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

项目摘要 哺乳动物基因组被普遍转录以产生复杂的非编码转录组。一种新型 一类称为DoG的长链非编码RNA（lncRNA）含有“基因下游”转录物， 最近发现的。响应于各种应激源，如病毒感染，DoG RNA通过以下途径表达： 在某些蛋白质编码基因的末端继续至少5 kb的通读转录。值得注意的是， 这种以前未知的RNA种类作为一个群体占所有基因间转录物的30%，但它们的 功能仍然完全未知。我发现先天免疫感应病毒核酸和 I型干扰素（IFN）抗病毒应答的激活导致来自数千个细胞的DoG RNA的表达， 基因，尤其是IFN基因本身。因此，我假设DoG RNA的功能可能是 调节其上游基因的起源，这是一个重要的调控过程，在先天性抗病毒 应答从机制上讲，我认为DoG RNA重塑了染色质和/或转录水平， 其上游基因的景观，以达到一个平衡的状态。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，我将评估来自于细胞的DoG RNA的作用。 Ifnb 1基因（Ifnb 1-DoG RNA）在IFN-β表达调控中的作用 转录方法来操纵DoG RNA水平。在目标2中，我将研究 Ifnb 1-DoG RNA通过表征Ifnb 1基因位点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 架构在目标3中，我将确定DoG RNA在体内的生理重要性。我将生成Ifnb 1- 通过首先产生靶向Ifnb 1下游的指导RNA敲入小鼠，然后 通过将这些小鼠与dCas 9转基因小鼠杂交。我将研究Ifnb 1-DoG RNA对先天免疫的影响 在体内平衡和病毒感染期间。I型IFN应答是免疫应答的关键组成部分。 我们的抗病毒防御机制，但可以导致人类疾病，如I型干扰素病和全身性 红斑狼疮时失调。本研究旨在进一步了解I型干扰素的调控 通过对一类新的lncRNA进行功能表征。从这项研究中获得的见解可能是 用于开发针对感染性和IFN介导的自身免疫性疾病的改进疗法。

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.