GENOMIC AND TRANSGENIC RESOURCES FOR CRANIOFACIAL ENHANCER STUDIES

用于颅面增强研究的基因组和转基因资源

基本信息

批准号：
8724906
负责人：
Axel Visel
金额：
$ 63.9万
依托单位：
UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-05-20 至 2019-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8724906
关键词：
8q24 Affect Biological Assay ChIP-seq Code Collaborations Commit Communities Complement Complex Computational Biology Computer Analysis Conceptions Congenital Abnormality DNA Data Data Set Development Disease Distal Distant E1A-associated p300 protein Embryo Enhancers Face FaceBase Functional RNA Gene Targeting Genes Genetic Genetic Variation Genome Genomics Health Histones Human Human Genetics Human Genome Individual Knock-out Knockout Mice Location Maps Modeling Morphology Mus Optics Phenotype Play Postdoctoral Fellow Predisposition Process Proteins Protocols documentation Regulator Genes Reporter Research Research Personnel Resolution Resources Role Secondary Palate Staging Structure Testing Time Tissues Transgenic Mice Transgenic Organisms Variant Work base clinical care comparative craniofacial genome-wide histone modification human tissue improved in vivo insight malformation member mouse genome mouse model new technology novel strategies programs repository spatiotemporal tomography trait transcriptome sequencing vector

项目摘要

Genetic studies have shown that distant-acting regulatory sequences (enhancers) embedded in the vast non-coding portion of the human genome play important roles in craniofacial development and susceptibility to craniofacial birth defects. The mechanistic exploration of these distant-acting enhancers continues to be difficult because the genomic location and in vivo function of most craniofacial enhancers remains unknown. As members of FaceBase 1, we generated first sets of annotation and functional data for distal enhancers controlling craniofacial development. These resources proved to be of significant value to the craniofacial research community. However, these efforts captured only a small proportion of the enhancers that are active during craniofacial development in vivo. Here we propose to characterize the gene regulatory landscape of craniofacial development more comprehensively using new and complementary approaches. The specific aims are: 1) We will map predicted enhancers by ChIP-seq from embryonic mouse and human facial tissues. In preliminary studies, we used ChIP-seq with the enhancer-associated protein p300 to identify several thousand enhancers predicted to be active in the mouse face at e11.5 and in the secondary palate at later stages of development. Using ChIP-seq for a panel of histone modifications (H3K4me1, H3K27ac, H3K27me3), which will require less tissue and increase the sensitivity of enhancer discovery by an order of magnitude, we will obtain higher-resolution data from all subregions of the developing mouse face at three stages of development (e11.5, e13.5, e15.5). We will complement this mouse-based effort with ChIP-seq on human embryonic face tissue to identify human-specific craniofacial enhancers not functionally conserved in mice. 2) In initial studies we characterized ~200 craniofacial enhancers in vivo in transgenic reporter assays. Taking advantage of protocols and collaborations established during FaceBase 1, we will continue to generate critically needed in vivo transgenic assays accompanied by optical projection tomography to characterize enhancers residing in new craniofacial loci identified by FaceBase 2 investigators and outside groups. This will include testing of enhancer variants associated with craniofacial malformations. The datasets, vectors and transgenic embryos produced through our efforts will be made available as resources to the craniofacial research community. We are deeply committed to our ongoing collaborative interactions with the Hub and other Spoke projects, contributing to and taking advantage of the unique research opportunities enabled through the FaceBase program.

遗传学研究表明，嵌入人类基因组大量非编码部分中的遥远作用调节序列（增强剂）在颅面发育和颅面先天性缺陷的敏感性中起着重要作用。这些遥远作用增强剂的机械探索仍然很困难，因为大多数颅面增强剂的基因组位置和体内功能仍然未知。作为面库1的成员，我们生成了控制颅面发育的远端增强子的第一组注释和功能数据。事实证明，这些资源对颅面研究界具有重要价值。但是，这些努力仅捕获了在体内颅面发育过程中活跃的一小部分增强子。在这里，我们建议使用新的和互补的方法更全面地表征颅面发展的基因调节景观。具体目的是：1）我们将通过胚胎小鼠和人面组织的chip-seq绘制预测的增强子。在初步研究中，我们使用与增强子相关的蛋白p300的ChIP-Seq鉴定了数千个预测在E11.5时在小鼠面上活跃的增强子，并且在后期发育阶段的次生口感中。使用chip-seq进行组蛋白修饰面板（H3K4ME1，H3K27AC，H3K27ME3），它将需要较少的组织，并通过数量级来提高增强子发现的敏感性，我们将从三个阶段的发展小鼠面对开发的所有子区域中获得更高分辨率的数据（e11.5 e11.5，e13.5）。我们将以人类胚胎面组织的芯片序列为基于小鼠的努力进行补充，以鉴定小鼠在功能上保守的人类特异性颅面增强子。 2）在最初的研究中，我们表征了300个在转基因报告基因测定中体内的颅面增强剂。利用面孔1期间建立的协议和协作，我们将继续生成急需的体内转基因测定法，并伴有光学投影层析成像，以表征居住在Facebase 2调查人员和外部组确定的新颅面基因座中的增强剂。这将包括测试与颅面畸形相关的增强子变体。通过我们的努力产生的数据集，向量和转基因胚胎将作为颅面研究界的资源提供。我们深入致力于与枢纽和其他讲话项目的持续合作互动，从而为通过Facebase计划启用了独特的研究机会做出了贡献。