Predicting Lung Chromatin Access Profiling in an Animal Model

预测动物模型中的肺染色质访问分析

• 批准号: 9386599
• 负责人: KURT H ALBERTINE
• 金额: $ 18.95万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2019-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9386599
• 关键词: Affect; Animal Model; B-Lymphocytes; Biochemical; Biological Assay; Biology; Biophysics; Birth; Blood Volume; Brain; Brain Injuries; Bronchopulmonary Dysplasia; CD4 Positive T Lymphocytes; Cells; Chemicals; Chromatin; Chromatin Remodeling Factor; Complex; DNA; DNA Sequence; DNA-Binding Proteins; Data; Development; Environmental Risk Factor; Epigenetic Process; Female; Future; Gene Expression; Genome; Genomics; Growth and Development function; Histones; Housekeeping Gene; Human; Human Genome; Individual; Infant; Injury; Leukocytes; Libraries; Location; Lung; Lymphocyte; Mechanical ventilation; Mechanics; Modeling; Modification; Molecular Analysis; Nucleic Acid Regulatory Sequences; Nucleosomes; Nucleotides; Organ; Pattern; Perinatal; Peripheral Blood Lymphocyte; Pregnancy; Premature Birth; Premature Infant; Proteins; Resolution; Respiratory Failure; Risk; Sheep; Site; Structure of parenchyma of lung; Technology; Testing; Tissues; Transposase; XCL1 gene; brain tissue; chromatin remodeling; disorder risk; epigenetic marker; fetal; genome-wide; innovation; lung development; lung injury; male; member; negative affect; novel strategies; particle; premature; response; single cell analysis; success

PROJECT SUMMARY/ABSTRACT Chemical modifications to specific histones and DNA sequences within nucleosomes attract chromatin remodeling complexes. Remodeling complexes create regions of open and restricted chromatin access to control gene expression. Environmental factors disrupt assigning epigenetic marks to histones and/or DNA that alter chromatin access, altering gene expression and increasing disease risk. The recent development of the cutting-edge technology assay for transposase-accessible chromatin, using ATAC sequencing (ATAC-seq), makes identification possible of chromatin access with nucleotide resolution on ~5000 cells. ATAC-seq determines the genomic location of open chromatin, DNA binding proteins, individual nucleosomes, and chromatin compaction. Defining chromatin access provides information about the functional state of DNA regulatory regions that may be altered by preterm birth and mechanical ventilation (PTMV). We will use ATAC-seq to identify the impact of PTMV on chromatin remodeling in our unique preterm lamb model of bronchopulmonary dysplasia (BPD). Our revised R21’s new data show that 1) chromatin landscape patterns are different in lung and brain from PTMV lambs versus healthy control lambs, 2) these differences are reflected within CD4+ T cells from PTMV lambs versus healthy control lambs, and 3) housekeeping genes are conserved among lamb CD4+ T cells, lung, brain, and human B cells. We hypothesize that PTMV negatively impact assignment of epigenetic marks necessary to direct chromatin remodeling and establish proper chromatin access throughout the genome. We will test our hypothesis by doing the following 2 specific aims. Specific Aim 1. Determine alterations to chromatin landscape induced by PTMV. Tissue-specific differences in chromatin landscapes will be identified by comparing results between lung and brain. Specific Aim 2. Compare alterations in chromatin landscape in CD4+ T cells with those identified in the lung and brain obtained in Aim 1. Tissue-specific differences in chromatin landscapes will be identified by comparing results between CD4+ T cells and lung and brain from the same lamb. Results of our revised R21 application will be significant because they will identify CD4+ T cells as accessible biomarkers of epigenetic changes in chromatin landscape in the lung and brain, which become adversely affected in preterm infants with evolving BPD but are not readily accessible for molecular analysis. Innovative approaches combine ATAC-seq with our preterm lamb model of BPD. Our collaborative, multiple- PI members bring expertise in epigenetics, preterm lamb model of BPD, and leukocyte biology. Translational potential arises from defining epigenetic biomarkers in CD4+ lymphocytes that correlate with altered gene expression in lung and brain tissue. Impact of our R21 project will be a novel approach that may be applicable to human preterm infants at risk for BPD, in part because ATAC-seq analysis now is available for single cells.

项目概要/摘要 核小体内特定组蛋白和 DNA 序列的化学修饰吸引染色质 改造综合体。重塑复合物创建了开放和限制染色质访问的区域 控制基因表达。环境因素会破坏组蛋白和/或 DNA 的表观遗传标记， 改变染色质通路，改变基因表达并增加疾病风险。 最近开发的转座酶可及染色质尖端技术检测，使用 ATAC 测序 (ATAC-seq) 使通过核苷酸分辨率识别染色质通路成为可能 〜5000 个细胞。 ATAC-seq 确定开放染色质、DNA 结合蛋白、个体的基因组位置 核小体和染色质压缩。定义染色质访问提供了有关功能的信息 DNA 调节区域的状态可能会因早产和机械通气 (PTMV) 而改变。我们 将使用 ATAC-seq 来确定 PTMV 对我们独特的早产羔羊模型中染色质重塑的影响 支气管肺发育不良（BPD）。我们修订后的 R21 的新数据表明 1) 染色质景观模式 PTMV 羔羊与健康对照羔羊的肺和脑部存在差异，2) 这些差异是 反映在 PTMV 羔羊与健康对照羔羊的 CD4+ T 细胞内，3) 管家基因 在羔羊 CD4+ T 细胞、肺、脑和人类 B 细胞中保守。我们假设 PTMV 呈负向 表观遗传标记的影响分配对于指导染色质重塑和建立适当的 染色质访问整个基因组。我们将通过实现以下两个具体目标来检验我们的假设。 具体目标 1. 确定 PTMV 引起的染色质景观的改变。组织特异性 通过比较肺和大脑之间的结果可以识别染色质景观的差异。 具体目标 2. 将 CD4+ T 细胞中染色质景观的变化与 目标 1 中获得的肺和大脑。将识别染色质景观的组织特异性差异 通过比较同一只羔羊的 CD4+ T 细胞与肺和大脑之间的结果。 我们修订的 R21 应用程序的结果将具有重要意义，因为它们将 CD4+ T 细胞识别为 肺和大脑染色质景观表观遗传变化的可获取生物标志物，这些变化成为 对患有 BPD 的早产儿产生不利影响，但不易进行分子分析。 创新方法将 ATAC-seq 与我们的早产羔羊 BPD 模型相结合。我们的协作、多元 PI 成员带来了表观遗传学、BPD 早产羔羊模型和白细胞生物学方面的专业知识。翻译性 潜力来自于定义 CD4+ 淋巴细胞中与改变基因相关的表观遗传生物标志物 在肺和脑组织中表达。我们的 R21 项目的影响将是一种可能适用的新颖方法 人类早产儿有 BPD 风险，部分原因是 ATAC-seq 分析现在可用于单细胞。