B cell development

B淋巴细胞通过抗体识别和摧毁病毒和细菌。当B细胞遇到并识别病原体表面的异物时，这些分子在免疫反应中分泌。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是由启动子序列和各种远端顺式调控元件调控的。其中的关键是增强子，它与启动子相关联，以组织特异性的方式增加目标基因的转录输出。增强剂与非调控DNA的典型区别在于它们对DNAs的消化和特定蛋白质的结合非常敏感，称为染色质修饰剂。基于这些参数，最近发现了40万个显示增强子样特征的基因组位置，覆盖了人类基因组的近10%。 增强剂通过招募转录因子、辅因子和RNA聚合酶II(介导转录的酶)来控制细胞特性。所有这些蛋白质都通过循环插入序列来调节启动子-增强子之间的相互作用。与启动子和绝缘体不同的是，不同类型的细胞几乎不同，增强剂在发育过程中发生了很大的变化。这一特征预测，哺乳动物细胞中的功能3D连接i)必须显示出高度的组织特异性，ii)应该密切反映细胞分化过程中转录组的变化。然而，这些想法还没有被充分探索，因为在开发过程中绘制启动子-增强子连接的图很困难。 在缺乏直接方法的情况下，增强子通常被分配给基于线性接近或共同染色质状态的同源启动子。这种策略有局限性，因为增强剂并不总是调节染色质图谱，也不总是与最近的启动子共享染色质图谱。为了克服这一挑战，在过去的一年里，我们应用了一种最近开发的协议(CHIA-PET)，该协议允许可视化启动子-增强子相互作用。在《细胞》上发表的一篇手稿中，我们绘制了小鼠干细胞和B淋巴细胞中的这些相互作用图。我们对比了这些互动组地图，发现了几个非常有趣的特征： 1-我们证实，增强剂的使用在不同的组织中差异很大。 2-出乎意料的是，我们发现这一特征不仅延伸到只在干细胞或B细胞中表达的基因，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，我们证明了这些不断变化的增强子可以招募细胞特异性因子。 这些发现很重要，因为它们表明，生物体依靠动态的增强剂以组织特有的方式控制基本的细胞功能。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那些研究自身免疫和其他疾病的人将具有非常高的价值。

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.