Characterization of Chromatin associated Long non-coding in immunity

免疫中染色质相关长非编码的表征

• 批准号: 8966645
• 负责人: Katherine A. Fitzgerald
• 金额: $ 20.94万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-12-01 至 2016-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8966645
• 关键词: Accounting; Address; Air; Antisense RNA; Arthritis; Atherosclerosis; Automobile Driving; B-Lymphocytes; Binding; Binding Proteins; Binding Sites; Biological; Biological Process; Cataloging; Catalogs; Categories; Cells; Chromatin; Code; Collection; Communities; Complex; Coupled; DNA Binding; DNA Sequence; Dendritic Cells; Density Gradient Centrifugation; Disease; Event; Future; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomics; Guilt; Health; Heart Diseases; High-Throughput DNA Sequencing; Host Defense; Human; Immune; Immune response; Immune system; Immunity; Inflammation; Inflammatory; Invaded; Malignant Neoplasms; Maps; Mass Spectrum Analysis; Microbe; Molecular; Neoplasm Metastasis; Nuclear Import; Nucleotides; Pathway interactions; Positioning Attribute; Proteins; Publishing; RNA; Regulation; Research Design; Rest; Signal Transduction; Site; Specificity; Sucrose; T-Lymphocyte; Technology; Tissues; Untranslated RNA; Vaccines; Viral; Work; X Inactivation; adaptive immunity; base; chromatin immunoprecipitation; combat; genome-wide; imprint; inducible gene expression; macrophage; meetings; microbial; nano-string; neutrophil; pathogen; prevent; response; screening; transcription factor; transcriptome sequencing

DESCRIPTION (provided by applicant): Innate immune responses combat infectious microbes by driving inflammation, host-defense pathways and adaptive immunity. Multiple genes within distinct functional categories are coordinately and temporally regulated by transcriptional "on" and "off" switches that account for the specificity of gene expression in response to microbial triggers. Well-defined DNA binding transcription factors, transcriptional co-regulators and chromatin modifying complexes collaborate to coordinate transcription of immune genes. Recent evidence indicates that non-coding RNAs also contribute to gene regulation in diverse biological contexts. A growing body of evidence including our own published studies supports their importance in the immune system. lncRNAs have been identified in macrophages, dendritic cells, neutrophils, T-cells and B-cells during their differentiation and/or activation. We have found that these lncRNAs in turn regulate expression of other immune genes. This proposal is based on our hypothesis that lncRNAs are associated with chromatin in immune cells in order to regulate transcription of immune genes. We propose to identify and catalogue chromatin-associated lncRNAs in both resting and activated human macrophages and employ cutting edge molecular approaches to functionally characterize the genomic targets of these regulators. These objectives will be met using two specific aims: In aim 1 we will identify chromatin-associated lncRNAs (ca-lncRNAs) in an unbiased manner in human macrophages using sucrose density gradient fractionation as well as chromatin Immunoprecipitation coupled to RNA-sequencing. The regulation of these ca-lncRNAs will then be profiled using Nanostring technology to assess the temporal regulation and signaling mechanisms regulating their expression in response to microbial products, viral and bacterial pathogens. In aim2 we will identify the genomic targets and protein-binding partners of chromatin-associated lncRNAs using RNA antisense purification (RAP) coupled to DNA-Sequencing or Mass Spectrometry, respectively. These studies will define functionally important lncRNAs acting at the level of chromatin to modulate macrophage transcriptional responses and define genomic targets of ca-lncRNAs regulated during host-pathogen interactions. This unbiased identification of functionally relevant lncRNAs will also provide a platform for future studies that characterize these genes in greater detail. They will also provide new strategies to study lncRNA in other biological contexts.

描述（由申请人提供）：先天免疫反应通过驱动炎症、宿主防御途径和适应性免疫来对抗传染性微生物。不同功能类别内的多个基因受到转录“开”和“关”开关的协调和暂时调节，这些开关解释了响应微生物触发的基因表达的特异性。明确的 DNA 结合转录因子、转录共调节因子和染色质修饰复合物协作协调免疫基因的转录。最近的证据表明，非编码 RNA 也有助于不同生物环境中的基因调控。越来越多的证据（包括我们自己发表的研究）支持它们在免疫系统中的重要性。 lncRNA 已在巨噬细胞、树突状细胞、中性粒细胞、T 细胞和 B 细胞的分化和/或激活过程中被发现。我们发现这些lncRNA反过来调节其他免疫基因的表达。该提议基于我们的假设，即 lncRNA 与免疫细胞中的染色质相关，以调节免疫基因的转录。我们建议对静息和激活的人类巨噬细胞中的染色质相关 lncRNA 进行识别和分类，并采用尖端分子方法来对这些调节因子的基因组靶标进行功能表征。 这些目标将通过两个具体目标来实现：在目标 1 中，我们将使用蔗糖密度梯度分级以及染色质免疫沉淀与 RNA 测序相结合，以公正的方式鉴定人类巨噬细胞中的染色质相关 lncRNA (ca-lncRNA)。然后将使用 Nanostring 技术对这些 ca-lncRNA 的调节进行分析，以评估响应微生物产物、病毒和细菌病原体而调节其表达的时间调节和信号传导机制。在 Target2 中，我们将分别使用 RNA 反义纯化 (RAP) 与 DNA 测序或质谱联用来鉴定染色质相关 lncRNA 的基因组靶标和蛋白质结合伴侣。这些研究将定义在染色质水平上发挥作用以调节巨噬细胞转录反应的功能重要的lncRNA，并定义在宿主-病原体相互作用期间调节的ca-lncRNA的基因组靶标。这种对功能相关lncRNA的公正鉴定也将为未来更详细地表征这些基因的研究提供一个平台。他们还将提供在其他生物学背景下研究 lncRNA 的新策略。

项目成果

Emerging role of long noncoding RNAs as regulators of innate immune cell development and inflammatory gene expression.

长链非编码 RNA 作为先天免疫细胞发育和炎症基因表达调节剂的新作用。

• 发表时间: 2016-03
• 影响因子: 5.4
• 作者: Elling, Roland;Chan, Jennie;Fitzgerald, Katherine A
• 通讯作者: Fitzgerald, Katherine A