Long noncoding RNAs in innate lymphoid cell biology

先天淋巴细胞生物学中的长非编码RNA

• 批准号: 9329977
• 负责人: Walter Mowel
• 金额: $ 4.4万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-01 至 2019-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9329977
• 关键词: ATAC-seq; Address; Affect; Alpha Cell; Antigen Receptors; Apoptosis; Asthma; Bacterial Infections; Bioinformatics; Biological Process; Biological Response Modifiers; Biology; Bone Marrow; CD4 Positive T Lymphocytes; CRISPR/Cas technology; Cell Proliferation; Cells; Cellular biology; Chromatin; Code; Defect; Development; Disease; Ectopic Expression; Embryonic Development; Functional disorder; Future; Gene Expression; Gene Expression Regulation; Genes; Genetic Polymorphism; Genetic Transcription; Genome; Genomic Segment; Helminths; Helper-Inducer T-Lymphocyte; Homeostasis; Human; Human Genome; Hypersensitivity; ID2 gene; IL2RB gene; Immune response; Immune system; Immunologic Monitoring; Immunologics; Infection; Inflammation; Inflammatory; Inflammatory Bowel Diseases; Insulin Resistance; Interleukin-15; Knowledge; Lead; Listeria monocytogenes; Lymphocyte; Lymphoid; Lymphoid Cell; Malignant Neoplasms; Mediator of activation protein; Mus; Myelogenous; Natural Killer Cells; Obesity; Pathology; Phenotype; Play; Population; Poxviridae; Proteins; RNA; Regulation; Regulator Genes; Role; Signal Transduction; Techniques; Testing; Therapeutic; Tissues; Toxoplasma gondii; Transcript; Transcription Repressor/Corepressor; Untranslated RNA; Virus Diseases; Western Blotting; base; cell type; cytokine; experimental study; immunoregulation; in vivo; novel; novel therapeutics; pathogen; progenitor; programs; response; targeted treatment; transcription factor

Project Summary: Innate lymphoid cells (ILCs) are recently described groups of innate lymphocytes critical for defense against a variety of pathogens, and their dysfunction has been associated with multiple pathologies. Therefore, understanding how innate lymphoid cells are regulated in vivo is key to developing novel treatments for a variety of diseases. It has become clear recently that although the majority of the human genome does not encode for proteins, noncoding regions are transcribed nonetheless. Indeed, long intergenic noncoding RNA (lincRNA) transcripts have been shown to have key regulatory function in a variety of contexts, such as embryonic development. However, the roles of lincRNAs in the immune system in vivo are not well understood. Importantly, the loci encoding lincRNAs in mice and humans are often conserved. Furthermore, the expression of lincRNAs is often regulated in a cell type-specific manner, more so than protein coding genes. This implies both that lincRNAs play important roles in regulating specific cells in mice and humans, and that they may be useful targets in future therapeutics. Therefore, I hypothesize that cell type-specific lincRNA expression in ILCs is critical for their homeostasis. To this end, we found a specific lincRNA, Ak083360, that is expressed in group 1 ILCs, and in the absence of Ak083360 I have found that both the numbers and function of group 1 ILCs are significantly reduced in multiple tissues. Furthermore, I found that expression of the Id2 transcript is greatly reduced in Ak083360-/- NK cells. Thus, I hypothesize that Ak083360 is critical for the homeostasis of group 1 ILCs through regulation of group 1 ILC development, and that it does this through specific regulation of the Id2 gene. To test this hypothesis, I will determine both the developmental stages and biological process, such as cell proliferation or apoptosis, that are dysregulated in Ak083360-/- mice. I will also determine whether Ak083360 is required for group 1 ILC responses in inflammatory settings. Furthermore, I found that the expression of the Id2 gene is altered in Ak083360-deficient group 1 ILCs, and will determine whether dysregulation of Id2 expression is responsible for this phenotype. Finally, I predict that Ak083360 regulates chromatin accessibility at the Id2 locus. To test this, I will determine the state of chromatin accessibility in Ak083360-/- group 1 ILCs using ATAC-seq, and will combine this with RNA pulldown and Western blotting to determine if Ak083360 interacts with specific protein partners. Altogether, successful completion of the described experiments will further our understanding of both gene regulation by lincRNAs in general and specific factors regulating ILC populations.

项目概要： 先天性淋巴样细胞（inate lymphoid cells，ILC）是近年来发现的一组先天性淋巴细胞，它们在免疫系统中起重要作用， 多种病原体，它们的功能障碍与多种病理学有关。因此，我们认为， 了解先天性淋巴样细胞在体内是如何调节的，是开发新的治疗方法的关键。 各种疾病。最近已经很清楚，尽管人类基因组的大部分不 尽管编码蛋白质，但非编码区仍被转录。事实上，长的基因间非编码RNA 已显示lincRNA转录物在多种情况下具有关键调控功能，例如 胚胎发育然而，lincRNA在体内免疫系统中的作用并不清楚 明白重要的是，小鼠和人类中编码lincRNA的基因座通常是保守的。此外，委员会认为， lincRNA的表达通常以细胞类型特异性的方式调节，比蛋白质编码更是如此。 基因.这意味着lincRNA在调节小鼠和人类的特定细胞中发挥重要作用， 并且它们可能是未来治疗中有用的靶点。因此，我假设细胞类型特异性 ILC中的lincRNA表达对其体内平衡至关重要。为此，我们发现了一种特定的lincRNA， Ak 083360，其在第1组ILC中表达，并且在Ak 083360不存在的情况下，我发现， 组1 ILC的数量和功能在多种组织中显著降低。此外，我发现， Ak 083360-/- NK细胞中Id 2转录本的表达大大减少。因此，我假设Ak 083360 通过调节第1组ILC的发育，对第1组ILC的稳态至关重要， 这是通过Id 2基因的特异性调节实现的。为了验证这一假设，我将确定两个发展 阶段和生物过程，如细胞增殖或凋亡，在Ak 083360-/- 小鼠我还将确定Ak 083360是否是炎症环境中第1组ILC反应所必需的。 此外，我发现Ak 083360缺陷的第1组ILC中Id 2基因的表达改变， 确定Id 2表达的失调是否是这种表型的原因。最后，我预测， Ak 083360调节Id 2位点的染色质可及性。为了验证这一点，我将确定染色质的状态 使用ATAC-seq在Ak 083360-/-组1 ILC中的可及性，并将联合收割机与RNA下拉结合， 蛋白质印迹以确定Ak 083360是否与特定蛋白质伴侣相互作用。总之，成功 所述实验的完成将进一步加深我们对lincRNA的基因调控的理解， 调节ILC群体的一般和具体因素。