Integrated, cell type specific functional genomics analyses of regulatory sequence elements and their dynamic interaction networks in neuropsychiatric brain tissues

神经精神脑组织中调节序列元件及其动态相互作用网络的综合、细胞类型特异性功能基因组学分析

• 批准号: 10609543
• 负责人: JOACHIM F HALLMAYER
• 金额: $ 164.33万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-20 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10609543
• 关键词: 3-Dimensional; ATAC-seq; Adult; Alleles; Autopsy; Biological Assay; Bipolar Disorder; Brain; Brain region; Cell Fraction; Cell Nucleus; Cells; Chromatin; Chromosome Mapping; Chromosomes; Code; Copy Number Polymorphism; Coupled; Critical Pathways; DNA; DNA mapping; Data; Data Analyses; Databases; Development; Dimensions; Disease; Disease Marker; Disease Pathway; Early Diagnosis; Early Intervention; Elements; Freezing; Future; Gene Expression Profile; Genetic; Genetic Diseases; Genetic Transcription; Genome; Genomics; Goals; Haplotypes; Human; Human Development; Human Genome; Individual; Knowledge; Link; Longevity; Maps; Mass Spectrum Analysis; Mental disorders; Nature; Neuroglia; Neurons; Nuclear; Nuclear Protein; Nuclear Proteins; Nucleic Acid Regulatory Sequences; Organoids; Pathology; Pathway interactions; Patients; Pattern; Phase; Preventive care; Proteomics; Regional Anatomy; Sampling; Schizophrenia; Series; Sorting; Source; Stretching; Techniques; Technology; Time; Tissues; Untranslated RNA; Variant; autism spectrum disorder; bioinformatics tool; brain tissue; cell type; clinical phenotype; complex data; computational pipelines; data integration; design; epigenomics; fetal; functional genomics; genetic architecture; induced pluripotent stem cell; innovation; mind control; neural; neuropsychiatric disorder; neuropsychiatry; novel; prenatal; psychiatric genomics; psychogenetics; rare variant; single-cell RNA sequencing; transcription factor; transcriptome; transcriptome sequencing; whole genome

Project Summary/Abstract After a century of debate about the fundamental nature of neuropsychiatric disorders, we know that genetics lie at their core, yet do not fully understand the critical underlying mechanisms of their disease-causing pathology. The overall goal of our proposal is the creation of comprehensive and integrated maps of chromatin accessibility, chromosome folding and transcriptional patterns, delineating regulatory regions in the genomes of key disease relevant anatomical regions of adult and fetal brains, in brains from patients with Schizophrenia, Autism Spectrum Disorder, Bipolar Affective Disorder and matched controls, and those with known CNVs (Copy-Number Variants) that may unmask regional or long-range targets of epigenomic regulatory interactions that may also be of great relevance in patients with the same clinical phenotype. We will use comprehensive and highly-resolving epigenomics assays, that were recently developed by us, and novel ways to integrate the data for the first time in neuropsychiatrically relevant brain tissues. We will generate comprehensive maps of the spectrum of organization and function of regulatory regions by integrating complementary techniques: single-cell ATAC-seq (scATAC-seq) to characterize chromatin openness and HiChIP to characterize long- range folding interactions of sorted neuronal and non-neuronal cells, both of which are coupled to single-cell RNA-seq and long-range RNA-seq for expression information, further complimented by information about transcription factors through proteomic analysis of nuclear fractions. These maps will then be combined with coding or non-coding/regulatory variants in the genomic sequence in the candidate regions and integrated into the overall PsychENCODE database, which will allow us to create and validate reference maps for epigenomic marks and interactions, determine aberrations to the reference state in patient tissue, and connect such aberrations to genetic disease loci as well as assemble such loci into disease pathways. This project will not only greatly expand our understanding of regulatory information encoded in the human genome and its impact on human brain development and neuropsychiatric disorders, but also produce the bioinformatics tools necessary to analyze the complex data being generated in PsychENCODE.

项目摘要/摘要 在对神经精神障碍的基本性质进行了一个世纪的辩论之后，我们知道基因决定了 在其核心，但还没有完全了解其致病病理的关键潜在机制。 我们提案的总体目标是创建全面和完整的染色质图谱 可获得性、染色体折叠和转录模式，描绘基因组中的调节区 在成人和胎儿大脑的关键疾病相关解剖区域，精神分裂症患者的大脑中， 自闭症谱系障碍、双相情感障碍和配对对照以及已知CNV的患者 (拷贝数变异体)可能揭示表观基因组调控相互作用的区域或远程靶点 这在临床表型相同的患者中也可能有很大的相关性。我们将使用全面的 以及我们最近开发的高分辨率表观基因组分析，以及整合 第一次在神经精神病学相关的脑组织中的数据。我们将生成全面的地图 通过整合互补技术，确定监管区域的组织和职能范围： 单细胞ATAC-seq(scATAC-seq)用于表征染色质开放，HiChIP用于表征长染色质 分离的神经元细胞和非神经元细胞的距离折叠相互作用，两者都耦合到单细胞 RNA-seq和长程RNA-seq用于表达信息，进一步补充了关于 转录因子通过核组分的蛋白质组学分析。然后，这些地图将与 候选区域中基因组序列中的编码或非编码/调控变异体并整合到 整个心理编码数据库，这将使我们能够创建和验证表观基因组的参考地图 标记和相互作用，确定患者组织中参考状态的像差，并将这样的 基因疾病基因座的变异以及将这些基因座组装成疾病途径。此项目不会 只会大大扩展我们对编码在人类基因组中的调控信息及其影响的理解 对人类大脑发育和神经精神障碍的研究，也产生了生物信息学的工具 有必要分析在心理编码中生成的复杂数据。