The four dimensions of nucleosome chain folding

真核细胞中的DNA反复缠绕在组蛋白蛋白周围，形成一串珠状的核小体链，进一步折叠成更高级别的染色质结构。在细胞分化和组织发育过程中，核小体链堆积密度和DNA可及性的变化控制着基因的表达和抑制。本项目将研究细胞核中核小体链的三维结构及其在组织发育和成熟过程中随时间的变化，称为第四维。这项研究的结果将为设计遗传和药物工具提供关键信息，这些工具能够改变核小体链折叠，从而调节分化细胞和组织的表观遗传学变化和发育可塑性。该项目将与研究生教育深度结合，为本科生提供新的研究机会，激励和培训他们在STEM领域的职业生涯。该项目的总体目标是揭示具有某些表观遗传状态的核小体链折叠基序，这些基序与锁定成熟细胞中的潜在基因和抑制组织再生有关。第一个研究目标是在参考人类细胞系中解析表观遗传不同染色质状态的纳米级染色质结构。第二个目标是确定小鼠视网膜发育过程中染色质凝聚的核小体链转变。一种独特的技术，EMANIC(电子显微镜辅助的核小体相互作用捕获)将被应用于解析核小体折叠基序。这项技术将与生化分析一起使用，将核小体链折叠与特定的表观遗传状态和染色质重排联系起来。通过将关键的结构信息：核小体重复长度、核小体间相互作用和核小体链柔性与计算模型相结合，该项目将为工程染色质表观遗传状态和修改与组织发育和再生过程相关的染色质功能提供新的结构线索。该奖项反映了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。

DNA in eukaryotic cells is repeatedly coiled around histone proteins forming 'beads-on-a-string' chains of nucleosomes that are further folded into higher-order chromatin structures. Changes in the nucleosome chain packing density and DNA accessibility govern gene expression and repression during cell differentiation and tissue development. This project will investigate the 3-dimensional structures of nucleosome chains in the cell nucleus and their transitions over time in the course of tissue development and maturation, referred to as the 4th dimension. The outcomes of this research will provide crucial information for designing genetic and pharmacological tools capable of altering nucleosome chain folding and thus modulating epigenetic changes and developmental plasticity in differentiated cells and tissues. This project will be deeply integrated with graduate education and provide new research opportunities for undergraduate students, inspiring and training them for careers in STEM.The overall goal of this project is to reveal nucleosome chain folding motifs that characterize certain epigenetic states and are associated with locking down the underlying genes in mature cells and inhibiting tissue regeneration. The first research aim is to resolve the nanoscale chromatin structure of epigenetically distinct chromatin states in a reference human cell line. The second aim is to determine nucleosome chain transitions underlying chromatin condensation during mouse retina development. A unique technique, EMANIC (electron microscopy-assisted nucleosome interaction capture) will be applied to resolve nucleosome folding motifs. This technique will be used in conjunction with biochemical assays to link the nucleosome chain folding with specific epigenetic states and chromatin rearrangements. By integrating crucial structural information: nucleosome repeat length, internucleosomal interactions, and nucleosome chain flexibility with computational modeling, this project will provide new structural cues for engineering chromatin epigenetic states and modifying chromatin functions related to tissue developmental and regenerative processes.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.