Protein Regulators of 3D Genome Architecture: Dynamics, Mechanism and Function

该研究项目将有助于我们对3D基因组折叠的理解。基因表达的适当调节在所有生物有机体中是必不可少的。在哺乳动物中，大多数基因由远端增强子调控，所述远端增强子可以位于远离其线性基因组上的靶基因的位置。也许正是出于这个原因，哺乳动物的基因组被折叠成3D结构域，以确保增强子通过空间与适当的基因相互作用。这项研究将为3D基因组结构域的未充分研究的潜在调节因子提供关键见解。该项目将为一名研究生和一名博士后创造跨学科培训机会，支持他们在学术界、生物医学行业和/或相关职业中发展为科学家。通过将该项目的成像方面与麻省理工学院的本科课程（20.309）相结合，为STEM学科代表性不足的群体的本科生提供夏季研究机会以及通过外联活动，将实现更广泛的影响。 CTCF是哺乳动物细胞中增强子和启动子之间最知名的绝缘子。CTCF与粘着蛋白复合物一起将基因组折叠成染色质环和环结构域。然而，并不是所有的环都在其锚点处具有CTCF，并且由于CTCF在所有细胞类型中表达，因此目前难以解释为什么环在细胞类型之间存在差异。此外，一些研究提供了证据表明，其他DNA结合蛋白强烈富集在环锚。本研究将详细研究这样一个候选成环因子ZNF 143。Micro-C的急性消耗将揭示其在3D基因组组织和循环中的作用。活细胞和超分辨率显微镜将揭示其动力学，目标搜索机制，停留时间，并提供3D基因组模型的定量约束。总的来说，这项研究将扩大关键基因组组织因素的知识超越CTCF。这个奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

The research project will contribute to our understanding of 3D genome folding. Proper regulation of gene expression is essential in all biological organisms. In mammals, most genes are regulated by distal enhancers that can be located far away from their target genes on the linear genome. Perhaps for this reason, mammalian genomes are folded into 3D domains that ensure enhancers interact with the appropriate genes through space. This research will provide key insights into an understudied potential regulator of 3D genome domains. The project will create interdisciplinary training opportunities for a graduate student and a post-doctoral associate, supporting their development as scientists in academia, biomedical industry and/or related careers. Additional broader impact will be achieved through integration of the imaging aspects of the project with an undergraduate course at MIT (20.309), summer research opportunities for undergraduates from underrepresented groups in STEM disciplines and through outreach activities. CTCF is the best-known insulator between enhancers and promoters in mammalian cells. CTCF, together with the cohesin complex, fold the genome into chromatin loops and loop domains. However, not all loops have CTCF at their anchors, and since CTCF is expressed in all cell types, it is currently difficult to explain why loops differ between cell types. Moreover, several studies have provided evidence that other DNA-binding proteins are strongly enriched at loop anchors. The research will study such a candidate looping factor, ZNF143, in detail. Acute depletion followed by Micro-C will reveal its role in 3D genome organization and looping. Live-cell and super-resolution microscopy will reveal its dynamics, target-search mechanism, residence time, and provide quantitative constraints on 3D genome models. Taken together, the research will expand knowledge of critical genome organizing factors beyond CTCF.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.