The Spatiotemporal Landscape of the Human Brain Epitranscriptome

人脑表观转录组的时空景观

• 批准号: 10189699
• 负责人: Christopher Edward Mason
• 金额: $ 65.42万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10189699
• 关键词: ASD patient; Address; Adenosine; Adult; Affect; Alleles; Alternative Splicing; Atlases; Autopsy; Bioinformatics; Biological; Biological Assay; Brain; Brain Diseases; Brain region; CRISPR/Cas technology; Cells; Cerebellar Cortex; Chemicals; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Copy Number Polymorphism; Cytosine; DNA Methylation; DNA Modification Process; Data; Data Set; Development; Disease susceptibility; Environment; Epigenetic Process; Event; Female; Future; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genes; Genetic; Genetic Transcription; Genotype-Tissue Expression Project; Goals; High-Throughput Nucleotide Sequencing; Human; Human Activities; Institutes; Knock-out; Link; Maps; Mediating; Mental disorders; Modeling; Modification; Molecular; Neuroglia; Neurologic; Neurons; Patients; Prefrontal Cortex; Proteins; Quantitative Trait Loci; RNA; RNA Editing; RNA Splicing; RNA methylation; Reader; Regulation; Resources; Sampling; Site; Somatosensory Cortex; System; Temporal Lobe; Testing; Time; Tissue Banks; Tissues; Transcript; Translations; Untranslated RNA; Variant; Visualization; area striata; autism spectrum disorder; autistic; base; bisulfite sequencing; clinically relevant; data resource; epigenetic regulation; epigenome; epitranscriptome; follow-up; genome sequencing; induced pluripotent stem cell; inter-individual variation; male; methylome; nervous system disorder; neurodevelopment; neuropsychiatric disorder; postnatal; postnatal development; repository; response; risk variant; spatiotemporal; transcriptome; translational medicine; whole genome; work-study

ABSTRACT The human Brainspan data was created to identify all transcripts involved in neural development and to help understand of how specific risk genes affect human brain development. In addition, these data will have important clinical relevance for translational medicine; these data can help discern which risk alleles associated with psychiatric and neurological disorders influence transcription and alternative splicing across different regions and developmental stages. Also, most Brainspan samples were processing for whole-genome sequencing (WGS) and/or DNA methylation analysis, which enables direct comparisons of single basepair changes, copy number variation, and RNA editing events in the developing human brain. As such, Brainspan data holds biologically and clinically important data on the genetic and molecular mechanisms underlying the development and increased disease susceptibility of the human brain. To expand upon this resource, we aim to create a matched profile of the human brains RNA modification landscape (epitranscriptome), for both methyl-6-adenosine (m6A) and 5-methyl-cytosine (5mC). We will profile the developmental trajectory of the RNA modifications and their activity in non-coding regions and impact on splicing, RNA editing, AU-rich regulation of transcripts, and association with DNA methylation changes (epigenetics). Finally, we will also test the impact of these modifications from patient-derived iPS cells that will be grown and assayed over five time points. This will be accomplished over five years, and across 1,075 samples, across the Mason and Sestan labs, with collaborators at the Broad institute available to help with assays and access to GTEx data from adult brains with m6A profiles. We will achieve these goals across three main aims. (1) Create a neuro-developmental map for epitranscriptome sites and levels, with an emphasis on m6A and m5C, for 35 brains from four time periods, and five regions of the brain, chosen based on their large differences seen in the BrainSpan data and prior implication in neurological development. (2) Detail the inter-individual variation in epitranscriptome levels and their epigenetic regulation using m6A variation with the changes in expression levels, and then link epigenetic changes to altered gene expression and m6A regulation. (3) We will delineate the epitranscriptome changes in autism brains and manifestation in patient-derived iPS cells, including an examination of epitranscriptome variation across 30 banked Autistic brain samples and testing of the impact on disruption of the readers and writers of RNA regulation (on induced pluripotent stem cells). These will represent the first-ever epitranscriptome maps from primary tissue of Autism brains and help guide future studies that examine the dysregulation of Autism gene expression networks and epitranscriptome states.

摘要 人类Braspiran数据的创建是为了识别与神经发育有关的所有转录，并 帮助了解特定的风险基因如何影响人脑发育。此外，这些数据将具有 转化医学的重要临床相关性；这些数据有助于辨别哪些风险等位基因与 精神和神经障碍影响转录和不同基因的选择性剪接 区域和发展阶段。此外，大多数布拉斯潘样本都在处理全基因组 测序(WGS)和/或DNA甲基化分析，允许直接比较单个碱基对 发育中的人脑中的变化、拷贝数变化和RNA编辑事件。因此，布拉斯潘 数据保存了关于遗传和分子机制的生物学和临床重要数据 人类大脑的发育和疾病易感性增加。 为了扩展这一资源，我们的目标是创建一个匹配的人脑RNA图谱 甲基-6-腺苷(M6A)和5-甲基胞嘧啶(5mC)的修饰图谱(表位转录组)。 我们将描述RNA修饰的发展轨迹及其在非编码区的活性 对剪接、RNA编辑、富含AU的转录本的调控以及与DNA甲基化的关联的影响 变化(表观遗传学)。最后，我们还将测试这些修改对患者来源的iPS细胞的影响 这将在五个时间点上进行培养和检测。这将在五年内完成，并将跨越 梅森和塞斯坦实验室的1075个样本，布罗德研究所的合作者可以提供帮助 通过分析和访问来自具有m6A特征的成人大脑的GTEx数据。 我们将通过三个主要目标实现这些目标。(1)创建神经发育地图 对来自四个时期的35个大脑的表位和水平进行转录，重点是M6A和M5C，以及 大脑的五个区域，根据BrainSpan数据和之前的巨大差异选择 对神经发育的影响。(2)详细说明表位转录水平的个体间差异和 它们利用m6A的表观遗传调控随表达水平的变化而变化，然后将表观遗传联系起来 改变基因表达和m6A调节。(3)我们将描述以下方面的外在翻译变化 自闭症患者的脑和患者来源的iPS细胞的表现，包括表位转录组学检查 对30个自闭症患者大脑样本进行了变异，并测试了其对读者和 RNA调控的作者(关于诱导的多能干细胞)。这将是有史以来第一次 自闭症大脑初级组织的表观转录组图并有助于指导未来研究 自闭症基因表达网络和表位转录组状态的失调。