权益分类	功能权益	普通用户	{{item.name}}会员
{{category.name}}	{{benefitItem.name}}

Toward a mechanistic understanding of genetic interactions

对遗传相互作用的机械理解

基本信息

批准号：
10627988
负责人：
Christine Queitsch
金额：
$ 53.29万
依托单位：
UNIVERSITY OF WASHINGTON
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-06-01 至 2026-05-31
项目状态：
未结题

项目摘要

A key challenge of the post-genomic era is the functional interpretation of the vast numbers of single nucleotide variants found in human genomes. This challenge is compounded by the fact that these variants contribute to complex traits and diseases by interacting with one another and with genetic variation in repetitive DNA elements. Assessing the phenotypic consequences of all genetic interactions amounts to an impossible numbers game. In order to prioritize certain variant combinations, I will use model organisms with powerful genetics, namely the yeast S. cerevisiae and the worm C. elegans, to identify and characterize genetic interactions with large impact on complex phenotypes. I propose three projects that capitalize on our previous studies. These projects are united by their focus on genetic interactions (i.e. epistasis), albeit they address different types of variant combinations and different mechanisms. The first project focuses on rDNA, a highly variable repetitive DNA element. Variation in rDNA copy number impacts gene expression, replication, genome stability, and mitochondrial abundance. Like other repetitive loci, rDNA is predisposed to interact epistatically with other variants because of its high mutation rate. Using newly developed C. elegans mapping populations and robotics-enabled phenotyping, our preliminary data show that rDNA copy number variation affects lifespan and fitness through epistasis. High-throughput analyses of healthspan traits such as stress resistance and fertility are ongoing. We will pursue fine-mapping of the most significant genomic loci implicated in epistasis with rDNA because their identity, possibly DNA replication or repair genes, may point to the molecular mechanism by which rDNA variation affects phenotype. In both yeast and worms, we will use the entire tool box of genetics and genomics to directly interrogate the pathways by which rDNA copy number variation affects replication, genome stability, and mitochondrial abundance. To enable accurate high-throughput measurements of rDNA copy number in model organisms and humans, we will optimize a promising FISH technology. The second project relies on the detailed genotype–phenotype maps we established for genes in the yeast mating pathway. Selecting single nucleotide variants of small and intermediate effects, we will combine variants in two genes and test the combinations for mating efficiency while also perturbing strong genetic modifiers and applying common stresses. To do so, we developed a sequencing strategy that allows us to simultaneously phenotype tens of thousands of single nucleotide variant combinations between pairs of genes. The third project will apply a technology of dominant negative polypeptides that we recently developed to identify at genome scale protein interaction surfaces and their dynamics. In yeast, we will explore to what extent genetic interactions reflect direct protein interactions. We will ask how easily (or not) protein interaction surfaces are perturbed by mutation, by evolutionary divergence, or by drugs or stress that perturb protein folding. Together, the results of these three projects will yield a broad and deep assessment of epistasis, testable hypotheses for human genetics and novel technologies for testing them.

