Exploration of cis-regulatory diversity underlying phenotypic innovation

表型创新背后的顺式调控多样性探索

基本信息

批准号：
10581623
负责人：
Alexandre Marand
金额：
$ 4.17万
依托单位：
UNIVERSITY OF GEORGIA
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-03-01 至 2023-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10581623
关键词：
Affect Alleles Atlases Award Binding Sites Biological Assay Candidate Disease Gene Cell Line Cell Nucleus Cells Cellular Morphology Chromatin Chromatin Structure Communication Complex Computer Analysis Computer Models Coupled DNA DNA sequencing Data Development Disease Etiology Faculty Foundations Future Gene Order Genes Genetic Genetic Models Genetic Polymorphism Genetic Transcription Genetic Variation Genome Genomic approach Genomics Genotype Geography Goals Grant Height Human Genome Image Individual Institution Investigation Link Linkage Disequilibrium Machine Learning Maize Maps Mediator Mentors Mentorship Microscopy Mission Modeling Molecular Outcome Pattern Phase Phenotype Plants Population Sizes Positioning Attribute Postdoctoral Fellow Primates Proliferating Quantitative Trait Loci Regulator Genes Regulatory Element Research Resolution Resources Role Specificity Techniques Testing Tissues Training Training Activity Transgenic Organisms United States National Institutes of Health Untranslated RNA Variant Weight Whole Organism Work Writing Zea mays career career development causal variant cell type cost design experimental study falls genetic approach genetic information genetic variant genome resource genome wide association study genome-wide human disease human model innovation model organism mouse genome mouse model single nucleus RNA-sequencing spatiotemporal stem success trait transcription factor transcriptome transcriptomics

项目摘要

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.

项目摘要 DNA测序的成本下降导致全基因组关联研究（GWAS）的扩散试图识别与疾病和其他重要表型相关的因果变异。但是，这是一个惊人的 93％的表型相关变体落在非编码区域内，通常数百千碱基来自最近的基因。最近的研究表明，此类变体在顺式调节中富集元素（CRE），可能会影响转录结果。 CRE由4-30 bp DNA图案组成通过序列特异性转录因子（TF）识别，该因子合作建立了转录模式以开发和细胞类型特异性方式。但是，尚不清楚CRE中的遗传变异如何机械上的转录模式，并有助于表型多样性单个细胞，组织和整个生物。该建议的目的是确定分子关系在各种细胞类型和遗传背景之间的遗传变异，CRE和基因转录中它们对细胞和生物表型的一致影响。 Zea Mays（玉米）的特征是广泛的内在表型和遗传变异可比在灵长类动物之间观察到的水平。该提案的遗传框架，282个玉米多样性面板，是由地理分散的个体专门构建的，以代表现存的全部范围物种内的变化。 282个玉米多样性面板中的连锁区脱骨衰减速率为10-40倍人类和小鼠基因组的人口大小明显较小，并具有等效分辨率。这项研究的基本原理是遗传变异，基因组资源，人群减少尺寸要求和最近的参考质量基因组（〜35）提出了理想模型研究由调节变化引起的表型多样性的机械基础。提议研究具有创新性，因为尖端的基因组方法（包括scatac-seq和snRNA-seq）将是与200个玉米基因型的基于显微镜的成像并行使用以检验中心假设这种Cre变化是基因转录的不同时空模式的基础细胞和生物水平的表型多样性。意识到拟议的目标将引入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景观。成功完成拟议的工作将为将来的审讯奠定基础遗传变异对人类疾病的机械作用，与NIH的任务有关。该应用程序是专门设计的，旨在通过相关的指导，赠款写作和科学交流中的培训活动。实现职业培训计划将促进申请人从博士后职位的成功过渡到教师在研究密集型机构中的位置。