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.

人脑发育需要发育基因的及时激活。随着细胞的分化，基因激活主要由非编码DNA元件调节，这种元件被称为增强子，通常位于远离目标基因的地方。随着DNA结合蛋白(转录因子)的输入，增强子与目标基因相互作用，引发它们的激活。转座元件(TES)是寄生的基因组元件，利用宿主基因组进行世代繁殖。尽管如此，一些TES呈现出对宿主基因组有用的特定特征。例如，TES的DNA序列可能包括由特定转录因子识别的特定序列基序。在这种情况下，TES可能会被基因组“增选”成为功能增强剂。这种寄主-寄生虫的互惠作用通常是细胞类型特有的，因为TES可能在某些细胞类型中被增选为增强剂，而在另一些细胞类型中被抑制。在这种背景下，一个年轻的TES家族，称为Sine-VNTR-Alu(SVA)，可能在人类神经发育过程中发挥重要作用。SVA是大猩猩(猩猩、大猩猩、黑猩猩、人类)所独有的，在人类基因组中存在的2700个拷贝中，有近一半是我们物种所独有的。有强有力的初步证据表明，人类特有的SVA通过作为增强剂来控制人类的神经发育。在这里，我们将研究SVA控制人类神经发育的机制。我们想要解决几个问题：1)人类神经发育的哪些阶段由SVA控制？2)SVA是只在特定类型的脑细胞中起到发育促进剂的作用，还是这种现象在大脑中普遍存在？3)SVA衍生的脑增强剂是否在人类群体中积累了其序列中的遗传变异？这种变异是否与人类特定的神经发育特征有关？为了回答这些问题，我们将使用诱导多能干细胞(IPSCs)产生脑器官来模拟人类神经发育。IPSCs是从体外培养的人类体细胞中提取的干细胞，已被改造成干细胞样细胞。IPSCs可以用特定的试剂处理，以触发类脑组织的快速发展，这种组织被称为脑器官。神经同一性的出现只需要10天，大脑特定区域的形成只需要20-30天。有机化合物在两个月内达到最大尺寸，但它们可以在培养中无限期保存。我们将把这个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，将使用单细胞基因组技术(单细胞RNA-seq和单细胞atac-seq)来评估在脑有机体生成过程中每个单个细胞中哪些SVA是活跃的，以及它们控制哪些基因。此外，我们将使用CRISPR干扰，这是CRISPR-Cas9技术的修改，该技术已经进行了优化，以招募抑制特定基因组位点的蛋白质。在这种情况下，CRISPR干扰将被用来在有机体生成的不同时间点抑制所有人类SVA，并评估其对不同类型脑细胞发育的影响。除了在有机化合物上进行的工作外，我们还将利用公开的人类全基因组序列来描述SVA衍生的神经发育增强剂的遗传和结构变异，并将在基因组广泛关联研究(GWASs)的背景下解释这种变异，这些研究已经由其他人进行，以预测与特定人类神经发育轨迹相关的遗传变异。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大脑组件的发育过程中基因打开和关闭的新机制。