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。对基因表达的适当调控在所有生物体内都是必不可少的。在哺乳动物中，大多数基因都受到远端增强子的调控，这些增强子可以位于远离其线性基因组上的靶基因的位置。也许是因为这个原因，哺乳动物的基因组被折叠成3D结构域，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基因组结构域的一个未被充分研究的潜在调控因素提供关键的见解。该项目将为研究生和博士后助理创造跨学科培训机会，支持他们在学术界、生物医药行业和/或相关职业中发展成为科学家。将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)结合起来，为科学、技术和经济管理学科中代表性不足群体的本科生提供暑期研究机会，并通过外联活动，实现更广泛的影响。CTCF是哺乳动物细胞中最著名的增强子和启动子之间的绝缘体。CTCF与粘附素复合体一起，将基因组折叠成染色质环和环域。然而，并不是所有的循环在它们的锚上都有CTCF，而且由于CTCF在所有细胞类型中都表达，目前很难解释为什么循环在细胞类型之间不同。此外，几项研究提供了证据，证明其他DNA结合蛋白在环锚上高度浓缩。本研究将对这样一个候选环路因子ZNF143进行详细的研究。伴随着Micro-C的急性耗尽将揭示其在3D基因组组织和环路中的作用。活细胞显微镜和超分辨显微镜将揭示其动力学、目标搜索机制、停留时间，并为3D基因组模型提供定量约束。总而言之，这项研究将扩大对关键基因组组织因素的了解，超越CTCF。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.