Computational and Biochemical Analysis of Microsatellite Life Cycle

微卫星生命周期的计算和生化分析

• 批准号: 8277920
• 负责人: Kristin A Eckert
• 金额: $ 34.23万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-07-16 至 2014-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8277920
• 关键词: Affect; Alleles; Applications Grants; Base Pairing; Biochemical; Bioinformatics; Birth; Cessation of life; Characteristics; Clinical; Computational Biology; Computer Simulation; DNA; DNA Replication Inhibition; DNA Sequence; DNA biosynthesis; DNA-Directed DNA Polymerase; Data; Death Rate; Development; Disease; Evolution; Forensic Medicine; Gene Expression; Generations; Genetic; Genetic Anticipation; Genetic Polymorphism; Genetic Recombination; Genome; Genomics; Goals; Guanine + Cytosine Composition; Health; Hereditary Disease; Human; Human Genetics; Human Genome; In Vitro; Individual; Interdisciplinary Study; Interruption; Knowledge; Lead; Length; Life Cycle Stages; Link; Maintenance; Measures; Metabolism; Microsatellite Repeats; Modeling; Molecular; Mutate; Mutation; Nucleotides; Open Reading Frames; Pathway interactions; Population Genetics; Positioning Attribute; Prevalence; Primates; Probability; Property; Public Health; Relative (related person); Research; Research Proposals; Sequence Analysis; Short Tandem Repeat; Staging; Techniques; Testing; Time; United States National Institutes of Health; Ursidae Family; Variant; base; biochemical model; comparative genomics; density; disorder risk; genetic risk factor; genome-wide; human disease; in vitro Assay; insertion/deletion mutation; insight; recombinational repair; research study; statistics; trend

DESCRIPTION (provided by applicant): Microsatellite sequences are abundant in the human genome and have mutation rates orders of magnitude higher than any other genomic sequences. As a result, microsatellites are frequently used as markers in forensics and population genetics. Importantly, microsatellites influence genome functions by being part of protein-coding regions or by regulating gene expression, and allele-length polymorphisms at microsatellites are implicated as genetic risk factors in several diseases. Because the full impact of microsatellite changes on genome function has yet to be elucidated, it is of utmost importance to gain knowledge about how microsatellite arise, mutate, and eventually cease to exist at individual loci in the human genome. The evolution of each microsatellite has been presented theoretically as a life cycle, with the stages of birth, active dynamic mutation activity, and death. However, the concept of the microsatellite life cycle has not been previously investigated in detail. The goal of this interdisciplinary proposal is to elucidate mechanisms defining microsatellite life cycle in the human genome. This will be accomplished by a combination of computational and biochemical approaches, and follows the NIH roadmap themes of Interdisciplinary research and Bioinformatics and computational biology. Specific Aim 1 is to determine the mechanisms of microsatellite birth. We will use biochemical experiments to determine the microsatellite threshold in terms of the minimal number of repeats (or length) required for dynamic mutations to occur. These thresholds will be determined for various motifs, and will be used in computational analyses to examine mechanisms and densities of new microsatellite births. The results of this aim will allow us for the first time to derive a regression model explaining variation in microsatellite birth densities across the genome. Specific Aim 2 will examine microsatellite interruption and death. Our preliminary studies demonstrate that microsatellite interruptions can be observed frequently in the human genome, and that DNA polymerases can directly produce such interruptions in vitro. This aim will use computational and biochemical techniques to measure the mutational consequences of interruptions and the extent to which they contribute to microsatellite death. Specific Aim 3 is to computationally determine the mechanisms contributing to variation in mature microsatellite mutation rates among and within individual human genomes, and to biochemically determine specific mechanisms contributed by intrinsic features. Overall, the results of this project will be of considerable significance for our understanding of the dynamics of genome evolution. Additionally, our research proposal has direct relevance to the issues of public health and clinical genetics. The new information gained by our research can be used to predict the probability of each microsatellite to undergo mutation or cease to exist, and the probability of any genomic region to bear a new microsatellite. This will have major importance for assessing an individual's disease risks, especially in the era when individual human genomes are being rapidly sequenced. PUBLIC HEALTH RELEVANCE: Repetitive DNA sequences, called microsatellites, are characteristic of primate genomes and are known to regulate gene expression, and mutations within microsatellite sequences are causally linked to the development of several human diseases. Our interdisciplinary project will elucidate the mechanisms whereby microsatellites arise, mutate, and disappear at distinct loci in individual human genomes. This research could have major consequences for predicting the risk of diseases caused by microsatellites.

