The Spatiotemporal Landscape of the Human Brain Epitranscriptome

摘要 创建人类Brainspan数据是为了识别参与神经发育的所有转录本， 帮助了解特定风险基因如何影响人类大脑发育。此外，这些数据将 转化医学的重要临床相关性;这些数据可以帮助辨别哪些风险等位基因相关 与精神和神经系统疾病的影响转录和选择性剪接在不同的 地区和发展阶段。此外，大多数Brainspan样本正在处理全基因组 测序（WGS）和/或DNA甲基化分析，这使得能够直接比较单个碱基对 变化，拷贝数变异和RNA编辑事件在发育中的人类大脑。因此，Brainspan 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。 为了扩大这一资源，我们的目标是建立一个匹配的人类大脑RNA的轮廓， 修饰景观（表转录组），对于甲基-6-腺苷（m6 A）和5-甲基-胞嘧啶（5 mC）。 我们将描绘RNA修饰的发展轨迹及其在非编码区的活性 以及对剪接、RNA编辑、富含AU的转录调控以及与DNA甲基化的关联的影响 表观遗传学（epigenetics）最后，我们还将测试来自患者来源的iPS细胞的这些修饰的影响。 将在五个时间点内进行培养和检测。这项工作将在五年内完成， 梅森和塞斯坦实验室的1,075个样本，布罗德研究所的合作者可以提供帮助 通过分析和获取具有m6 A谱的成年大脑的GTEx数据。 我们将通过三个主要目标实现这些目标。(1)创建一个神经发育图， 来自四个时间段的35个大脑的表观转录组位点和水平，重点是m6 A和m5 C，以及 大脑的五个区域，根据BrainSpan数据和之前的数据中看到的巨大差异选择 对神经发育的影响。(2)详细描述表转录组水平的个体间差异， 其表观遗传调控利用m6 A变异与表达水平的变化，进而联系表观遗传 改变基因表达和m6 A调节。(3)我们将描绘出 自闭症大脑和患者来源的iPS细胞的表现，包括epitranscriptome的检查 30个自闭症大脑样本的差异，以及对阅读者中断的影响和 RNA调节（关于诱导多能干细胞）的作者。这将是有史以来 从自闭症大脑的主要组织中提取的epitranscriptome图谱，有助于指导未来的研究， 自闭症基因表达网络和表转录组状态的失调。

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.