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

基本信息

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
项目类别：
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

项目摘要

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 (MHC-II) 蛋白由 HLA-DR、-DQ 和 -DP α/β 基因编码通过将加工过的抗原肽呈递给 CD4+ T 细胞来配对并发挥作用，从而启动和/或维持 MHC-II 的表达受到转录调节并组成型表达。抗原呈递细胞，例如 B 细胞，但可以在非免疫细胞中被 IFNγ 诱导，因此，MHC-II-。介导的免疫反应和适应性免疫主要在转录水平上受到控制。 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，其中仅 CIITA 是细胞类型限制性的，由 IFNγ 诱导。几年前，我们发现 MHC-II 基因表达受到限制。还受到一系列结合 CTCF 和粘连蛋白的转录绝缘子元件的调节，并且这些元件是彼此和 MHC-II 启动子之间长程染色质相互作用的焦点这些元素共同形成了有利于基因的三维染色质结构。事实上，当 B 细胞分化为浆细胞并失去 MHC-II 表达时，这种结构就被改变了。虽然这个模型是正确的并且在过去 5 年中一直有效，但我们现在提供了令人兴奋的新证据。此处提供的新数据确定了位于 HLA-之间的超级增强子（SE）。 DRB1 和 -DQA1 基因（称为 DR/DQ-SE）是系统最大表达和其“3D”架构介导 Raji B 细胞中 DR/DQ-SE 的缺失，导致细胞因子减少。 HLA-DR 和 -DQ 的表达，刺激同种异体 CD4 T 细胞反应的能力降低，以及另外，启动子相关的组蛋白修饰和所有局部 CTCF-绝缘子相互作用。公认 MHC 蛋白在顺式调控区内具有高度多态性、非编码多态性 MHC-II 位点更广泛，并且与 MHC-II 表达和疾病密切相关，这表明 DR/DQ-SE 对 MHC-II 表达的转录调节是免疫和疾病的关键组成部分。除了我们所介绍的内容之外，我们对这个区域及其运作方式一无所知。知识，本应用旨在了解该 SE 如何发挥作用来控制 MHC-II 表达和目标 1 将阐明 DR/DQ-SE 和的基本分子和生化成分。确定多态性如何影响其功能目标 2 将确定 SE 的影响范围并进行测试。目标 3 将研究 SE 的建立和退役方式。我们的研究将深入了解人类 (SNP) 多样性如何影响免疫力，以及最终如何影响免疫力至关重要的一组免疫系统基因受到调节。所获得的知识将具有广泛的意义。对基因调控的影响，并将为适应性免疫的初始步骤如何提供新的见解我们的结果可能对未来的免疫疗法产生重要影响。和疫苗接种，以及用于治疗传染病、自身免疫、癌症和移植。