Mutation Rate Variation Among Human Genomic Regions

人类基因组区域的突变率变异

• 批准号: 6463901
• 负责人: WEN-HSIUNG LI
• 金额: $ 21.82万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-05-01 至 2005-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6463901
• 关键词: Cercopithecidae; CpG islands; DNA; DNA replication; Gorillas; Pan; Pongo; animal genetic material tag; autosome; baboons; chromosome aberrations; computer assisted sequence analysis; gender difference; gene frequency; gene mutation; genetic polymorphism; genetic recombination; genome; human genetic material tag; molecular cloning; nucleic acid sequence; polymerase chain reaction; sex chromosomes; single nucleotide polymorphism; statistics /biometry

Our goal is to understand variability in the rates and patterns of mutation among regions of the human genome and the causes of this variation. Specifically, we shall address the following issues: 1. How different are the mutation rates among homologous sequences on different types of chromosome (autosomes, X chromosome, and Y chromosome)? The aim is to estimate the magnitude of difference between male and female mutation rates. 2. How variable are the mutation rates among regions of a chromosome or chromosomes of the same type? 3. Does the pattern of mutation different among genomic regions? Issues 2 and 3 are the essence of the regional mutation pressure hypothesis, which postulates that the rate and pattern of mutation varies among regions of the mammalian genome. We shall test this hypothesis and study the origin and evolution of GC-rich isochores. 4. Is the variation in the level of single nucleotide polymorphism (SNO) among human genomic regions due in a large extent to variations in mutation rate. To study these issues, we propose to pursue the following work. 1. To search for pairs of non-coding regions that are homologous (very similar) between X and Y chromosomes, or between Y and an autosome, or between X and an autosome, and choose several (5 to 7) pairs of regions that are suitable for estimating sex differences in mutation rate. Each pair of regions will be sequenced in several higher primates (e.g.. chimpanzee, gorilla, orangutan, siamang, gibbon, and possibly Old World monkeys. 2. Select approximately 15 unique Y-linked DNA segments each of 2-5 kb in length, These segments should be non-coding, should have no homologue on any autosome or X chromosome, and should have a wide coverage of GC contents. Sequence each segment in several higher primates. 3. Similarly, select approximately 50 unique autosomal DNA segments each of approximately 5 kb in length. We will try to select segments that have SNP data and have suitable GC contents and recombination rates. Sequence each of them in chimpanzee, gorilla, orangutan, siamang, baboon and colobus. 4. To conduct statistical analyses of the new and existing data to address the above issues.

我们的目标是了解人类基因组区域之间突变速率和模式的变异性以及这种变异的原因。具体而言，我们将解决以下问题：1。不同类型染色体（常染色体、X染色体和Y染色体）上同源序列的突变率有多大差异？目的是估计男性和女性突变率之间的差异程度。2.一条染色体或同一类型的染色体的不同区域之间的突变率有多大的差异？3.基因组区域之间的突变模式是否不同？问题2和问题3是区域突变压力假说的本质，该假说假设突变的速率和模式在哺乳动物基因组的不同区域之间存在差异。我们将测试这一假设，并研究富含GC的等容线的起源和演化。4.人类基因组区域之间单核苷酸多态性（SNO）水平的变化在很大程度上是由于突变率的变化。为了研究这些问题，我们建议开展以下工作。1.寻找X和Y染色体之间，或Y和常染色体之间，或X和常染色体之间同源（非常相似）的非编码区对，并选择几对（5至7对）适合于估计突变率性别差异的区域。每对区域将在几种高等灵长类动物中进行测序（例如，黑猩猩、大猩猩、猩猩、合趾猴、长臂猿，可能还有旧大陆的猴子。2.选择约15个独特的Y-连锁DNA片段，每个长度为2-5 kb，这些片段应是非编码的，在任何常染色体或X染色体上应没有同源物，并应具有广泛的GC含量覆盖范围。对几种高等灵长类动物的每个片段进行测序。3.类似地，选择约50个独特的常染色体DNA片段，每个片段长度约为5 kb。我们将尝试选择具有SNP数据并且具有合适的GC含量和重组率的片段。对黑猩猩、大猩猩、猩猩、暹罗猴、狒狒和疣猴中的每一个进行测序。4.对新的和现有的数据进行统计分析，以解决上述问题。