B cell development

B细胞发育

• 批准号: 8939422
• 负责人: rafael c casellas
• 金额: $ 315.29万
• 依托单位: NATIONAL INSTITUTE OF ARTHRITIS AND MUSCULOSKELETAL AND SKIN DISEASES
• 依托单位国家: 美国
• 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/8939422
• 关键词: Antibodies; Arthritis; Autoimmune Process; Automobile Driving; B-Cell Development; B-Lymphocytes; Bacteria; Binding; Bioinformatics; Cell Differentiation process; Cell physiology; Cells; Chromatin; DNA; Deoxyribonucleases; Development; Digestion; Disease; Distal; Enhancers; Enzymes; Fc Receptor; Gene Expression Profile; Gene Targeting; Genes; Genetic Enhancer Element; Genetic Transcription; Genomics; Goals; Housekeeping Gene; Human Genome; Hypersensitivity; Imagery; Immune response; Immunoglobulin Class Switching; Immunoglobulin Somatic Hypermutation; Introns; Laboratories; Lupus; Mammalian Cell; Manuscripts; Maps; Mediating; Molecular; Molecular Biology; Mus; Organism; Output; Peripheral; Positron-Emission Tomography; Process; Proteins; Protocols documentation; Publishing; RNA Polymerase II; Reaction; Recruitment Activity; Regulatory Element; Site; Specificity; Stem cells; Surface; Techniques; Tissues; Transcription Process; Transgenic Organisms; V(D)J Recombination; Virus; base; cell type; cofactor; disease-causing mutation; domain mapping; genome-wide; interest; pathogen; promoter; tool; transcription factor; tumorigenesis

B lymphocytes recognize and destroy viruses and bacteria though antibodies. These molecules are secreted during the immune response, when B cells encounter and recognize foreign material on the surface of pathogens. How B cells are activated however is not entirely resolved. One key mechanism that controls this activation is transcription, the process whereby genes are expressed. Transcription during B cell development is orchestrated by promoter sequences and a variety of distal cis-regulatory elements. Key among these are enhancers, which associate with promoters to increase the transcriptional output of target genes in a tissue-specific manner. Enhancers are typically distinguished from non-regulatory DNA by their hypersensitivity to digestion with DNAses, and binding of specific proteins known as chromatin modifiers. Based on these parameters, 400,000 genomic sites displaying enhancer-like features were recently discovered, spanning nearly 10% of the human genome. Enhancers control cell identity by recruiting transcription factors, cofactors, and RNA Polymerase II, the enzyme that mediates transcription. All of these proteins mediate promoter-enhancer interactions by looping out of intervening sequences. In contrast to promoters and insulators, which vary little across cell types, the enhancer landscape changes considerably during development. This feature predicts that functional 3D connectivity in mammalian cells i) must display a high degree of tissue specificity and ii) should closely reflect transcriptome changes during cell differentiation. However, these ideas have not been fully explored because of the difficulty of mapping promoter-enhancer connections during development. In the absence of direct approaches, enhancers have been typically assigned to cognate promoters based on linear proximity or shared chromatin states. This strategy has limitations because enhancers do not always regulate nor share chromatin profiles with the nearest promoter. To overcome this challenge, this past year we applied a recently developed protocol (ChIA-PET) that permits visualization of promoter-enhancers interactions. In a manuscript published in Cell (Kieffer-Kwon et al, we mapped these interactions in mouse stem cells and B lymphocytes. We compared and contrasted these interactome maps and discovered several very interesting features: 1- We confirmed that enhancer usage varies widely across tissues. 2- Unexpectedly, we find that this feature extends not only to genes only expressed in stem cells or B cells, but also on those expressed ubiquitously (the so called housekeeping genes). 3- By means of genomic techniques we showed that these changing enhancers recruit cell-specific factors. These findings are important because they showed that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner. Because mutations that cause diseases such as lupus and arthritis occur at enhancer elements, our techniques to map these domains and their interactions in a genome-wide manner will be highly valuable to those studying autoimmune and other disorders.

B淋巴细胞通过抗体识别并破坏病毒和细菌。当B细胞遇到并识别病原体表面上的异物时，这些分子在免疫反应期间分泌。但是，如何激活B细胞并未完全解决。控制这种激活的一种关键机制是转录，这是表达基因的过程。 B细胞发育过程中的转录由启动子序列和各种远端顺式调节元件进行策划。其中的关键是增强子，它们与启动子相关联，以以组织特异性方式增加靶基因的转录输出。增强子通常通过对DNass对消化的过敏性以及被称为染色质修饰剂的特定蛋白质的结合来区分非调节DNA。基于这些参数，最近发现了400,000个显示出具有增强剂特征的基因组位点，占人类基因组的近10％。 增强剂通过募集转录因子，辅助因子和RNA聚合酶II（介导转录的酶）来控制细胞身份。所有这些蛋白质通过循环介导的启动子增强剂相互作用。与启动子和绝缘子相反，在开发过程中，增强子景观的变化很大。此功能预测，哺乳动物细胞中的功能3D连通性i）必须显示高度的组织特异性，ii）应在细胞分化过程中紧密反映转录组变化。但是，由于难以在开发过程中绘制启动子增强剂的连接，因此尚未完全探索这些想法。 在没有直接方法的情况下，通常将增强子基于线性接近或共享染色质状态分配给了认知启动子。该策略具有局限性，因为增强剂并不总是与最近的启动子进行调节或共享染色质谱。为了克服这一挑战，在过去的一年中，我们应用了最近开发的协议（CHIA-PET），该协议允许可视化启动子增强剂相互作用。在细胞中发表的手稿中（Kieffer-kwon等人，我们在小鼠干细胞和B淋巴细胞中绘制了这些相互作用。我们比较并对比了这些相互作用的图像，并发现了一些非常有趣的特征： 1-我们证实，增强子的使用范围在整个组织之间变化很大。 2-出乎意料的是，我们发现此特征不仅扩展到仅在干细胞或B细胞中表达的基因，而且还扩展到无处不在表达的基因（所谓的管家基因）。 3-通过基因组技术，我们表明这些变化的增强剂募集了细胞特异性因素。 这些发现很重要，因为它们表明生物依赖于动态增强子景观以组织特异性方式控制基本的细胞功能。由于引起狼疮和关节炎等疾病的突变发生在增强子元素上，因此我们以全基因组方式绘制这些领域及其相互作用的技术对于研究自身免疫和其他疾病的人来说非常有价值。