From a Long List to Causal Variants: High-Throughput Gene Regulatory Assays in Developing Tissues

摘要 我的实验室正在研究最近进化出的人类特征的遗传基础，这些特征在过去没有被观察到。 黑猩猩或其他类人猿。我们正在努力实现这一目标， 人类基因组中进化最快的区域。虽然这一系列的研究 以前一直在追求，研究一直集中在基因组的5%，显示出强大的 在非人类哺乳动物中的跨物种序列约束，因此显然是功能性的。 然而，我们现在知道有许多功能区域没有显示出强烈的跨物种 不同哺乳动物之间的限制。同样真实的是，许多表型转换在 与人类相似分支，如大脑扩张和直立姿势，也见于其他哺乳动物 血统例如，海豚和大象的大脑比人类大。狐猴和 大足类动物（例如袋鼠）也具有通常垂直于地面的脊椎。为 基于这些原因，我们假设许多基因组元素是人类适应的基础， 疾病风险将不仅限于表现出强烈跨物种的5%的基因组 保护其他哺乳动物。因此，我的实验室正在冒险进入人类的其他95%， 基因组，寻找在人类中迅速变化的区域，但也可能在其他基因组中变化。 物种这使我们面临着最初限制研究人员的问题， 5%的哺乳动物基因组高度受限。我们如何确定2089个地区中 是功能性的，我们如何知道人类谱系上的序列变化是否会改变他们的基因？ 功能？这是基因组学研究中常见的脱节现象： 数以千计的有趣的突变，无论是人类快速进化的区域，还是来自 全基因组关联研究，但为深入研究这些突变建立小鼠模型 只能进行一到十次突变这导致了两个数量级的脱节 在我们可以识别的突变和我们可以进一步分析的突变之间。绝 人类基因组中2089个进化最快的区域中的大多数都位于 蛋白质编码外显子，并可能调节基因的空间和时间表达， 发展虽然存在用于测试细胞系中增强子活性的高通量方法，但是， 细胞类型的活动通常是事先不知道的，细胞系不捕捉的复杂性， 在发育过程中短暂存在的细胞类型。为我们自己的工作解决这个问题， 为了被其他研究小组采用，我们正在开发一种检测该基因的方法。 在发育组织中和单细胞分辨率下的数千个DNA片段的调控潜力。

Abstract My laboratory is pursuing the genetic basis of recently evolved human traits that are not observed in chimpanzees, or other great apes. We are working towards this goal by identifying and functionally characterizing the fastest evolving regions in the human genome. While this line of research has been pursued before, the studies have always focused on the 5% of the genome that shows strong cross-species sequence constraint in non-human mammals, and is therefore clearly functional. However, we now know there are many functional regions that do not show strong cross-species constraint across diverse mammals. It is also true that many phenotypic transitions seen on the branch to humans, such as brain expansion and upright posture, are also seen in other mammalian lineages. For example, dolphins and elephants have larger brains than humans. Lemurs and macropods (e.g. kangaroos) also have a spine that is generally perpendicular to the ground. For these reasons, we hypothesize that many genomic elements underlying human adaptations and disease risks will not be restricted to the 5% of the genome showing strong cross-species conservation in other mammals. My laboratory is therefore venturing into the other 95% of the human genome, in search of regions that have rapidly changed in humans, but may also vary among other species. This has caused us to be faced with the problems that originally restricted researchers to the 5% of mammalian genomes that is highly constrained. How do we identify which of our 2089 regions are functional, and how do we know if the sequence changes on the human lineage change their function? This is a common disconnect in genomics research: a computational screen has generated thousands of interesting mutations, whether it be fast evolving regions in humans, or haplotypes from genome-wide association studies, but making mouse models for in depth study of these mutations can only be done for one to ten mutations. This results in a disconnect of two orders of magnitude between the mutations we can identify for further analysis and those we can further analyze. The vast majority of the 2089 fastest evolving regions in the human genome are located outside of protein-coding exons and are likely regulating the spatial and temporal expression of genes during development. While there are high-throughput methods for testing enhancer activity in cell lines, the cell type of activity is not usually known beforehand, and cell lines do not capture the complexity of cell types transiently present during development. To address this problem for our own work, and with the intention of it being adopted by other groups, we are developing a method to assay the gene regulatory potential of thousands of DNA segments in developing tissue and at single cell resolution.