclear envelopathies".