Role of the DR/DQ super enhancer in MHC-II expression

DR/DQ 超级增强子在 MHC-II 表达中的作用

• 批准号: 10650867
• 负责人: JEREMY M. BOSS
• 金额: $ 48.01万
• 依托单位: EMORY UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-16 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10650867
• 关键词: 3-Dimensional; ATAC-seq; Address; Affect; Allogenic; Antigen-Presenting Cells; Antigens; Architecture; Autoimmune Diseases; Autoimmunity; B cell differentiation; B-Cell Development; B-Lymphocytes; Binding; Binding Proteins; Biochemical; Bioinformatics; Biological Assay; CD4 Positive T Lymphocytes; CREB1 gene; CRISPR/Cas technology; Cells; Chromatin; Chromatin Loop; Chromatin Structure; Chromosome 6; Communicable Diseases; Complex; Data; Development; Disease; Elements; Enhancers; Future; Gene Expression; Gene Expression Regulation; Gene Structure; Genes; Genetic Polymorphism; Genetic Transcription; Goals; HLA-DQA1; HLA-DR Antigens; HLA-DRB1; Helper-Inducer T-Lymphocyte; Histocompatibility Antigens Class II; Human; Human Genome; Immune; Immune System Diseases; Immune response; Immune system; Immunity; Immunization; Immunotherapy; Individual; Infection; Insulator Elements; Interferon Type II; Knowledge; Link; Literature; MHC Class II Genes; MHC class II transactivator protein; Malignant Neoplasms; Mediating; Messenger RNA; Modeling; Molecular; Nucleic Acid Regulatory Sequences; Peptides; Plasma Cells; Process; Promoter Regions; Property; Proteins; Regulation; Regulatory Element; Regulatory T-Lymphocyte; Reporter Genes; Research; Role; Science; Series; Structure; System; T cell response; T-Cell Activation; T-Lymphocyte; Technology; Testing; Therapeutic; Tissues; Transcriptional Regulation; Transplantation; Untranslated RNA; Vaccination; Variant; Work; adaptive immune response; adaptive immunity; base; cell type; chromatin remodeling; chromosome conformation capture; cohesin; cytokine; design; experimental study; gene function; histone modification; human disease; improved; infectious disease treatment; insight; novel; programs; promoter; recruit; stem; transcription factor; transcriptome sequencing

Major histocompatibility complex class-II (MHC-II) proteins are encoded by HLA-DR, -DQ, and -DP α/β gene pairs and function by presenting processed antigenic peptides to CD4+ T cells thereby initiating and/or sustaining adaptive immune responses. MHC-II expression is transcriptionally regulated and expressed constitutively in antigen-presenting cells, such as B cells, but may be induced in non-immune cells by IFNγ. Thus, MHC-II- mediated immune responses and adaptive immunity is controlled primarily at the level of transcription. All MHC- II genes are coregulated by a common set of proximal promoter transcription elements and factors of which only CIITA is cell type limiting and induced by IFNγ. Several years ago, we showed that MHC-II gene expression was also modulated by a series of transcriptional insulator elements that bound CTCF and cohesin and that these elements were the focal points of long-range chromatin interactions between each other and MHC-II promoter regions. Together these elements formed a three-dimensional chromatin architecture that favored gene expression. Indeed, as B cells differentiated into plasma cells and lost MHC-II expression, this architecture was also lost. While this model is correct and has stood for the last 5 years, we now provide exciting new evidence that it is incomplete. New data presented herein identifies a super enhancer (SE) located between the HLA- DRB1 and -DQA1 genes (termed the DR/DQ-SE) that is required for maximal expression of the system and for its “3D” architecture. CRISPR/Cas9 mediated deletion of the DR/DQ-SE in Raji B cells resulted in decreased expression of HLA-DR and -DQ, reduced ability to stimulate an allogenic CD4 T cell response, and loss of promoter associated histone modifications and all local CTCF-insulator interactions. Additionally, while it is accepted that MHC proteins are highly polymorphic, non-coding polymorphisms within cis-regulatory regions of the MHC-II locus are more extensive and strongly linked to MHC-II expression and disease, suggesting that transcriptional regulation of MHC-II expression by the DR/DQ-SE is a key component of immunity and disease. Aside from what we present, nothing else is known about this region and how it works. To fill this gap in knowledge, this application seeks to understand how this SE functions to control MHC-II expression and immunity. Aim 1 will elucidate fundamental molecular and biochemical components of the DR/DQ-SE and determine how polymorphisms affect its function. Aim 2 will determine the range of the SE’s influence and test a model of how it may operate. Aim 3 will examine how the SE is established, and decommissioned. Together, our studies will provide insight into how human (SNP) diversity influences immunity, and ultimately how this critically important set of immune system genes are regulated. The knowledge gained will have broad implications on gene regulation and will provide new insight into how the initial steps of adaptive immune responses may be controlled. Our results could have important implications for future immune-based therapies and vaccinations, and for treatments of infectious disease, autoimmunity, cancer, and transplantation.

