A novel class of long non-coding RNA in regulation of the type I interferonresponse

一类新型长非编码RNA调节I型干扰素反应

• 批准号: 10535470
• 负责人: Annsea Park
• 金额: $ 5.1万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-01 至 2024-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10535470
• 关键词: Address; Affect; Antiviral Response; Architecture; Autoimmune Diseases; Biological Assay; Cell Nucleus; Cells; Cellular Stress; ChIP-seq; Chromatin; Chromatin Loop; Chromatin Modeling; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Complex; Defense Mechanisms; Epigenetic Process; Equilibrium; Gene Expression; Genes; Genetic; Genetic Transcription; Genome; Guide RNA; Homeostasis; Human Genome; Infection; Interferon Activation; Interferon Type I; Interferon-beta; Interferons; Knock-in Mouse; Malignant Neoplasms; Measures; Mediating; Modeling; Molecular; Mus; Natural Immunity; Nucleic Acids; Organism; Phenotype; Physiological; Post-Transcriptional RNA Processing; Process; Proteins; RNA; Recombinant Interferon Beta; Regulation; Role; Serum; Signal Transduction; System; Systemic Lupus Erythematosus; Testing; Therapeutic; Tissues; Transcript; Transgenic Mice; Transposase; Untranslated RNA; Vesicular stomatitis Indiana virus; Viral; Viral Genes; Virus Diseases; Virus Replication; antiviral immunity; chromatin remodeling; chromosome conformation capture; genome editing; genomic locus; histone modification; human disease; immune activation; immunopathology; improved; in vivo; innate immune sensing; insight; knock-down; mammalian genome; novel; posttranscriptional; programs; response; senescence; stressor; transcriptome; viral resistance

Project Summary The mammalian genome is pervasively transcribed to generate a complex non-coding transcriptome. A novel class of long non-coding RNA (lncRNA) called DoGs for “Downstream-of-Gene”-containing transcripts was recently discovered. In response to various stressors such as viral infections, DoG RNAs are expressed by readthrough transcription that continues past the ends of some protein-coding genes for at least 5kb. Remarkably, this previously unknown RNA species as a group accounts for up to 30% of all intergenic transcripts, yet their function remains completely unknown. I discovered that innate immune sensing of viral nucleic acids and activation of the type I interferon (IFN) antiviral response leads to expression of DoG RNAs from thousands of genes, most notably from the IFN gene itself. I therefore hypothesize that a DoG RNA may function to regulate its upstream gene of origin, and that this is an essential regulatory process in innate antiviral responses. Mechanistically I propose that a DoG RNA remodels the chromatin and/or transcriptional landscape of its upstream gene to achieve a poised state. This would be beneficial for organisms because rapid responses to viral infections can be achieved. In Aim 1, I will evaluate the role of the DoG RNA from the Ifnb1 gene (Ifnb1-DoG RNA) in regulating IFN-β expression using genetic, transcriptional, and post- transcriptional approaches to manipulate DoG RNA levels. In Aim 2, I will investigate the molecular basis of Ifnb1-DoG RNA function by characterizing the chromatin and transcriptional landscape of the Ifnb1 gene locus. I will test whether DoG RNA expression affects post-transcriptional processing, epigenetic marks, and chromatin architecture. In Aim 3, I will determine the physiological importance of DoG RNA in vivo. I will generate Ifnb1- DoG RNA deficient mice by first generating guide RNA knock-in mice that targets downstream of Ifnb1 and then by crossing these with dCas9 transgenic mice. I will study the effect of the Ifnb1-DoG RNA on innate immunity at homeostasis and during viral infections with these mice. The type I IFN response is a critical component of our antiviral defense mechanism, but can lead to human disease such as type I interferonopathies and systemic lupus erythematosus when dysregulated. This study aims to advance our understanding of type I IFN regulation by functionally characterizing a novel class of lncRNAs. Insights gained from this study can potentially be leveraged to develop improved therapeutics for infectious and IFN-mediated autoimmune diseases.

项目概要 哺乳动物基因组普遍转录以产生复杂的非编码转录组。一本小说 一类称为 DoG 的长非编码 RNA (lncRNA)，用于包含“基因下游”的转录本 最近发现的。为了应对病毒感染等各种应激源，DoG RNA 通过以下方式表达： 通读转录，持续超过某些蛋白质编码基因的末端至少 5kb。值得注意的是， 这种以前未知的 RNA 物种作为一个群体占所有基因间转录本的 30%，但它们的 功能仍然完全未知。我发现病毒核酸的先天免疫感应和 I 型干扰素 (IFN) 抗病毒反应的激活导致数千个细胞中 DoG RNA 的表达 基因，最显着的是来自 IFN 基因本身。因此我推测 DoG RNA 的功能可能是 调节其上游起源基因，这是先天抗病毒的重要调节过程 回应。从机制上讲，我建议 DoG RNA 重塑染色质和/或转录 使其上游基因景观达到平衡状态。这对生物体是有益的，因为 可以实现对病毒感染的快速反应。在目标 1 中，我将评估 DoG RNA 的作用 Ifnb1 基因 (Ifnb1-DoG RNA) 通过遗传、转录和后转录调控 IFN-β 表达 操纵DoG RNA水平的转录方法。在目标 2 中，我将研究其分子基础 Ifnb1-DoG RNA 通过表征 Ifnb1 基因座的染色质和转录景观来发挥功能。 我将测试 DoG RNA 表达是否影响转录后加工、表观遗传标记和染色质 建筑学。在目标 3 中，我将确定 DoG RNA 在体内的生理重要性。我将生成 Ifnb1- DoG RNA 缺陷小鼠首先生成靶向 Ifnb1 下游的指导 RNA 敲入小鼠，然后 通过将这些小鼠与 dCas9 转基因小鼠杂交。我将研究 Ifnb1-DoG RNA 对先天免疫的影响 在这些小鼠的体内平衡和病毒感染期间。 I 型干扰素反应是 我们的抗病毒防御机制，但可能导致人类疾病，例如 I 型干扰素病和全身性疾病 失调时患红斑狼疮。本研究旨在增进我们对 I 型干扰素调节的理解 通过对一类新型 lncRNA 进行功能表征。从这项研究中获得的见解可能会 用于开发针对传染性和干扰素介导的自身免疫性疾病的改进疗法。