3D Genome Organization and Gene Expression in Drosophila

项目摘要/摘要 拓扑关联域(TADS)是一种三维组织单位，它将遥远的遗传基因座带入 与它们的调控元件密切相关，并划定高度相互作用的染色质区域。早期研究 这表明TADS在基因调控中起着关键作用，因为它们被发现在垂直方向上高度保守。 Brates和果蝇。然而，最近的研究表明，TAD经常被重组，并且重新组织- 结构不会影响基因的表达。关于TAD保护和TAD的作用都缺乏明确性 TADS在基因表达调控中的作用是理解基因调控进化的关键障碍。这个 3D基因组进化的fi领域的长期目标是阐明3D基因组组织之间的关系。 基因和基因表达。这一建议的目的是描述三维基因组进化与生物多样性之间的关系。 通过表征TAD结构和基因表达的保守性和发散性来研究基因和基因表达 涉及11种果蝇。我的初步数据显示，TAD和基因表达进化的速度可能 不同的TAD亚型基于染色质的丰富。因此，我的中心假设是TAD进化的速度- 基因表达的差异因TAD亚型而异。我将通过以下方式验证这一假设 以下是物种fic的目标：1)进行系统发育比较分析，以评估TAD的保护 11种果蝇的结构和伴随基因表达的fi图谱和2)使用CRISPR测试 谱系特有的fic TAD中断对3D基因组组织和基因表达的直接影响。建议数 研究代表了一种创新的方法，因为它将利用物种之间的自然变异 以描述果蝇TADS与基因表达的关系。TAD边界的破坏已经被 与异常的增强子-启动子接触和基因错误调控有关，导致发育异常 和癌症。这些结果将有助于今后的研究，确定导致物种fic遗传前的遗传因素。 压抑模式和疾病状态，并提高对基因调控进化的整体理解。 培训计划侧重于对申请者进行计算基因组和分子遗传学方面的正规教育。 通过课程、讲习班和在赞助商的实验室环境中完成拟议的研究来提供方法。 此建议书中概述的培训将为申请者完成领导研究团队的职业目标做好准备。 研究野生生物和模式生物的基本进化过程，作为发现基因的多方面方法 健康和疾病的基础。这项提案的共同发起人拥有进化基因组学方面的专业知识 和遗传结构变异，罗格斯大学拥有足够的资源、设施和智力环境 在培训期间为申请人提供支持，并确保成功过渡到独立和达到 她的目标。

Project Summary/Abstract Topologically associating domains (TADs) are three-dimensional organizational units that bring distant genetic loci into close proximity with their regulatory elements and demarcate regions of highly-interacting chromatin. Early studies suggested that TADs play a critical role in gene regulation since they were found to be highly conserved in verte- brates and Drosophila. However, more recent research suggests that TADs are frequently reorganized and that re- structuring does not affect gene expression. The lack of clarity surrounding both TAD conservation and the role of TADs in regulating gene expression represents a critical barrier to understanding genetic regulatory evolution. The long-term goal within the field of 3D genome evolution is to elucidate the relationship between 3D genome organiza- tion and gene expression. The objective of this proposal is to describe the relationship between 3D genome evolu- tion and gene expression by characterizing the conservation and divergence of TAD structures and gene expression across 11 species of Drosophila. My preliminary data show that the rate of TAD and gene expression evolution may vary by TAD subtype based on chromatin enrichment. Therefore, my central hypothesis is that rate of TAD evolu- tion and the associated divergence in gene expression varies by TAD subtype. I will test this hypothesis through the following specific aims: I will 1) implement a phylogenetic comparative analysis to evaluate the conservation of TAD architecture and accompanying gene expression profiles across 11 Drosophila species and 2) use CRISPR to test the effects of lineage-specific TAD disruptions on 3D genome organization and gene expression directly. The proposed research represents an innovative approach because it will take advantage of natural variation between species of Drosophila to describe the relationship between TADs and gene expression. Disruption of TAD boundaries has been associated with aberrant enhancer-promoter contacts and gene misregulation, leading to developmental abnormalities and cancer . These results will assist in future research identifying genetic factors causing species-specific genetic ex- pression patterns and disease states, and improve overall understanding of the evolution of gene regulation. The training plan focuses on formal education of the applicant in computational genomic and molecular genetic approaches through courses, workshops, and completion of the proposed research in the Sponsor's laboratory setting. The training outlined in this proposal will prepare the applicant to accomplish her career goal of leading a research team studying basic evolutionary processes in wild and model organisms as a multifaceted approach to discover the genetic underpinning of health and disease. The Co-Sponsors for this proposal have the expertise in evolutionary genomics and genetic structural variation, and Rutgers University has the resources, facilities, and intellectual environment to support the applicant through the training period and ensure a successful transition to independence and attainment of her goal.