Modeling gene expression trajectories in the developing brain: methods and applications

大脑功能和发育依赖于基因表达的精确控制。成千上万的基因必须在空间和时间维度上得到精细的调控，以实现大脑区域的适当专门化和相互连接。此外，这种调节必须在神经细胞的长寿命中持续，在许多情况下，这是用年来衡量的。因此，与转录和RNA加工相关的分子过程对中枢神经系统中细胞的正常功能尤为重要。近年来，基因组技术的进步促进了人类组织转录组学和表观基因组学发育数据集的生成，这些数据集已经公开提供。这些国际努力为系统地评估整个大脑发育过程中、跨大脑区域和细胞类型的复杂分子景观提供了一个起点。虽然已经开发了一些全球分析方法，但这些大型数据集在很大程度上仍未被探索。细粒度动力学的异构体表达和复杂的RNA加工机制仍然没有表征，这是本提案的主要焦点。我们的总体目标是在高时间和空间分辨率下研究大脑转录过程的发育调节。我们特别关注连接表观遗传（染色质相关）和RNA加工机制的过程。为此，我们建议开发一个基于模型的框架来描述个体基因和外显子在时间和大脑区域中的表达轨迹。在这个框架内，我们的目标是确定新的替代外显子，基因启动子，仅在狭窄的发育窗口中使用的聚腺苷化位点，并随后研究潜在的染色质相关决定因素。总之，这个项目将对我们理解大脑中基因表达的转录和表观遗传调控的基本机制产生直接影响。此外，我们采取的高度跨学科的方法将导致综合基因组分析专业知识的发展，向研究界开放。

Brain function and development depend on precise control of gene expression. Thousands of genes must be finely regulated both in spatial and temporal dimensions to achieve proper specialization and inter-connectivity of brain regions. Moreover, this regulation must be sustained throughout the long lifespan of neural cells, which in many cases is measured in years. Molecular processes related to transcription and RNA processing, thus, are particularly important for proper function of cells in the central nervous system. In recent years, the advances in genomic technologies have facilitated the generation of comprehensive transcriptomic and epigenomic developmental datasets from human tissues, which have been made publicly available. These international efforts provide a starting point for systematically assessing the complex molecular landscape throughout brain development and across brain regions and cell types. While some global analytical approaches have been developed, these large datasets remain largely unexplored. Fine grained dynamics of isoform expression and complex RNA processing mechanisms are still uncharacterized, and are the main focus of this proposal. Our overall goal is to study, at high temporal and spatial resolution, developmental regulation of transcriptional processes in the brain. We particularly focus on processes linking epigenetic (chromatin-related) and RNA processing mechanisms. For this, we propose to develop a model-based framework to describe expression trajectories of individual genes and exons across time and across brain regions. Within this framework, we aim to identify novel alternative exons, gene promoters, polyadenylation sites used exclusively in narrow developmental windows, and subsequently study the underlying chromatin-related determinants.Altogether, this program will have a direct impact on our understanding of fundamental mechanisms of transcription and epigenetic regulation of gene expression in the brain. Furthermore, the highly interdisciplinary approach we undertake will result in the development of expertise in integrated genomic analyses, open to the research community.