Long noncoding RNA expressing genomic elements that control antibody diversification and chromosomal integrity in B cells

表达控制 B 细胞抗体多样化和染色体完整性的基因组元件的长非编码 RNA

• 批准号: 10531294
• 负责人: Uttiya Basu
• 金额: $ 58.96万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-12-07 至 2027-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10531294
• 关键词: 3-Dimensional; Antibodies; Architecture; B-Cell Development; B-Lymphocytes; Binding Sites; Biochemical; Biological Assay; Biological Models; Biology; CRISPR/Cas technology; CSPG6 gene; Cell Line; Chromatin Conformation Capture and Sequencing; Chromosomal translocation; Chromosomes; Complex; Control Locus; DNA; DNA Maintenance; DNA Sequence Alteration; Data; Detection; Development; Disease; Elements; Enhancers; Event; Experimental Genetics; Genes; Genetic; Genetic Enhancer Element; Genetic Polymorphism; Genetic Recombination; Genetic Transcription; Genome; Genomics; Grant; High-Throughput Nucleotide Sequencing; Homeostasis; Human; Hybrids; IGH@ gene cluster; IgA Deficiency; Immune system; Immunity; Immunoglobulin A; Immunoglobulin Class Switching; Immunoglobulin Somatic Hypermutation; Immunoglobulin Switch Recombination; Immunoglobulins; Immunologics; Impairment; Libraries; Lymphoma; Lymphomagenesis; Mediating; Modeling; Molecular; Molecular Mechanisms of Action; Mutation; Nomenclature; Patients; Peyer' s Patches; Physiological; Physiology; Post-Transcriptional RNA Processing; Proteins; Publishing; RNA; RNA analysis; RNA-Protein Interaction; Regulation; Regulatory Element; Research Design; Role; Scanning; Site; Structure; Syndrome; System; Transcript; Untranslated RNA; chromatin immunoprecipitation; cohesin; dysbiosis; exosome; experimental study; genome integrity; genome-wide; genomic locus; humoral immunity deficiency; mammalian genome; microbiome; mouse genome; mouse model; novel; prevent; recruit; repaired; trafficking; transcriptomics

PROJECT SUMMARY Background. It is now evident that the majority of the mammalian genome has the potential to express non- coding RNAs (ncRNAs). However, the functionality and mechanism(s) of regulation of these ncRNAs are just beginning to be explored. One challenge that biologists encounter is the detection of these ncRNAs, which often tend to be transcriptionally tightly controlled and rapidly degraded. Using mouse models that allow easy detection of lncRNA, we have recently identified a set of long noncoding RNAs (lncRNA) that are expressed surrounding the immunoglobulin loci genes. These lncRNAs are placed inside topologically associating domains (TADs) that are formed during B cell development. Experiments using mouse models that lack these lncRNAs (published and preliminary data) demonstrate roles in class switch recombination and somatic hypermutation mechanisms. Objectives/Hypothesis. Here we investigate the direct role of lncRNAs in regulating genome local architecture and DNA topology via cis and trans mechanisms. In aim 1: we evaluate the physiological role of lncRNA-expressing loci in regulating IgH recombination via organizing TADIgH; in aim 2, we understand the molecular mechanisms through which lncRNAs are used to control genome architecture; and in aim 3, we focus on understanding the function of lncRNA SµGLT in control of CSR. Study Design: Using mouse models and cell lines that are deficient in specific lncRNAs we aim to investigate their immunologically relevant functions. For evaluating the molecular mechanism of action of the lncRNAs we use biochemical assays to purify lncRNA interacting proteins and perform chromosomal architecture assays such as HiC and 4C-seq. Finally, we perform high-throughput sequencing experiments to evaluate the lncRNA's effect(s) on SHM in the Ig loci genes and elsewhere. Disease Relevance: The proposed studies will lead to a better understanding of the mechanisms in B cell development and function. The lncRNAs being investigated in this application carry polymorphisms in patients with IgA deficiency syndrome and thus our study is relevant for human physiology. Finally, antibody diversification mechanisms are essential for immune system homeostasis but when these mechanisms fail there are increased genomic alterations that are associated with lymphomas. Thus, this study is related with both immunity and lymphomagenesis.

项目摘要 背景。现在有证据表明，大多数哺乳动物基因组具有表达非 - 编码RNA（NCRNA）。但是，这些NCRNA调节的功能和机制只是 开始探索。生物学家遇到的一个挑战是对这些NCRNA的检测 通常倾向于在抄录中受到紧密控制并迅速降解。使用允许轻松的鼠标模型 检测LNCRNA，我们最近确定了一组表达的长期非编码RNA（LNCRNA） 围绕免疫球蛋白局部基因。这些lncrnas放置在拓扑结合的内部 在B细胞发育过程中形成的域（TAD）。实验使用缺乏这些的鼠标模型 LNCRNA（已发布和初步数据）在类开关重组和躯体中展示了作用 超数机制。 目标/假设。在这里，我们研究了LNCRNA在调节基因组局部的直接作用 通过顺式和反式机制进行结构和DNA拓扑。在AIM 1中：我们评估 通过组织tadigh来调节IGH重组的LNCRNA局部表达局部；在AIM 2中，我们了解 LNCRNA用于控制基因组结构的分子机制；在AIM 3中，我们 专注于理解LNCRNA SµGLT控制CSR的功能。 研究设计：使用缺乏特定LNCRNA的小鼠模型和细胞系，我们旨在调查 他们的免疫学相关功能。用于评估LNCRNAS的分子作用机理 使用生化测定法纯化lncRNA相互作用蛋白质并执行染色体架构测定 例如HIC和4C-Seq。最后，我们执行高通量测序实验以评估 lncRNA对IG基因座基因和其他地方的SHM的影响。 疾病相关性：拟议的研究将使人们对B细胞的机制有更好的了解 发展和功能。在此应用中研究的LNCRNA在患者中携带多态性 与IgA缺乏综合症有关，因此我们的研究与人类生理学有关。最后，抗体 多元化机制对于免疫系统稳态至关重要，但是当这些机制失败时 与淋巴瘤相关的基因组改变增加。那，这项研究与 免疫和淋巴作用。