Chromatin and epigenetic memory

染色质和表观遗传记忆

基本信息

批准号：
10266504
负责人：
Keiko Ozato
金额：
$ 109.4万
依托单位：
EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH & HUMAN DEVELOPMENT
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10266504
关键词：
Adult Binding Bone Marrow Bromodomain Cell division Cells Chromatin Chromosome Mapping Coupled Defect Deposition Embryo Encephalomyocarditis virus Enhancers Environment Epigenetic Process Erythrocytes Exposure to Faculty Family Fetal Liver Fibroblasts Genes Genetic Transcription Genome Goals Hematopoiesis Hematopoietic Heterochromatin Histone H3 Histones IFNAR1 gene Immune Immune response In Vitro Inflammatory Inflammatory Response Inherited Interferon Type I Interferon Type II Interferon-alpha Interferon-beta Interferons Knock-out Knockout Mice Link Location Lymphocyte Mediating Memory Mitotic Chromosome Myeloid Cells Natural Immunity Nuclear Nutritional Phenotype Physiological Play Positive Transcriptional Elongation Factor B Process Reporting Rest Role STAT1 gene Saccharomyces cerevisiae Shapes Signal Pathway Signal Transduction Surface Variant Virus Diseases Work Yeasts conditional knockout epigenetic memory epigenetic regulation factor EF-P interest macrophage promoter response telomere transcriptome sequencing

项目摘要

1 Interferon creates transcriptional memory We report that interferon (IFN) stimulation leaves a lasting mark on chromatin over many ISG. This chromatin mark correlated with a memory phonotype: cells that were previously exposed to IFN led to faster and higher ISG induction when restimulated by IFN as compared to nave cells that were not exposed to IFN before. This memory, which we call IFN memory closely resembled a memory response reported in Yeast (Saccharomyces cerevisiae) for genes that respond to nutritional signaling. Type I IFN (IFN alpha and IFN beta)and IFN-gamma both generated memory in fibroblasts and bone marrow derived macrophages, respectively. IFN memory was not attributed to changes in IFN signaling pathways, since levels of IFNAR and phosphorylated STAT1 were similar between nave and memory cells. IFN memory was inherited through several cycles of fibroblast cell divisions. Moreover, this memory gave a functional advantage, in that cells previously exposed to IFN were more effective in the protection against encephalo-myocarditis virus (EMCV) infection. RNA-seq analysis found that about 2,000 ISG induced after IFN stimulation. These ISG were divided into two groups, those with positive memory and those with negative memory. ISG with positive memory showed an elevated response after the 2nd stimulation, while ISG with negative memory were unresponsive or showed reduced response to the 2nd IFN. Positive memory was more prevalent in fibroblasts than negative memory, but in macrophages negative memory was more predominant. Lastly, positive IFN memory correlated with specific chromatin marks, i.e., the acquisition of H3K36me3 mark and H3.3 deposition. Our results illustrate that IFN stimulation creates epigenetic memory by which cells acquire a new, adaptive faculty to respond to changing environments. 2 BRD4 is required for immune responses in a context dependent manner. To study the role of BRD4 in the immune responses we studied ted Brd4 conditional knockout (KO) mice where the Brd4 gene was deleted from the cells of hematopoietic lineage. The initial work found that fetal liver in Brd4 KO mice was grossly abnormal. It had very few HSCs (lineage negative, Sca1+ cKit+ cells) Consequently, Brd4 KO embryos failed to generate erythrocytes, lymphocytes and myeloid cells, and died at around embryonic day 16 to day 17. We concluded that BRD4 is indispensable for embryonic hematopoiesis. However, Brd4 deletion in developing macrophages caused relatively modest defects. Brd4 KO mice generated macrophages with normal surface phenotypes. In vitro deletion of Brd4 from bone marrow had similar results. Furthermore, LPS induction of ISG and other inflammatory factors was only partially reduced in Brd4 KO macrophages, illustrating that BRD4 is largely dispensable for macrophage differentiation and LPS induced inflammatory responses. Nevertheless, BRD4 occupied many genes, over the promoter to the gene body, even on the genes that did not require BRD4 for expression. In addition, BRD4 was broadly present in numerous enhancers both in resting and inflammatory macrophages. The results indicate that there are multiple compensatory mechanisms that cover the lack of BRD4.

1个干扰素创建转录内存我们报告说，干扰素（IFN）刺激在许多ISG上留下了持久的标记。该染色质标记与记忆音型相关：与以前未暴露于IFN的中介细胞相比，IFN恢复以前暴露于IFN的细胞会导致更快，更高的ISG诱导。我们称之为IFN记忆的记忆与对营养信号反应的基因相似的记忆反应（酿酒酵母）中报告的记忆反应。 I型IFN（IFNα和IFNβ）和IFN-gamma分别在成纤维细胞和骨髓中产生记忆，分别衍生出巨噬细胞。 IFN记忆并非归因于IFN信号通路的变化，因为IFNAR和磷酸化的STAT1水平在中殿和记忆细胞之间相似。 IFN记忆是通过成纤维细胞分裂的几个循环继承的。此外，这种记忆具有功能优势，因为先前暴露于IFN的细胞更有效地防止脑肌动炎病毒（EMCV）感染。 RNA-seq分析发现，IFN刺激后约有2,000个ISG诱导。这些ISG分为两组，具有积极的记忆力和具有负记忆的那些组。在第二个刺激后，具有正记忆的ISG显示出较高的响应，而具有负记忆的ISG无反应或对第二个IFN的响应降低。在成纤维细胞中，积极记忆比阴性记忆更为普遍，但是在巨噬细胞中，负记忆更为主导。最后，阳性IFN记忆与特定的染色质标记相关，即H3K36me3标记和H3.3沉积的采集。我们的结果表明，IFN刺激会产生表观遗传记忆，细胞通过该记忆获得新的自适应教师来响应不断变化的环境。 2 BRD4是在上下文依赖性方式中进行免疫反应所必需的。为了研究BRD4在免疫反应中的作用，我们研究了TED BRD4条件敲除（KO）小鼠，其中BRD4基因从造血谱系细胞中删除。最初的工作发现BRD4 KO小鼠中的胎儿肝脏严重异常。因此，BRD4 KO胚胎几乎没有产生红细胞，淋巴细胞和髓样细胞的HSC（谱系阴性，SCA1+ CKIT+细胞），并且在16至17天的胚胎第16天左右死亡。但是，在发展巨噬细胞中的BRD4删除会导致相对适度的缺陷。 BRD4 KO小鼠产生了具有正常表面表型的巨噬细胞。骨髓中BRD4的体外缺失具有相似的结果。此外，在BRD4 KO巨噬细胞中仅部分降低了ISG和其他炎症因子的LPS诱导，这表明BRD4在很大程度上可以用于巨噬细胞分化，而LPS诱导的炎症反应。然而，即使在不需要BRD4进行表达的基因上，BRD4也占据了基因体的许多基因。此外，BRD4在静止和炎症性巨噬细胞中的众多增强剂中广泛存在。结果表明，有多种补偿机制涵盖了缺乏BRD4。