Exploration of cis-regulatory diversity underlying phenotypic innovation

项目摘要 DNA测序成本的下降导致了全基因组关联研究(GWAS)的激增 寻找与疾病和其他重要表型相关的因果变异。然而，令人震惊的是 93%的表型相关变异落在非编码区，通常在几百个碱基之外 来自最近的基因。最近的研究表明，这些变异体在顺式调控中富含 元素(CRE)，并可影响转录结果。CRE由4-30个核苷酸的DNA基序组成 由协同建立转录模式的序列特异性转录因子(TF)识别 以发育和细胞类型特定的方式。然而，目前还不清楚Cres中的遗传变异是如何 对转录模式的机械扰动，并促进表型多样性在 单个细胞、组织和整个生物体。这项提议的目的是确定分子间的关系 在不同细胞类型和遗传背景的遗传变异中，Cres和基因转录，以及 它们对细胞和生物体表型的协同作用。 玉米具有广泛的种内表型和遗传变异，具有可比性 在灵长类动物中观察到的水平。这项提案的遗传框架，282玉米多样性小组， 是由地理上分散的个体专门构建而成的，以代表现存的 物种内的变异。在282个玉米多样性小组中，连锁不平衡衰减率为10-40倍 人类和小鼠的基因组，在同等分辨率的情况下，提供显著较小的种群规模。 这项研究的基本原理是，丰富的遗传变异、基因组资源、减少的种群 大小要求和最近扩展的参考质量基因组(~35)提供了一个理想的模型 研究调控变异引起表型多样性的机制基础。建议数 研究是创新的，包括scatac-seq和snrna-seq在内的尖端基因组方法将是 与基于显微镜的成像并行使用200个玉米基因型来检验中心假设 Cre变异是基因转录的不同时空模式的基础，这些模式共同表现在 细胞和生物水平的表型多样性。提出的目标的实现将迎来一个新的 了解细胞类型特异性的决定因素和进化基因的表型后果 监管环境。拟议工作的圆满完成将为今后的审讯奠定基础 基因变异对人类疾病的机械作用，与美国国立卫生研究院的任务有关。 这份申请是专门为促进申请者的职业发展而设计的。 指导、赠款撰写和科学交流方面的培训活动。事业成就感 培训计划将有助于申请人成功地从博士后职位过渡到教职人员 在一家研究密集型机构工作。

Project Summary The falling costs of DNA sequencing has resulted in a proliferation of genome-wide association studies (GWAS) seeking to identify causal variants associated with disease and other important phenotypes. However, a striking 93% of phenotype-associated variants fall within non-coding regions, often several hundreds of kilobases away from the nearest gene. Recent studies have demonstrated that such variants are enriched within cis-regulatory elements (CREs) and can affect transcriptional outcomes. CREs are composed of clusters of 4-30 bp DNA motifs recognized by sequence-specific transcription factors (TFs) that cooperatively establish patterns of transcription in a development and cell type-specific manner. However, it remains unclear how genetic variants within CREs mechanistically perturb patterns of transcription and contribute towards phenotypic diversity at the scale of individual cells, tissues and whole organisms. The aim of this proposal is to determine the molecular relationships among genetic variants, CREs, and gene transcription across diverse cell types and genetic backgrounds, and their concerted effects on cellular and organismal phenotypes. Zea mays (maize) is characterized by extensive intraspecies phenotypic and genetic variation comparable to the levels observed among primates. The genetic framework of this proposal, the 282 maize diversity panel, was specifically constructed from geographically dispersed individuals to represent the full spectrum of extant variation within the species. The rate of linkage-disequilibrium decay in the 282 maize diversity panel is 10-40X that of human and mouse genomes, affording significantly smaller population sizes with equivalent resolution. The rationale for this study is that the abundance of genetic variation, genomic resources, reduced population size requirements and recent expansion of reference-quality genomes (~35) present an ideal model to investigate the mechanistic basis of phenotypic diversity stemming from regulatory variation. The proposed research is innovative in that cutting edge genomic approaches, including scATAC-seq and snRNA-seq, will be utilized in parallel with microscopy-based imaging across 200 maize genotypes to test the central hypothesis that CRE variation underlies distinct spatiotemporal patterns of gene transcription that collectively manifest in phenotypic diversity at cellular and organismal levels. Realization of the proposed aims will usher a new understanding of the determinants of cell type-specificity and the phenotypic consequences of evolving gene regulatory landscapes. Successful completion the proposed work will lay the foundation for future interrogation of the mechanistic role of genetic variants towards human disease, relevant to the missions of the NIH. This application was specifically designed to enhance the applicants career development through associated training activities in mentorship, grant writing, and scientific communication. Accomplishment of the career training plan will facilitate the successful transition of the applicant from a post-doctoral position to a faculty position at a research-intensive institution.