Statistical and high-throughput models of enhancer function and evolution

增强子功能和进化的统计和高通量模型

• 批准号: 10846272
• 负责人: SCOTT V. EDWARDS
• 金额: $ 5.9万
• 依托单位: HARVARD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10846272
• 关键词: Admission activity; African American; African American population; Area; Bioinformatics; Biological Assay; Biology; Burn injury; Complement; DNA Transposable Elements; Doctor of Philosophy; Enhancers; Evolution; Exhibits; Faculty; Family; Future; Genome; Goals; Laboratories; Mentors; Methods; Modeling; Modernization; Oral candidiasis; Parents; Proliferating; Research; Research Project Grants; Role; Science; Students; Technical Expertise; Tissues; Training; Universities; Voice; Work; Writing; career; comparative; comparative genomics; genome sequencing; novel; pan-genome; parent grant; programs; skills; vertebrate genome

Project Summary This diversity supplement proposes to train Mr. Christian Burns, an African American master’s student, in modern methods of comparative genomics and genome biology. African Americans are severely underrepresented in evolutionary biology and this supplement will assist Mr. Burns in reaching his goal of gaining admission to a top PhD program and furthering his career towards becoming a faculty at an R1 university. Our main Aim is to train Mr. Burns in basic skills in genome biology, including long-read genome sequencing, assembly, annotation and comparative analysis. This training will be accomplished through a research project building on recent work in the PI laboratory that revealed dramatic differences in transposable element (TE) abundance in two closely related, cryptic species of thrushes (family Turdidae). Catharus bicknelli and C. minimus are estimated to have diverged only ~15,000 years before present, yet exhibit up to 10% difference in TE abundance depending on the TE subfamily. This project will expose Mr. Burns to cutting-edge approaches in bioinformatics, including PacBio HiFi genome assembly, assembly quality assessment, genome alignment, TE abundance and annotation, and pangenome analysis. This project is related to the parent proposal because of the well-known relationship between enhancer origin and function and TE proliferation: many TEs in vertebrate genomes are discovered to underlie enhancers with diverse functions in multiple tissues. The parent proposal is focused on understanding how changes in evolutionary rate of enhancers can be estimated and tied to changes in function through high throughput enhancer assays, and this supplement will complement Aim 2 of the parent grant by exploring possible connections between TE proliferation and the origin of novel enhancer functions. Mr. Burns will receive in-depth mentoring focusing on four areas critical to achieving his career goals: Finding your voice in science; the importance of writing; acquisition of technical skills; and envisioning and planning for a future in STEM. Together these research and mentoring activities will strengthen the career prospects of Mr. Burns in evolutionary biology and equip him with lasting technical and conceptual skills to allow him to achieve his career goals.

项目摘要 这份多元化增刊提议培训非裔美国人克里斯蒂安·伯恩斯先生 硕士生，比较基因组学和基因组生物学的现代方法。 非裔美国人在进化生物学中的代表性严重不足， 补充将有助于伯恩斯先生在实现他的目标，获得录取的顶级博士 计划和进一步发展他的职业生涯，成为一名教师在R1大学。我们 主要目的是培训伯恩斯先生在基因组生物学方面的基本技能，包括长期阅读 基因组测序、组装、注释和比较分析。本次培训将 通过建立在PI实验室最近工作基础上的研究项目来完成 这揭示了转座因子（TE）丰度的显着差异，在两个密切的 画眉科的一个有亲缘关系的隐蔽种类。Catharus bicknelli和C. minimus 据估计，它们在距今15,000年前就已经分开了， TE丰度的差异取决于TE亚家族。这个项目将揭露先生。 Burns到生物信息学的尖端方法，包括PacBio HiFi基因组 组装、组装质量评估、基因组比对、TE丰度和 注释和泛基因组分析。本项目与母提案相关 由于增强子来源和功能与TE之间的关系众所周知 增殖：脊椎动物基因组中的许多TE被发现是增强子的基础， 在多种组织中发挥不同的功能。家长提案的重点是理解 如何估计增强子进化速率的变化，并将其与 通过高通量增强子测定发挥作用，这种补充将补充 通过探索TE增殖与 新增强子功能的起源。伯恩斯先生将接受深入的指导， 在四个领域实现他的职业目标至关重要：在科学中找到你的声音; 写作的重要性;获得技术技能;以及设想和规划一个 未来的STEM这些研究和指导活动将共同加强 伯恩斯先生在进化生物学的职业前景，并装备他持久的技术 和概念技能，使他能够实现自己的职业目标。