The Role of the De-condensed Structure of Nascent Chromatin During T Cell Differentiation

新生染色质解压缩结构在 T 细胞分化过程中的作用

• 批准号: 10092898
• 负责人: LORRAINE IACOVITTI
• 金额: $ 65.36万
• 依托单位: THOMAS JEFFERSON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-02-03 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10092898
• 关键词: Address; Antigens; Area; Binding; Biological; Biology; Cell Differentiation Induction; Cell Differentiation process; Cell Lineage; Cell Proliferation; Cell model; Cells; Chromatin; Chromatin Structure; Complex; DNA; DNA biosynthesis; Data; Development; Epigenetic Process; Event; Future; Genes; Genetic Transcription; Genome; Goals; Health; Histones; Hour; Human; Lead; Maintenance; Modeling; Molecular; Mothers; Nature; Nucleosomes; Proteins; Role; Specific qualifier value; Structure; T cell differentiation; T-Lymphocyte; T-Lymphocyte Subsets; Techniques; Testing; Transcriptional Regulation; Undifferentiated; base; cell type; daughter cell; dopaminergic neuron; gene conservation; human disease; human embryonic stem cell; in vivo; molecular modeling; novel strategies; programs; recruit; stem cell differentiation; transcription factor

Project Summary: During cell differentiation, transcriptional programs are changed, and then must be maintained in turn. Chromatin-based epigenetic mechanisms are at the core of maintenance and switching of transcriptional programs. The fundamental issues of the nature of epigenetic marking and of the mechanisms that switch this marking during differentiation remain unclear due to lack of relevant experimental approaches. We developed new experimental paradigms that allow investigating the structure of chromatin during DNA replication at a single-cell and at a gene-specific levels. Using our new techniques, we found striking differences in the structure of chromatin during differentiation of the pluripotent human embryonic stem cells (hESC) and the antigen-inexperienced (naïve) T cells. During the first several hours after induction of differentiation of hESCs to dopamine neuron lineage, or T cells to different T cell subsets, accumulation of H3K27me3 is significantly delayed on nascent DNA. Since the occurrence of H3K27me3 in the genome coincides with the dense structure of nucleosomes, this suggests the existence of a temporarily de-condensed structure of nucleosomes on nascent DNA shortly after induction of cell differentiation. Our preliminary data indicate that the de-condensed, `open' structure of chromatin may be essential for recruitment to DNA of the lineage-specific transcription factors (TFs) that are essential to induce changes in transcriptional programs during cell differentiation. Thus, our results present a molecular explanation of how the vast areas of the repressed genome can be activated during cell differentiation. The goals of this proposal are to test two unique hypotheses using different models of differentiation to various lineages for pluripotent hESCs and for specialized T cells: 1) To examine whether the period of `open' post-replicative chromatin in early differentiating cells is a result of complex interplay of activities of several histone-modifying proteins; and 2) To examine whether this open post-replicative chromatin creates a `window of opportunity' for high accessibility of lineage- specifying TFs that are required to change the transcriptional program during cell differentiation. Examining these unique hypotheses may provide a universal chromatin-based molecular mechanism for biological plasticity of the cell.

项目概要： 在细胞分化过程中，转录程序发生变化，然后必须维持在 基于染色质的表观遗传机制是维持和转换的核心。 表观遗传标记和转录程序的本质问题。 由于缺乏相关的研究，在分化过程中转换这种标记的机制仍不清楚。 我们开发了新的实验范式来研究 使用我们的新方法，在单细胞和基因特异性水平上进行 DNA 复制过程中染色质的结构。 技术，我们发现在分化过程中染色质结构存在显着差异 多能人类胚胎干细胞 (hESC) 和未经历抗原的（幼稚）T 细胞。 hESC 分化为多巴胺神经元谱系或 T 细胞分化为多巴胺神经元谱系后的最初几个小时 不同的 T 细胞亚群中，H3K27me3 在新生 DNA 上的积累显着延迟。 H3K27me3 在基因组中的出现与核小体的致密结构相吻合，这 表明不久后新生 DNA 上存在暂时解压缩的核小体结构 我们的初步数据表明，在诱导细胞分化后，出现了解压缩的“开放”结构。 染色质可能对于谱系特异性转录因子 (TF) 招募至 DNA 至关重要 这对于在细胞分化过程中诱导转录程序的变化至关重要。 结果对如何激活被抑制的基因组的广大区域提供了分子解释 该提案的目标是使用不同的方法来测试两个独特的假设。 多能 hESC 和特化 T 细胞向各种谱系的分化模型：1) 检查早期分化细胞中复制后染色质的“开放”时期是否是以下因素的结果 几种组蛋白修饰蛋白活性的复杂相互作用；以及 2) 检查这是否存在 开放的复制后染色质为谱系的高可及性创造了“机会之窗”- 指定在细胞分化过程中改变转录程序所需的 TF。 检查这些独特的假设可能会提供一种通用的基于染色质的分子机制 细胞的生物可塑性。

项目成果

Delayed Accumulation of H3K27me3 on Nascent DNA Is Essential for Recruitment of Transcription Factors at Early Stages of Stem Cell Differentiation.

• DOI: 10.1016/j.molcel.2017.03.006
• 发表时间: 2017-04-20
• 期刊: Molecular cell
• 影响因子: 16
• 作者: Petruk S;Cai J;Sussman R;Sun G;Kovermann SK;Mariani SA;Calabretta B;McMahon SB;Brock HW;Iacovitti L;Mazo A
• 通讯作者: Mazo A

A Proximity Ligation-Based Method to Detect RNA-DNA Association.

一种基于邻近连接的方法来检测 RNA-DNA 关联。

• DOI: 10.1007/978-1-4939-9537-0_10
• 发表时间: 2019
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Fenstermaker,TylerK;Sun,Guizhi;Mazo,Alexander;Petruk,Svetlana
• 通讯作者: Petruk,Svetlana

Changes in nascent chromatin structure regulate activation of the pro-fibrotic transcriptome and myofibroblast emergence in organ fibrosis.

• DOI: 10.1016/j.isci.2023.106570
• 发表时间: 2023-05-19
• 期刊: ISCIENCE
• 影响因子: 5.8
• 作者: Basta, Morgan D.;Petruk, Svetlana;Summer, Ross;Rosenbloom, Joel;Wermuth, Peter J.;Macarak, Edward;Levin, Alex V.;Mazo, Alexander;Walker, Janice L.
• 通讯作者: Walker, Janice L.

A stress-free strategy to correct point mutations in patient iPS cells.

纠正患者 iPS 细胞点突变的无压力策略。

• DOI: 10.1016/j.scr.2021.102332
• 发表时间: 2021-05
• 期刊: Stem cell research
• 影响因子: 1.2
• 作者: Cai J;Kropf E;Hou YM;Iacovitti L
• 通讯作者: Iacovitti L

Detection of RNA-DNA association by a proximity ligation-based method.

通过基于邻近连接的方法检测 RNA-DNA 关联。

• DOI: 10.1038/srep27313
• 发表时间: 2016
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Petruk,Svetlana;Fenstermaker,TylerK;Black,KathrynL;Brock,HughW;Mazo,Alexander
• 通讯作者: Mazo,Alexander