Developmental and evolutionary dynamics of tissue-specific mammalian enhancers.

组织特异性哺乳动物增强子的发育和进化动力学。

• 批准号: 8595085
• 负责人: Alexander Nord
• 金额: $ 5.22万
• 依托单位: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-01 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8595085
• 关键词: Accounting; Address; Adult; Antibodies; Beryllium; Binding; Binding Sites; Biological; Biological Assay; Biological Models; Biological Process; Biomedical Research; Brain; Cataloging; Catalogs; Computer Analysis; Coupled; DNA; DNA Sequence; Data; Data Set; Development; Disease; Elements; Embryo; Embryonic Development; Embryonic Heart; Enhancers; Evolution; Exhibits; Functional RNA; Gene Expression; Gene Expression Regulation; Genetic Transcription; Genomics; Goals; Heart; Histones; Human; Laboratories; Liver; Maps; Methods; Molecular Evolution; Mus; Pathway interactions; Pattern; Play; Pregnancy; Prosencephalon; Regulator Genes; Regulatory Element; Role; Sampling; Sequence Analysis; Series; Specificity; Staging; Techniques; Testing; Time; Tissue Sample; Tissues; Transgenic Mice; Validation; Work; biomedical resource; body system; brain tissue; chromatin immunoprecipitation; comparative genomics; design; epigenomics; genome wide association study; genome-wide; human disease; in vivo; insight; interest; mammalian genome; mouse development; novel; postnatal; prenatal; pressure; public health relevance; research study; transcription factor

DESCRIPTION (provided by applicant): Enhancers are remotely acting non-coding DNA elements that regulate the tissue-specific and developmental expression of genes. Enhancers are thought to be a major driver of vertebrate evolution, and there is increasing evidence that they play important roles in human disorders. Two complementary, powerful approaches to identify tissue-specific enhancers at a genomic scale are the use of extreme evolutionary conservation of non-coding sequences and, more recently, the mapping of enhancer-associated epigenomic marks by chromatin immunoprecipitation coupled to sequencing (ChIP-seq). Surprisingly, ChIP-seq studies of different embryonic mouse tissues revealed that enhancers active in some tissues, such as the embryonic brain, are under severe evolutionary sequence constraint whereas enhancers active in other tissues, such as the embryonic heart, are only mildly constrained. These results raise the possibility that patterns of evolutionary constraint generally differ between enhancers active in different tissues. Alternatively, it is possible that he degree of enhancer constraint in a specific tissue changes during development, and those differences in timing of these changes account for the observed differences in enhancer conservation between tissues. I propose to examine these two possibilities through a combination of experimental and computational approaches aimed at the identification and sequence analysis of genome-wide sets of enhancers active in the mouse from mid-gestation through adulthood in three tissues with different developmental trajectories. The specific aims include: 1) Identify active enhancers through ChIP-seq performed on brain, liver and heart tissue sampled across eight time points of pre- and postnatal mouse development; 2) Classify the degree of evolutionary constraint associated with active enhancers in the three tissues at all time points sampled; 3) Validate changes in activity through development in vivo using mouse transgenic enhancer assays for a selected set of enhancers. This study is expected to elucidate the evolutionary constraint signatures of enhancers active in different tissues at the same developmental time point, as well as possible constraint differences between enhancers active in the same tissue at different developmental stages. Importantly, the results will help to explain why gene expression in evolutionarily old organ systems like the heart appears to be under the control of poorly conserved enhancers. This is expected to have direct implications for our understanding of the role of enhancers in vertebrate evolution. In addition to enabling fundamental evolutionary insights, the data sets generated through this proposal will also provide a valuable resource for biomedical studies, since they are expected to reveal large numbers of currently unrecognized enhancers with transient developmental activities in three tissues of major biomedical interest.

描述（由申请人提供）：增强子是调节基因组织特异性和发育表达的远程作用的非编码DNA元件。增强剂被认为是脊椎动物进化的主要驱动力，并且有越来越多的证据表明它们在人类疾病中起着重要作用。在基因组量表下鉴定组织特异性增强子的两种互补的强大方法是使用非编码序列的极端进化保守性，最近，通过染色质免疫沉淀与测量伴侣（Chip-seq）相结合的染色质免疫沉淀与增强子相关的表观基因组标记的映射。令人惊讶的是，对不同胚胎小鼠组织的芯片zeq研究表明，在某些组织中活跃的增强子（例如胚胎脑）处于严重的进化序列约束下，而在其他组织（例如胚胎心脏）（例如胚胎心脏）中活跃的增强剂仅受到轻度约束。这些结果提出了一种可能性，即在不同组织中活跃的增强子之间的进化约束模式通常有所不同。另外，他在发育过程中特定组织变化中的增强子约束程度可能会导致这些变化的时间差异造成了组织之间观察到的增强子保存的差异。我建议通过相结合的实验和计算方法的结合来检查这两种可能性，这些方法和计算方法旨在鉴定和序列分析整个基因组范围的增强子集中，从妊娠中期到成年中的三种具有不同发育轨迹的组织中的成年期活跃的小鼠。具体目的包括：1）通过对大脑，肝脏和心脏组织进行的CHIP-seq确定活跃的增强子，这些chip-seq在产后和产后小鼠发育的八个时间点上采样； 2）分类与三个组织中的活性增强子相关的进化约束程度； 3）使用小鼠转基因增强剂测定法对选定的一组增强子来验证活性变化。预计这项研究将阐明在同一发育时间点在不同组织中活跃的增强子的进化约束特征，以及在不同发育阶段处于同一组织中的增强子之间的可能约束差异。重要的是，结果将有助于解释 为什么像心脏这样的进化旧器官系统中的基因表达似乎受到保守较差的增强子的控制。预计这将对我们对增强子在脊椎动物进化中的作用的理解产生直接影响。除了实现基本的进化见解外，通过本提案生成的数据集还将为生物医学研究提供宝贵的资源，因为预计它们会揭示大量目前未认可的增强子在主要生物医学兴趣的三个组织中具有短暂性发育活性。