主要组织相容性复合体-II类蛋白由人类白细胞抗原-DR、-DQ和-DPα/β基因编码 通过将经过处理的抗原肽呈递给CD4+T细胞从而启动和/或维持 适应性免疫反应。MHC-II的表达受转录调控，并在 抗原提呈细胞，如B细胞，但可由干扰素γ在非免疫细胞中诱导。因此，MHC-II- 介导的免疫反应和获得性免疫主要在转录水平上受到控制。所有MHC- II基因由一组共同的近端启动子转录元件和因子共同调控，其中只有 CITA是细胞类型限制性的，由干扰素γ诱导。几年前，我们发现MHC-II基因的表达是 也受一系列转录绝缘体元件的调节，这些元件结合了CTCF和粘附素 元件是彼此与MHC-II启动子之间长距离染色质相互作用的焦点 地区。这些元件一起形成了有利于基因的三维染色质结构 表情。事实上，随着B细胞分化为浆细胞并失去MHC-II的表达，这种结构 也输了。虽然这个模型是正确的，并且在过去的5年里一直存在，但我们现在提供了令人兴奋的新证据。 它是不完整的。本文提供的新数据确定了一种超级增强子(SE)，位于人类白细胞抗原- DRB1和-DQA1基因(称为DR/DQ-SE)是系统和 它的“3D”架构。CRISPR/Cas9介导的Raji B细胞DR/DQ-SE缺失 人类白细胞抗原DR和DQ的表达，刺激同种异体CD4T细胞反应的能力降低，以及 启动子相关的组蛋白修饰和所有局部CTCF-绝缘体相互作用。此外，虽然它是 公认MHC蛋白是高度多态的，非编码多态的顺式调控区域 MHC-II基因座范围更广，与MHC-II的表达和疾病有很强的联系，这表明 DR/DQ-SE对MHC-II表达的转录调控是免疫和疾病的重要组成部分。 除了我们介绍的内容外，我们对这个地区及其运作方式一无所知。填补这一空白 知识，本应用程序试图了解该SE如何发挥作用来控制MHC-II的表达和 豁免权。目标1将阐明DR/DQ-SE的基本分子和生化成分以及 确定多态如何影响其功能。目标2将确定SE的影响和测试的范围 它可能会如何运作的一个模型。AIM 3将研究SE是如何建立和退役的。一起， 我们的研究将深入了解人类(SNP)多样性如何影响免疫力，并最终如何影响 一组至关重要的免疫系统基因受到调控。所获得的知识将具有广博的 对基因调控的影响，并将为获得性免疫的初始步骤提供新的见解 反应可能是可控的。我们的研究结果可能对未来基于免疫的治疗有重要意义 和疫苗，以及传染病、自身免疫、癌症和移植的治疗。