Defining gene regulatory networks driving cortical evolution and brain development

定义驱动皮质进化和大脑发育的基因调控网络

基本信息

批准号：
10616776
负责人：
Luis de la Torre-Ubieta
金额：
$ 67.94万
依托单位：
UNIVERSITY OF CALIFORNIA LOS ANGELES
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-07-01 至 2026-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10616776
关键词：
ATAC-seq Adult Affect Atlases Automobile Driving Biochemical Biological Biological Assay Brain CISH gene CRISPR interference CRISPR/Cas technology Cell Nucleus Cells ChIP-seq Chromatin Chromosome Mapping Code Cognition Cognitive Data Development Disease Engineering Enhancers Equilibrium Evolution Excision Experimental Models FGFR2 gene Gene Expression Gene Expression Regulation Gene Targeting Genes Genetic Determinism Genetic Variation Genome Genomics Human Human Development Impairment LYN gene Length Libraries Macaca Maps Mass Spectrum Analysis Methodology Molecular Morphogenesis Mus Neocortex Neuroglia Neurons Nuclear Nucleic Acid Regulatory Sequences Outcome Phenotype Pregnancy Proliferating Protein Isoforms Proteins Proteomics Radial Reading Regulator Genes Regulatory Element Research Personnel Resolution Risk Role Specificity Structure Technology Testing Therapeutic Tissues Untranslated RNA Validation Work brain size cell type falls gene regulatory network gene repression genetic variant genomic variation insight neocortical nerve stem cell neurogenesis neuropsychiatric disorder next generation sequencing novel progenitor programs promoter social spatiotemporal transcription factor transcriptome

项目摘要

PROJECT SUMMARY/ABSTRACT Neuropsychiatric disorders often affect our most distinguishing cognitive and social capabilities, which are thought to have developed as a result of the expansion of the human neocortex. The unique mechanisms orchestrating cortical neurogenesis and differentiation in the developing human neocortex forming the basis of this expansion are beginning to be described. However, although genetic variation in non-coding gene-regulatory regions, rather than in protein coding genes, drives these evolutionary changes, the cis gene regulatory elements (GREs), including promoters and enhancers, and the transcription factors (TFs) governing cortical neurogenesis remain to be characterized. To begin to investigate this understudied mechanism, we and others have leveraged next generation sequencing approaches to profile chromatin accessibility and interaction in parallel with gene expression to create GRE maps of varying levels of spatiotemporal specificity. We previously identified thousands of developmentally dynamic GREs and their putative gene targets by contrasting GRE activity in progenitor versus neuron-enriched laminae of mid-gestation human neocortex, and functionally validated the role of select GREs in cortical neurogenesis using primary human neural progenitor cells. Further, we found that human-gained enhancers (HGEs), a subset of GREs more active in the human than the macaque or mouse neocortex, regulate genes enriched in outer radial glia (oRG), a neural progenitor with prominent roles in cortical gyrification. This work supports the hypothesis that human developmentally dynamic GREs and HGEs direct gene expression programs controlling the proliferation and differentiation of progenitor pools key to cortical expansion. In this proposal, we seek to test this hypothesis and move from a tissue- and gene-level resolution atlas to a cellular- and gene isoform-level resolution atlas. We will perform single nucleus ATAC-seq to identify cell-specific GREs and leverage a novel single-cell isoform sequencing (scIso-seq) technology to investigate a previously understudied mechanism of gene regulation – alternative promoter usage. This new atlas will inform our work to functionally define the GREs impacting cortical neurogenesis at scale using CRISPR interference (CRISPRi) libraries containing capture tags enabling simultaneous reading of transcriptome and sgRNA at the single-cell level. Finally, we will define and characterize the TFs directing the balance of proliferation versus differentiation of progenitors. These results will enable us identify the cellular basis of genomic variation causing risk for neuropsychiatric disease, and influencing cognition and brain structure. Together this work will create a robust single cell-resolution functional annotation of non-coding GREs and TFs acting in developing human neocortex and elucidate evolutionary mechanisms driving cortical expansion. Broadly, this work will provide a blueprint for scalable approaches to study non-coding genetic variation and cellular diversity.

项目概要/摘要神经精神疾病通常会影响我们最显着的认知和社交能力，这些能力是被认为是由于人类新皮质扩张而发展起来的独特机制。在发育中的人类新皮质中协调皮质神经发生和分化，形成然而，这种扩展正在开始被描述，尽管遗传变异是非编码基因的调节。驱动这些进化变化的是顺式基因调控元件，而不是蛋白质编码基因中的区域（GRE），包括启动子和增强子，以及控制皮质神经发生的转录因子（TF）为了开始研究这一尚未充分研究的机制，我们和其他人已经利用了这一机制。下一代测序方法可与基因并行分析染色质可及性和相互作用表达来创建不同水平的时空特异性的 GRE 图。通过对比 GRE 活动，数以千计的发育动态 GRE 及其假定的基因目标祖细胞与妊娠中期人类新皮质的神经元富集层，并进行功能验证使用原代人类神经祖细胞，选择 GRE 在皮质神经发生中的作用。人类获得的增强子 (HGE)，是 GRE 的一个子集，在人类中比猕猴或小鼠更活跃新皮质，调节富含外放射状胶质细胞（oRG）的基因，外放射状胶质细胞是一种在皮质中发挥重要作用的神经祖细胞这项工作支持了人类发育动态 GRE 和 HGE 直接引导的假设。控制皮层关键祖细胞库增殖和分化的基因表达程序在本提案中，我们试图检验这一假设并从组织和基因水平的分辨率出发。我们将进行单核 ATAC-seq 来鉴定。细胞特异性 GRE 并利用新型单细胞异构体测序 (scIso-seq) 技术来研究之前研究的基因调控机制——替代启动子的使用，这个新的图谱将提供信息。我们的工作是使用 CRISPR 干扰功能性地定义大规模影响皮质神经发生的 GRE (CRISPRi) 文库包含捕获标签，可同时读取转录组和 sgRNA 最后，我们将定义和表征指导增殖与平衡的 TF。这些结果将使我们能够确定导致基因组变异的细胞基础。这项工作将共同创造一个神经精神疾病的风险，并影响认知和大脑结构。对人类发育中的非编码 GRE 和 TF 进行稳健的单细胞分辨率功能注释从广义上讲，这项工作将提供新皮质并阐明驱动皮质扩张的进化机制。研究非编码遗传变异和细胞多样性的可扩展方法的蓝图。

项目成果

期刊论文数量（2）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Defining the evolutionary and gene regulatory logic of vertebrate neuronal diversity.

定义脊椎动物神经元多样性的进化和基因调控逻辑。

DOI：
发表时间：
2022-01-05
期刊：
影响因子：
16.2
作者：
de la Torre
通讯作者：
de la Torre

Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms.

人类新皮质的发育亚型多样性揭示了神经精神风险机制。

DOI：
发表时间：
2023-10-11
期刊：
影响因子：
0
作者：
Patowary, Ashok;Zhang, Pan;Jops, Connor;Vuong, Celine K;Ge, Xinzhu;Hou, Kangcheng;Kim, Minsoo;Gong, Naihua;Margolis, Michael;Vo, Daniel;Wang, Xusheng;Liu, Chunyu;Pasaniuc, Bogdan;Li, Jingyi Jessica;Gandal, Michael J;de la Torre
通讯作者：
de la Torre