Tissue-specific evolutionarily conserved regulation of gene expression

基因表达的组织特异性进化保守调控

• 批准号: RGPIN-2015-04677
• 负责人: Mitchell, Jennifer
• 金额: $ 2.19万
• 依托单位: University of Toronto
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2018
• 资助国家: 加拿大
• 起止时间: 2018-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=659903
• 关键词: Tissue; specific; evolutionarily; conserved; regulation

Virtually every cell in a multicellular organism contains the same DNA genome yet each celltype looks and functions differently to perform its required role in the organism. It is the differences in the way each gene in the genome is expressed in each cell type that accounts for these dramatic differences in cellular functions. Even though there is a wide variety in appearance between vertebrates separated by millions of years of evolution, they are fundamentally made up of similar cell-types and organs. Brain, liver and heart from different vertebrate species share more common gene expression within the same organ than between different organs within the same species. This commonality indicates that the mechanisms that regulate gene expression in each tissue are highly conserved through evolution. We lack, however, an understanding of these mechanisms and are not able to pinpoint most of the regions of the genome that are not in genes, but that are responsible for this remarkable conservation.****This proposal will investigate the mechanisms that specify tissue-specific gene expression through identifying active enhancers of gene expression that are functionally conserved through 450 million years of evolution. Identifying these enhancers is challenging as they are short and often located in regions of the genome without genes where sequence conservation is low. Although a small number of developmentally important enhancers have been predicted based on very similar DNA sequences found in vertebrates ranging from fish to humans, this small number does not account for the remarkable genome-wide conservation in gene expression across these species. The proposed research will allow for a better understanding not only of how to identify enhancers of expression in complex genomes but also which DNA-binding proteins regulate gene expression in different cellular contexts. ****The objectives of this proposal are; ***1) To determine how gene expression is modulated in different cell types by identifying active enhancers in embryonic stem cells, trophoblasts and fibroblasts using computational approaches and genome-wide experimental validation of enhancer activity. ***2) To determine how enhancer activity and gene expression is modulated through evolution by investigating gene expression levels and identifying enhancers active in fibroblasts from 10 vertebrate species. ***This will be the first investigation of enhancer activity across evolution and the first genome-wide identification of active enhancers in vertebrate genomes. This innovative approach will focus on well characterized cell types which can be maintained in cell culture to develop the research methods, but over the long term we will apply our expertise to more complex situations in living organisms to develop an understanding of how gene expression is controlled through development and how this has changed during evolution.*** **

事实上，多细胞生物体中的每个细胞都含有相同的DNA基因组，但每种细胞类型的外观和功能都不同，以执行其在生物体中所需的角色。正是基因组中每个基因在每种细胞类型中表达方式的差异，解释了细胞功能的这些巨大差异。尽管在数百万年的进化过程中，脊椎动物之间的外观差异很大，但它们基本上是由相似的细胞类型和器官组成的。来自不同脊椎动物物种的脑、肝和心脏在同一器官内比在同一物种内的不同器官之间共享更多共同的基因表达。这种共性表明，在每个组织中调节基因表达的机制在进化过程中是高度保守的。然而，我们缺乏对这些机制的理解，无法确定基因组中大多数不在基因中的区域，但这些区域负责这种显着的保守性。该提案将通过鉴定在4.5亿年进化中功能保守的基因表达的活性增强子来研究指定组织特异性基因表达的机制。鉴定这些增强子是具有挑战性的，因为它们很短，并且通常位于序列保守性低的基因组区域。虽然已经基于从鱼类到人类的脊椎动物中发现的非常相似的DNA序列预测了少量发育上重要的增强子，但这一小部分并不能解释这些物种中基因表达的显著全基因组保守性。拟议的研究不仅可以更好地理解如何识别复杂基因组中的表达增强子，还可以更好地理解哪些DNA结合蛋白在不同的细胞环境中调节基因表达。* 本提案的目标是：*1）通过使用计算方法和增强子活性的全基因组实验验证来鉴定胚胎干细胞、滋养层细胞和成纤维细胞中的活性增强子，以确定基因表达如何在不同细胞类型中调节。*2）通过研究基因表达水平和鉴定在来自10种脊椎动物物种的成纤维细胞中有活性的增强子，确定增强子活性和基因表达如何通过进化来调节。* 这将是第一次跨进化研究增强子活性，也是第一次在脊椎动物基因组中全基因组范围内鉴定活性增强子。这种创新方法将专注于可以在细胞培养中保持的良好表征的细胞类型，以开发研究方法，但从长远来看，我们将把我们的专业知识应用于生物体中更复杂的情况，以了解基因表达如何通过发育来控制，以及在进化过程中如何改变。**