Evolutionary Conserved Sequences in the Human Genome

描述(由申请人提供)：目前对整个哺乳动物基因组进行测序的技术能力超过了目前对这些序列中包含的信息进行解码的计算和实验能力。跨物种序列比较是破译基因组信息的一种有效方法，因为功能元件在进化过程中是保守的，而非功能序列是漂移的。由于一个物种内基因组的不同区域以及物种之间的同源序列的进化速度差异很大，因此对人类基因组的全面比较分析将需要将其与多种哺乳动物的基因组序列进行比较。以目前对哺乳动物基因组测序的成本来说，要获得更多哺乳动物的深度序列复盖太昂贵了。因此，我们面临的选择是放弃通过多物种比较获得的信息，或者采用高分辨率扫描方法，如本提案中所述，用于比较人类序列和多个哺乳动物的DNA。在拟议的研究的第一阶段，我们将分析来自初步研究的数据，在该研究中，使用寡核苷酸高密度阵列将人类21号染色体的300kb区域与五种哺乳动物的DNA进行了比较。我们将改进目前使用高密度阵列检测和表征进化保守序列的算法。此外，我们还将展示使用高密度阵列和定向双脱氧测序相结合的多物种比较分析可以获得多个哺乳动物中具有生物学意义的保守元件的同源序列。在这项提议的第二阶段，我们将通过将高密度阵列与狗、猫、牛、猪和马的DNA杂交来筛选大约32Mb的人类21号染色体的保守序列。这项提议的目的是通过与整个人类基因组中的多种哺乳动物进行比较分析，证明高密度阵列方法识别保守的人类元件的可行性和成本效益。

DESCRIPTION (provided by applicant): The present technical ability to sequence entire mammalian genomes outpaces current computational and experimental abilities to decode the information contained within these sequences. Cross-species sequence comparisons are a powerful method for decoding genomic information due to the fact that functional elements are conserved through evolution whereas nonfunctional sequences drift. Because the rate of evolution varies widely in different regions of a genome within a species as well as for orthologous sequences between species, a comprehensive comparative analysis of the human genome will require that it be compared with the genomic sequences of multiple mammals. At the current cost of sequencing mammalian genomes it is too expensive to obtain in-depth sequence coverage of more than a few mammals. Thus, we are left with the choice of forgoing the information that would be obtained by multi-species comparisons or employing a high-resolution scanning approach, such as described in this proposal, for comparing human sequences with the DNA of multiple mammals. In phase I of the proposed research, we will analyze the data from a pilot study in which a 300-kb region of human chromosome 21 has been compared with the DNA of five mammals using oligonucleotide high-density arrays. We will improve the current algorithms employed for detecting and characterizing evolutionarily conserved sequences using high-density arrays. In addition, we will demonstrate that multi-species comparative analysis using high-density arrays combined with targeted dideoxy-sequencing can obtain the homologous sequences of biologically interesting conserved elements across multiple mammals. During phase II of this proposal, we will screen approximately 32 Mb of human chromosome 21 for conserved sequences by hybridizing high-density arrays with orthologous dog, cat, cow, pig, and horse DNA. The goal of this proposal is to demonstrate the feasibility and cost-effectiveness of the high-density array approach for identifying conserved human elements by comparative analysis with multiple mammals across the entire human genome.