Nuclear organization and its role in gene regulation

核组织及其在基因调控中的作用

• 批准号: 10406421
• 负责人: Jane Amanda Skok
• 金额: $ 74.24万
• 依托单位: NEW YORK UNIVERSITY SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-04-03 至 2027-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10406421
• 关键词: Address; Affinity; Binding; Biological; Biological Process; Cell Cycle; Cells; Chemicals; Chromatin; Chromatin Loop; Chromosome Structures; Chromosomes; DNA; Developmental Process; Disease; Epigenetic Process; Future; Gene Expression; Gene Expression Regulation; Genes; Genetic Recombination; Genetic Transcription; Genome; Goals; Growth Factor; Health; Individual; Link; Mediating; Methodology; Mitosis; Mitotic; Modernization; Molecular; Nuclear; Nutrient; Phase; Phenotype; Play; Population; Positioning Attribute; Process; RNA; Regulatory Element; Role; Signal Transduction; Site; Stress; Structure; Time; Toxic effect; Work; cohesin; computational pipelines; condensin; daughter cell; epigenetic memory; molecular imaging; preservation; programs; promoter; response

SUMMARY: My lab’s work has been at the forefront of studies showing that nuclear organization and long-range chromatin interactions play an essential role in recombination and gene regulation. We combine molecular and imaging (DNA/RNA FISH) approaches with in house generated computational pipelines, and are thus one of a handful of labs that has expertise in both the experimental and analytical aspects of chromosome folding. In this application we will extend our work to focus on two main interlinked problems of significant biological importance: Project 1: Understanding bookmarking in the context of mitotic chromatin folding. In mitosis (M), the promoters of M-phase active genes are “bookmarked” maintaining the accessibility of some regulatory elements. This provides a mechanism for the rapid activation of a subset of genes, allowing cells exiting from mitosis to preserve a memory of the epigenetic program of the previous cell cycle. Since regulatory factors associate with chromatin with distinct affinities, some factors will be retained on M-phase chromatin better than others, and furthermore, because binding occurs in a dynamic manner, sites at which factors remain bound will not be uniform across a population of cells. The inefficiency of bookmarking, combined with cell-to-cell variability, imparts daughter cells with a degree of epigenetic plasticity, enabling them to alter their phenotype in response to environmental signals, which can have a significant impact on developmental and biological processes. However, little is known about the mechanisms underlying this process, and in particular how condensin II-mediated chromatin folding during mitosis impacts accessibility. Project 2: Mechanisms underlying the chromatin organization and gene regulation of quiescent cells. Cells can adapt and survive under conditions of stress, toxicity, nutrient or growth factor depletion/and chemical insult, by exiting the cell cycle and entering a reversible dormant state known as quiescence (G0). Previous studies showed that CTCF/cohesin-mediated TAD structure is restored after entry into G1, but chromosome structure in mammalian G0 cells has not been studied carefully using modern molecular methodologies. Gene expression is globally repressed in G0 cells, but we now know that quiescent cells actively transcribe specific genes. Notably, chromatin in quiescent cells is predominantly compact, as in M phase. Accordingly, we hypothesize that cells exiting M into G0 partially preserve the compact organization of mitotic cells by retaining condensin II-mediated loops. The goal of our future studies is to determine whether (i) condensin II binding at the start of M-phase functions to bookmark a subset of active promoters, (ii) whether there is variability in the sites that are bookmarked between individual cells, and (iii) whether condensin II- mediated chromatin looping and bookmarking are mechanistically linked to the unique genome organization and transcriptional programs of G0 cells. Given our combined experimental and computational expertise in the field of nuclear organization, we are uniquely positioned to address these timely, relevant questions.

概括： 我实验室的工作一直处于研究的前沿，表明核组织和远程染色质 相互作用在重组和基因调控中发挥着重要作用，我们将分子和成像结合起来。 （DNA/RNA FISH）方法采用内部生成的计算管道，因此是少数几种方法之一 拥有染色体折叠实验和分析方面专业知识的实验室。 应用程序，我们将扩展我们的工作，重点关注重要生物的两个主要相互关联的问题 重要性：项目 1：了解有丝分裂染色质折叠背景下的书签。 有丝分裂 (M)，M 期活性基因的启动子被“标记”，以保持某些基因的可访问性 这提供了一种快速激活基因子集的机制，允许细胞。 退出有丝分裂以保留上一个细胞周期的表观遗传程序的记忆。 与染色质相关的调节因子具有不同的亲和力，一些因子将保留在 M 期 染色质比其他染色质更好，而且，由于结合以动态方式发生，因此 保持绑定的因素在细胞群中不会是统一的，书签的效率低下。 与细胞间的变异性相结合，赋予子细胞一定程度的表观遗传可塑性，从而使 它们会根据环境信号改变表型，这会对 然而，人们对其背后的机制知之甚少。 过程，特别是有丝分裂过程中凝缩蛋白 II 介导的染色质折叠如何影响可及性。 项目 2：静止细胞染色质组织和基因调控的潜在机制。 细胞可以在压力、毒性、营养或生长因子耗尽的条件下适应和生存/和 化学损伤，通过退出细胞周期并进入称为静止（G0）的可逆休眠状态。 之前的研究表明，CTCF/cohesin介导的TAD结构在进入G1后会恢复，但是 哺乳动物 G0 细胞的染色体结构尚未使用现代分子生物学仔细研究 G0 细胞中的基因表达受到全面抑制，但我们现在知道静止细胞 值得注意的是，静止细胞中的染色质主要是紧凑的，如 M 中那样。 因此，我们得出结论，从 M 进入 G0 的细胞部分保留了紧密的组织。 我们未来研究的目标是确定是否通过保留凝缩蛋白 II 介导的环来抑制细胞有丝分裂。 (i) 凝缩蛋白 II 在 M 期功能开始时结合，为活性启动子子集添加书签，(ii) 是否 各个细胞之间标记的位点存在差异，以及 (iii) 凝缩蛋白 II 是否- 介导的染色质循环和书签在机制上与独特的基因组组织相关 鉴于我们在实验和计算方面的综合专业知识，G0 细胞的转录程序。 在核组织领域，我们处于独特的地位，可以解决这些及时、相关的问题。