描述（由申请人提供）：微卫星序列在人类基因组中丰富，并且具有比任何其他基因组序列高几个数量级的突变率。因此，微卫星经常被用作法医学和群体遗传学的标记。重要的是，微卫星通过作为蛋白质编码区的一部分或通过调节基因表达来影响基因组功能，并且微卫星的等位基因长度多态性被认为是几种疾病的遗传风险因素。由于微卫星变化对基因组功能的全面影响尚未阐明，因此了解微卫星如何在人类基因组中的各个位点产生、突变并最终停止存在是至关重要的。每个微卫星的进化在理论上被描述为一个生命周期，包括出生、活跃的动态突变活动和死亡。然而，微型卫星寿命周期的概念以前没有进行过详细的研究。这个跨学科的建议的目标是阐明机制定义微卫星生命周期在人类基因组中。这将通过计算和生物化学方法的结合来实现，并遵循NIH跨学科研究和生物信息学和计算生物学的路线图主题。具体目标1是确定微卫星产生的机制。我们将使用生物化学实验来确定微卫星阈值，即动态突变发生所需的最小重复次数（或长度）。这些阈值将被确定为各种图案，并将用于计算分析，以检查新的微卫星出生的机制和密度。这一目标的结果将使我们能够第一次推导出一个回归模型，解释整个基因组中微卫星出生密度的变化。具体目标2将研究微卫星中断和死亡。我们的初步研究表明，在人类基因组中经常可以观察到微卫星中断，并且DNA聚合酶可以在体外直接产生这种中断。这一目标将使用计算和生物化学技术来测量中断的突变后果以及它们导致微卫星死亡的程度。具体目标3是通过计算确定个体人类基因组之间和内部成熟微卫星突变率变化的机制，并通过生物化学确定内在特征贡献的特定机制。总的来说，该项目的结果将对我们理解基因组进化的动态具有相当大的意义。此外，我们的研究计划与公共卫生和临床遗传学问题直接相关。我们的研究获得的新信息可以用来预测每个微卫星发生突变或停止存在的概率，以及任何基因组区域携带新微卫星的概率。这对于评估个人的疾病风险具有重大意义，特别是在个人基因组被快速测序的时代。公共卫生相关性：重复的DNA序列，称为微卫星，是灵长类动物基因组的特征，已知可以调节基因表达，微卫星序列内的突变与几种人类疾病的发生有因果关系。我们的跨学科项目将阐明微卫星在人类基因组不同位点出现、突变和消失的机制。这项研究可能对预测微卫星引起的疾病风险产生重大影响。

项目成果

A genome-wide view of mutation rate co-variation using multivariate analyses.

• DOI: 10.1186/gb-2011-12-3-r27
• 发表时间: 2011
• 期刊: Genome biology
• 影响因子: 12.3
• 作者: Ananda G;Chiaromonte F;Makova KD
• 通讯作者: Makova KD

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis.

• DOI: 10.1371/journal.pcbi.1004956
• 发表时间: 2016-06
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Campos-Sánchez R;Cremona MA;Pini A;Chiaromonte F;Makova KD
• 通讯作者: Makova KD

Complexes between two GAA Repeats within DNA introduced into Cos-1 cells.

DNA 内两个 GAA 重复序列之间的复合物被引入 Cos-1 细胞中。

• DOI: 10.4161/mge.23194
• 发表时间: 2012
• 期刊: Mobile genetic elements
• 作者: Krasilnikova,MariaM

A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome?

• DOI: 10.1101/gr.134395.111
• 发表时间: 2012-06
• 期刊: Genome research
• 影响因子: 7
• 作者: Fungtammasan A;Walsh E;Chiaromonte F;Eckert KA;Makova KD
• 通讯作者: Makova KD

Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.

• DOI: 10.1093/molbev/msw139
• 发表时间: 2016-10
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Fungtammasan A;Tomaszkiewicz M;Campos-Sánchez R;Eckert KA;DeGiorgio M;Makova KD
• 通讯作者: Makova KD