Nuclear pore complex proteins-directed 3D nuclear architecture in neural development and disease

3D染色质组织是谱系特异性基因表达和基因组不稳定的基础，两者都受到核孔复合体等核结构蛋白的影响。最近的研究和我们的初步数据表明，核孔复合体蛋白(Nups)直接或间接地与染色质相互作用，为表观遗传调节因子、转录因子和DNA修复提供结构支架。此外，Nup153，NUP之一，被发现与CTCF/Cohesion复合体相互作用，从而可能组织拓扑相关结构域(TAD)。我们的初步基因组分析也表明，Nup153在拓扑和定向基因调控中发挥着突出的作用。越来越多的证据表明，染色质在毛孔周围重组以平衡基因调节和基因组稳定性的机制。尽管如此，对NUPS的累积损伤、NUPS导向的3D基因组结构背后的机制以及它对调控和基因组不稳定性的影响之间的因果关系在很大程度上仍然难以捉摸，特别是在神经细胞中，我们预计这将对疾病的发展产生很大影响。在拟议的项目中，通过结合跨学科的专业知识，我们将研究：1)在神经分化过程中，核孔处的3D基因组组织是如何重组的，2)NUPS的破坏在多大程度上导致3D染色质组织的破坏，3)基因组不稳定性和NUPS定向的3D核结构之间的平衡的空间关系是什么。了解核孔3D基因组结构组织的时空机制对于揭示细胞类型特定的表观遗传程序是如何维持的，同时也保持稳定性是至关重要的。放松对这些机制的管制可能会导致神经发育功能障碍，可能导致癌症和神经发育疾病。为此，我们将使用不同发育阶段的神经细胞作为模型，利用多组学方法来揭示核孔周围多层表观遗传特征之间的关系。通过整合HiChIP、CHIP-SEQ、ATAC-SEQ、AP-SEQ和END-SEQ，我们将表征在Nup153分化和丢失时，3D-染色质相互作用中核孔的核结构变化、表观遗传调节因子的结合、染色质的可及性以及DNA损伤。我们还将询问已发现的染色质结构变化与癌症和神经发育障碍的基因组突变之间的空间关系。这些分析将揭示与核孔相关的基因组脆弱性的风险。

3D chromatin organization underlies lineage-specific gene expression and genome instability, which both are affected by nuclear structural proteins such as the nuclear pore complex. Recent studies and our pilot data indicate that nuclear pore complex proteins (Nups) directly or indirectly interact with chromatin and provide a structural scaffold for epigenetic regulators, transcription factors and DNA repair. Furthermore, Nup153, one of Nups was found to interact with the CTCF/cohesion complex to possibility organize topology associated domains (TAD). Our preliminary genomic analyses also indicate prominent roles for Nup153 in topological and directional gene regulation. This accumulating evidence suggests mechanisms of chromatin reorganization around pores to balance gene regulation and genome stability. Still, causal relationships among the accumulated damage on Nups, mechanisms behind Nups-directed 3D genome architecture, and its impact on regulation and genome instability remain largely elusive, especially in neural cells, where we expect high impact on disease development. In the proposed project, by combining interdisciplinary expertise, we will address, 1) how 3D genome organization at the nuclear pores is reorganized during neural differentiation, 2) to what extent disruption of Nups leads to disorganization of 3D chromatin organization, 3) what the spatial relationship of the balance between genome instability and Nups-directed 3D nuclear architecture is. Understanding spatio-temporal mechanisms underlying the organization of 3D genome-architecture at the nuclear pore is vital to unravel how cell type-specific epigenetic programs are maintained, while also preserve stability. Deregulation of these mechanisms can lead to dysfunctional neurodevelopment with cancer and neurodevelopmental diseases as potential consequences. To this end, using neural cells at different developmental stages as a model, we will employ multi-omics approaches to unravel relationships of multilayered epigenetic characteristics around nuclear pores. By integrating HiChIP, ChIP-seq, ATAC-seq, AP-seq, and END-seq, we will characterize changes of nuclear architecture at nuclear pores in 3D-chromatin interactions, binding of epigenetic regulators, chromatin accessibility, and DNA damage, upon differentiation and loss of Nup153. We will also interrogate the spatial relationship between identified changes in chromatin architecture and genomic mutations in cancer and neurodevelopmental disorders. The analyses will uncover the risk of genomic vulnerability associated with nuclear pores.