Dynamics and determinants of copy number variation in evolving populations

进化群体中拷贝数变异的动态和决定因素

• 批准号: 1818234
• 负责人: David Gresham
• 金额: $ 95.04万
• 依托单位: New York University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-15 至 2022-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1818234&HistoricalAwards=false
• 关键词: Dynamics; determinants; copy; number; variation

DNA copy number variation underlies differences in many inherited traits and is involved in diverse processes ranging from drug resistance in pathogens to domestication of animals. The study aims to characterize the dynamics of copy number variation in evolving populations and to understand the properties of the genome that facilitate their generation. Using evolution experiments in the lab, the project will investigate the dynamics with which copy number variation arises as populations evolve under selection. The project will test the role of different processes that generate copy number variation using a panel of mutants. Completion of this study will provide important new insights into the generation and selection of copy number variation leading to a more complete understanding of evolutionary processes with potential applications to microbial drug resistance and industrial microbiology. To broaden the impact of the scientific training activities, the study will provide opportunities for undergraduate and high school students from traditionally under-represented groups to undertake mentored research in our laboratory. In addition, a freely available, online textbook integrating instruction in genetics, statistics and computer programming will be completed as part of the project. To gain quantitative insights into the role of CNVs in evolving populations, the project will use a newly developed CNV reporter system that comprises a constitutively expressed fluorescent protein gene linked to loci at which CNVs are recurrently selected. Using long term experimental evolution of budding yeast (Saccharomyces cerevisiae) in nutrient-limited chemostats, the project will use the CNV reporter to quantify the evolutionary dynamics of CNVs at three loci that have distinct genomic architectures. To identify the number of unique CNVs that are generated and selected in each evolving population, the project will employ a lineage tracking method using random molecular barcodes and FACS-based isolation of CNV-containing lineages. Using next generation DNA sequencing of lineages containing CNVs, the project will define the mechanisms by which CNVs are formed. The project will study the role of different pathways on CNV formation using strains mutant for DNA replication and repair components. To test the effect of different sequence elements the project will alter the genomic architecture of the three loci and test the effect on CNV dynamics and diversity. Finally, the project will also test whether transcriptional activation impacts CNV formation rates.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

DNA拷贝数变异是许多遗传性状差异的基础，并涉及从病原体耐药性到动物驯化等多种过程。该研究旨在描述进化种群中拷贝数变化的动态特征，并了解促进其产生的基因组特性。利用实验室的进化实验，该项目将研究种群在选择下进化时拷贝数变化的动态。该项目将使用一组突变体来测试产生拷贝数变化的不同过程的作用。这项研究的完成将为拷贝数变异的产生和选择提供重要的新见解，从而更全面地了解进化过程，并在微生物耐药性和工业微生物学方面具有潜在的应用价值。为了扩大科学训练活动的影响，该研究将为传统上代表性不足的群体的本科生和高中生提供在我们实验室进行指导研究的机会。此外，作为该项目的一部分，还将完成一本免费的在线教科书，其中包括遗传学、统计学和计算机编程方面的教学。为了定量了解CNV在进化种群中的作用，该项目将使用新开发的CNV报告系统，该系统包括一个组成性表达的荧光蛋白基因，该基因与反复选择CNV的位点相关。该项目将利用芽殖酵母（Saccharomyces cerevisiae）在营养受限的化学调节器中的长期实验进化，使用CNV报告器来量化具有不同基因组结构的三个位点上CNV的进化动力学。为了确定在每个进化群体中产生和选择的独特cnv的数量，该项目将采用一种使用随机分子条形码和基于facs的含有cnv的谱系分离的谱系跟踪方法。利用含有CNVs的下一代DNA测序，该项目将定义CNVs形成的机制。该项目将利用菌株突变体进行DNA复制和修复组件，研究不同途径在CNV形成中的作用。为了测试不同序列元素的影响，该项目将改变三个位点的基因组结构，并测试对CNV动态和多样性的影响。最后，该项目还将测试转录激活是否会影响CNV的形成速率。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy

• DOI: 10.1093/nar/gkaa206
• 发表时间: 2020-05-21
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Spealman, Pieter;Burrell, Jaden;Gresham, David
• 通讯作者: Gresham, David

Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states

• DOI: 10.15252/msb.20199167
• 发表时间: 2020-05
• 期刊: Molecular Systems Biology
• 影响因子: 9.9
• 作者: Siyu Sun;A. Baryshnikova;Nathan Brandt;D. Gresham

Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics.

• DOI: 10.1371/journal.pbio.3001633
• 发表时间: 2022-05
• 期刊: PLOS BIOLOGY
• 影响因子: 9.8
• 作者: Avecilla, Grace;Chuong, Julie N.;Li, Fangfei;Sherlock, Gavin;Gresham, David;Ram, Yoav
• 通讯作者: Ram, Yoav

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

• DOI: 10.1371/journal.pbio.3000069
• 发表时间: 2018-12-01
• 期刊: PLOS BIOLOGY
• 影响因子: 9.8
• 作者: Lauer, Stephanie;Avecilla, Grace;Gresham, David
• 通讯作者: Gresham, David

Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove

• DOI: 10.5194/bg-18-2259-2021
• 发表时间: 2021-04-06
• 期刊: BIOGEOSCIENCES
• 影响因子: 4.9
• 作者: de Santana, Carolina Oliveira;Spealman, Pieter;Chinalia, Fabio Alexandre
• 通讯作者: Chinalia, Fabio Alexandre