Control of human neurodevelopment by a group of hominoid-specific transposons

一组人科动物特异性转座子控制人类神经发育

• 批准号: BB/Y000854/1
• 负责人: Marco Trizzino
• 金额: $ 80.46万
• 依托单位: Imperial College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2024
• 资助国家: 英国
• 起止时间: 2024 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FY000854%2F1
• 关键词: Control; human; neurodevelopment; group; hominoid

Human brain development requires the timely activation of developmental genes. As cells differentiate, gene activation is modulated primarily by non-coding DNA elements, called enhancers, usually located far away from their target genes. Following the input of DNA-binding proteins (transcription factors), the enhancers interact with the target genes, eliciting their activation.Transposable Elements (TEs) are parasitic genomic elements that take advantage of the host genomes to propagate across generations. Nonetheless, some TEs present specific characteristics that are useful to the host genome. For instance, the DNA sequence of the TEs may include particular sequence motifs that are recognized by specific transcription factors. When this is the case, the TEs may be "co-opted" by the genome to become functional enhancers. This host-parasite mutualism is usually cell type specific, in that the TEs may be co-opted as enhancers in some cell-types and repressed in others. In this context, a young family of TEs, called SINE-VNTR-Alu (SVA), may play an important role during human neurodevelopment. SVAs are exclusive of the great apes (orangutan, gorilla, chimpanzee, humans), and nearly half of the ~2,700 copies present in the human genome are exclusive of our species.There is strong preliminary evidence suggesting that the human-specific SVAs control human neurodevelopment by acting as enhancers. Here, we will investigate the mechanisms by which SVAs control human neurodevelopment. There are several questions we would like to address: 1) which stages of human neurodevelopment are controlled by the SVAs? 2) Do SVAs function as developmental enhancers only in specific brain cell types, or is this phenomenon universal in the brain? 3) Have the SVA-derived brain enhancers accumulated genetic variation in their sequence across human populations? And is this variation associated with specific neurodevelopmental human traits?To answer these questions, we will model human neurodevelopment in vitro using cerebral organoid generation from induced pluripotent stem cells (iPSCs). The iPSCs are stem cells derived from human somatic cells that have been engineered in vitro to become stem-like cells. The iPSCs can be treated with specific reagents to trigger the rapid development of brain-like tissues, termed cerebral organoids. Only 10 days are required for the appearance of neural identity and 20-30 days for defined brain regions to form. The organoids reach the maximum size in two months, but they can be kept in culture indefinitely. We will couple this system with single cell genomics and genome editing. More specifically, single cell genomic techniques (single-cell RNA-seq and single-cell ATAC-seq) will be employed to assess which SVAs are active in every individual cell during brain organoid generation, and which genes they control. Additionally, we will employ CRISPR-interference, which is a modification of the CRISPR-Cas9 technology that has been optimized to recruit proteins that repress specific genomic sites. In this case, the CRISPR-interference will be used to repress ALL the human SVAs at different time-points during organoid generation and assess the consequences on the development of the different brain cell types. In addition to the work performed on organoids, we will harness publicly available human whole genome sequences to profile genetic and structural variation in SVA-derived neurodevelopmental enhancers and will interpret this variation in the context of Genome Wide Association Studies (GWASs) that have been performed by others to predict genetic variants associated with specific human neurodevelopmental traits.Together these experiments will provide novel insights into human neurodevelopment, specifically unveiling novel mechanisms by which genes are turned on and off during the development of all the different brain components.

人脑的发育需要发育基因的及时激活。当细胞分化时，基因激活主要由非编码 DNA 元件（称为增强子）调节，通常远离靶基因。输入 DNA 结合蛋白（转录因子）后，增强子与目标基因相互作用，引发其激活。转座元件 (TE) 是寄生基因组元件，它们利用宿主基因组进行代际传播。尽管如此，一些 TE 仍呈现出对宿主基因组有用的特定特征。例如，TE 的 DNA 序列可能包括被特定转录因子识别的特定序列基序。在这种情况下，TE 可能会被基因组“选择”成为功能增强子。这种宿主-寄生虫互利共生通常是细胞类型特异性的，因为 TE 在某些细胞类型中可能被选为增强子，而在其他细胞类型中则被抑制。在这种背景下，一个名为 SINE-VNTR-Alu (SVA) 的年轻 TE 家族可能在人类神经发育过程中发挥重要作用。 SVA 是类人猿（猩猩、大猩猩、黑猩猩、人类）所独有的，而人类基因组中约 2,700 个拷贝中的近一半是我们物种所独有的。有强有力的初步证据表明，人类特异性的 SVA 控制着人类。通过充当增强剂来神经发育。在这里，我们将研究 SVA 控制人类神经发育的机制。我们想解决几个问题：1）人类神经发育的哪些阶段是由 SVA 控制的？ 2) SVA 是否仅在特定脑细胞类型中发挥发育促进剂的作用，还是这种现象在大脑中普遍存在？ 3) SVA 衍生的大脑增强子是否在人类群体中积累了序列遗传变异？这种变异是否与特定的人类神经发育特征相关？为了回答这些问题，我们将利用诱导多能干细胞 (iPSC) 生成大脑类器官来模拟人类神经发育。 iPSC 是源自人类体细胞的干细胞，经过体外改造成为干细胞样细胞。 iPSC 可以用特定试剂处理，以触发类脑组织（称为脑类器官）的快速发育。神经特征的出现只需要 10 天，特定的大脑区域形成则需要 20-30 天。类器官在两个月内达到最大尺寸，但它们可以无限期地保存在培养物中。我们将该系统与单细胞基因组学和基因组编辑结合起来。更具体地说，单细胞基因组技术（单细胞 RNA-seq 和单细胞 ATAC-seq）将用于评估在大脑类器官生成过程中每个单独细胞中哪些 SVA 处于活跃状态，以及它们控制哪些基因。此外，我们将采用 CRISPR 干扰，这是对 CRISPR-Cas9 技术的修改，经过优化以招募抑制特定基因组位点的蛋白质。在这种情况下，CRISPR 干扰将用于在类器官生成过程中的不同时间点抑制所有人类 SVA，并评估对不同脑细胞类型发育的影响。除了在类器官上进行的工作外，我们还将利用公开的人类全基因组序列来分析 SVA 衍生的神经发育增强子的遗传和结构变异，并将在已进行的全基因组关联研究 (GWAS) 的背景下解释这种变异这些实验将为人类神经发育提供新的见解，特别是揭示在所有不同的大脑组件发育过程中基因打开和关闭的新机制。