后基因组时代的一个关键挑战是对大量单核苷酸变异的功能解释在人类基因组中发现。这些变异导致复杂的性状和特征，这一事实使这一挑战变得更加复杂。通过相互作用以及重复 DNA 元件的遗传变异来预防疾病。评估表型所有基因相互作用的后果相当于一场不可能的数字游戏。为了优先考虑某些变体组合中，我将使用具有强大遗传学的模型生物，即酿酒酵母和蠕虫 C. 线虫，识别和表征对复杂表型有重大影响的遗传相互作用。我建议三个利用我们之前的研究的项目。这些项目的共同之处在于它们对遗传相互作用的关注（即上位性），尽管它们涉及不同类型的变体组合和不同的机制。第一个项目重点 rDNA，一种高度可变的重复 DNA 元件。 rDNA 拷贝数的变化影响基因表达，复制、基因组稳定性和线粒体丰度。与其他重复基因座一样，rDNA 易于相互作用由于其高突变率，与其他变体具有上位性。使用新开发的秀丽隐杆线虫绘制种群图和机器人技术支持的表型分析，我们的初步数据表明 rDNA 拷贝数变异影响寿命和通过上位适应。对抗压性和生育能力等健康寿命特征的高通量分析正在进行中。我们将追求对与 rDNA 上位性相关的最重要的基因组位点进行精细绘图，因为它们同一性，可能是 DNA 复制或修复基因，可能指向 rDNA 变异的分子机制影响表型。在酵母和蠕虫中，我们将使用遗传学和基因组学的整个工具箱来直接探究 rDNA 拷贝数变异影响复制、基因组稳定性和线粒体的途径丰富。为了能够对模型生物体和人类中的 rDNA 拷贝数进行准确的高通量测量，我们将优化一项有前景的 FISH 技术。第二个项目依赖于我们详细的基因型-表型图谱为酵母交配途径中的基因建立。选择小效应和中等效应的单核苷酸变体，我们将组合两个基因中的变体并测试组合的交配效率，同时也扰乱强遗传修饰剂和施加常见压力。为此，我们开发了一种测序策略，使我们能够同时对基因对之间数以万计的单核苷酸变异组合进行表型分析。第三个该项目将应用我们最近开发的显性失活多肽技术，以在基因组规模上进行鉴定蛋白质相互作用表面及其动力学。在酵母中，我们将探索遗传相互作用在多大程度上直接反映蛋白质相互作用。我们将问蛋白质相互作用表面如何容易（或不易）受到突变的干扰，通过进化分歧，或扰乱蛋白质折叠的药物或压力。这三个项目的成果共同将对上位性、人类遗传学的可测试假设和测试新技术进行广泛而深入的评估他们。

项目成果

期刊论文数量（8）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Dynamic chromatin accessibility deploys heterotypic cis/trans-acting factors driving stomatal cell-fate commitment.

DOI：
10.1038/s41477-022-01304-w
发表时间：
2022-12
期刊：
NATURE PLANTS
影响因子：
18
作者：
Kim, Eun-Deok;Dorrity, Michael W.;Fitzgerald, Bridget A.;Seo, Hyemin;Sepuru, Krishna Mohan;Queitsch, Christine;Mitsuda, Nobutaka;Han, Soon-Ki;Torii, Keiko U.
通讯作者：
Torii, Keiko U.

First discovered, long out of sight, finally visible: ribosomal DNA.

DOI：
10.1016/j.tig.2022.02.005
发表时间：
2022-06
期刊：
TRENDS IN GENETICS
影响因子：
11.4
作者：
Hall, Ashley N.;Morton, Elizabeth;Queitsch, Christine
通讯作者：
Queitsch, Christine

Binding and Regulation of Transcription by Yeast Ste12 Variants To Drive Mating and Invasion Phenotypes.

酵母 Ste12 变体转录的结合和调节以驱动交配和入侵表型。

DOI：
10.1534/genetics.119.302929
发表时间：
2020
期刊：
Genetics
影响因子：
3.3
作者：
Zhou,Wei;Dorrity,MichaelW;Bubb,KerryL;Queitsch,Christine;Fields,Stanley
通讯作者：
Fields,Stanley

LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana.

LTP2 亚型在拟南芥幼苗早期性状中表现出基因型与环境的相互作用。

DOI：
10.1101/2023.05.11.540469
发表时间：
2023
期刊：
bioRxiv : the preprint server for biology
影响因子：
0
作者：
Alexandre,CristinaM;Bubb,KerryL;Schultz,KarlaM;Lempe,Janne;Cuperus,JoshT;Queitsch,Christine
通讯作者：
Queitsch,Christine

Impact on splicing in Saccharomyces cerevisiae of random 50-base sequences inserted into an intron.

插入内含子的随机 50 个碱基序列对酿酒酵母剪接的影响。