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

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.