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消灭病毒和细菌。当B细胞遇到并识别病原体表面上的异物时，这些分子在免疫应答期间分泌。然而，B细胞是如何被激活的还没有完全解决。控制这种激活的一个关键机制是转录，即基因表达的过程。B细胞发育过程中的转录由启动子序列和多种远端顺式调控元件协调。其中关键的是增强子，其与启动子相关联以组织特异性方式增加靶基因的转录输出。增强子通常通过其对DNA酶消化的超敏性和被称为染色质修饰剂的特异性蛋白质的结合而与非调节性DNA区分开。基于这些参数，最近发现了400，000个显示增强子样特征的基因组位点，跨越了近10%的人类基因组。 增强子通过募集转录因子、辅因子和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环出插入序列来介导启动子-增强子相互作用。与启动子和绝缘子不同，它们在细胞类型中变化不大，而增强子景观在发育过程中变化很大。该特征预测哺乳动物细胞中的功能性3D连接性i）必须显示高度的组织特异性，并且ii）应该密切反映细胞分化期间的转录组变化。然而，由于在发育过程中绘制启动子-增强子连接的困难，这些想法尚未得到充分探索。 在没有直接方法的情况下，通常基于线性接近或共享的染色质状态将增强子分配给同源启动子。这种策略具有局限性，因为增强子并不总是调节，也不与最近的启动子共享染色质谱。为了克服这一挑战，在过去的一年里，我们应用了一个最近开发的协议（ChIA-PET），允许可视化的启动子-增强子相互作用。在发表于Cell的一篇手稿中（Killing-Kwon等人，我们绘制了小鼠干细胞和B淋巴细胞中的这些相互作用。我们比较和对比了这些相互作用组图谱，发现了几个非常有趣的特征： 1- 我们证实，增强子的使用在不同组织中有很大差异。 2- 出乎意料的是，我们发现这一特征不仅延伸到仅在干细胞或B细胞中表达的基因，而且还延伸到那些普遍表达的基因（所谓的管家基因）。 3- 通过基因组技术，我们表明，这些不断变化的增强子招募细胞特异性因子。 这些发现很重要，因为它们表明生物体依赖于动态增强子景观以组织特异性方式控制基本细胞功能。由于导致狼疮和关节炎等疾病的突变发生在增强子元件上，因此我们以全基因组方式绘制这些结构域及其相互作用的技术对于研究自身免疫性疾病和其他疾病的人来说非常有价值。