The 3D Genomes of Memory B cells and Plasma Cells

记忆 B 细胞和浆细胞的 3D 基因组

• 批准号: 8873979
• 负责人: Alexandra Bortnick
• 金额: $ 5.42万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-01-15 至 2016-01-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8873979
• 关键词: Adopted; Affect; Affinity; Antibodies; Antibody Formation; Antibody Response; Antigens; B cell differentiation; B-Cell Development; B-Lymphocytes; Binding; Binding Sites; Cell Nucleus; Cell physiology; ChIP-seq; Chromosomes; Data; Development; Distant; E protein; Enhancers; Epigenetic Process; Gene Expression; Gene Expression Profile; Genes; Genetic; Genetic Transcription; Genome; Genomics; Global Change; Goals; Histones; Immunization; Immunoglobulin Class Switching; Immunoglobulin Somatic Hypermutation; Immunoglobulin Switch Recombination; Immunoglobulin-Secreting Cells; Invaded; Knock-out; Laboratories; Location; Lymphoid Tissue; Maintenance; Memory B-Lymphocyte; Mus; Nuclear; Nuclear Lamina; Nucleic Acid Regulatory Sequences; Nucleotides; Output; Peripheral; Plasma Cells; Positioning Attribute; Process; Protein Binding; RNA; Recruitment Activity; Regulation; Regulatory Element; Role; Serum; Site; Staging; Structure; Structure of germinal center of lymph node; TCF3 gene; Therapeutic; Tumor Suppressor Proteins; base; cell type; epigenome; genome-wide; helix-loop-helix protein differentiation inhibitor; in vivo; novel; pathogen; plasma cell development; plasma cell differentiation; promoter; public health relevance; research study; response; three dimensional structure; transcription factor; transcriptome sequencing

DESCRIPTION (provided by applicant): The genome is organized not merely as strings of nucleotides but as intricate folded structures that permit long-range interactions between genetic segments. Enhancers in particular have emerged as critical cis-regulatory elements that control gene transcription even at large distances from target promoters. These 3D structures are organized in the nucleus within transcriptionally permissive and repressive compartments, reflecting a previously unappreciated layer of regulation. In this regard, our laboratory has recently used high- throughput chromosome capture (Hi-C) to identify global changes in both the nuclear location of genes and the genomic interactions between distant promoters and enhancers during the developmental progression from the pre-pro-B to pro-B cell stage. Germinal centers are distinct anatomical structures that arise in peripheral lymphoid tissues in response to invading pathogens. During consecutive rounds of proliferation and affinity- based selection, via mechanisms that remain unclear, two effector B cell types emerge: memory B cells and antibody-secreting plasma cells. Plasma cells constitutively secrete antibody, sustaining serum antibody titers for months to years in mice and decades in people. In contrast, memory B cells remain quiescent but poised, ready to generate antibody-secreting cells upon antigen re-exposure. Our laboratory has found that E- and Id-proteins modulate germinal center B cell, plasma cell, and memory B cell differentiation. How these factors activate distinct patterns of gene expression in plasma cells versus memory B cells, how they act in concert with other factors, and how they are regulated themselves remains largely unknown. In this proposal, I hypothesize that germinal center B cells sequester lineage-specific transcription factors within nuclear compartments, and that tightly regulated mechanisms control their differential release in memory B cells and plasma cells. Here, we will characterize the binding sites of E-proteins in germinal center B cells, memory B cells, and plasma cells, describe their epigenomes, and determine which genes are recruited to the nuclear lamina. Overall, the experiments within this proposal will serve to better define the requirements for serum antibody maintenance and may suggest new ways to optimize these titers.

描述（由申请人提供）：基因组不仅是核苷酸的字符串，而且是允许遗传段之间长距离相互作用的复杂折叠结构。特别是增强子已经成为关键的顺式调节元件，即使在距离靶启动子远距离的距离很大，也可以控制基因转录。这些3D结构在转录允许和压抑室内的核中组织，反映了先前未批准的调节层。在这方面，我们的实验室最近使用高吞吐量染色体捕获（HI-C）来确定基因核位置的全球变化以及在Pre-Pro-B前发育过程中远处启动子和增强子之间的基因组相互作用pro-B细胞阶段。生发中心是响应入侵病原体的周围淋巴组织中产生的不同解剖结构。在连续的增殖和基于亲和力的选择中，通过尚不清楚的机制，出现了两种效应子B细胞类型：记忆B细胞和分泌抗体细胞。浆细胞组成性分泌抗体，在小鼠中维持血清抗体滴度数月至数十年的人。相比之下，记忆B细胞保持静止，但保持稳定，准备在抗原再暴露后生成分泌抗体的细胞。我们的实验室发现，E-和ID蛋白会调节生发中心B细胞，浆细胞和记忆B细胞分化。这些因素如何激活浆细胞与记忆B细胞中基因表达的不同模式，它们如何与其他因素一起起作用以及如何调节其本身仍然很大程度上是未知的。在此提案中，我假设生发中心B细胞隔离了核区室内的谱系特异性转录因子，并且严格调节的机制控制了它们在记忆B细胞和浆细胞中的差异释放。在这里，我们将表征E蛋白在生发中心B细胞，记忆B细胞和浆细胞中的结合位点，描述它们的表观基因组，并确定将哪些基因募集到核层。总体而言，该提案中的实验将有助于更好地定义血清抗体维持的要求，并可能提出优化这些滴度的新方法。