RIG: Comparative Genomics of Indels in Primate Lineages

比较基因组学的主要目标是通过比较生物体之间的序列来确定功能元件。目前下一代技术的快速发展使比较整个基因组、识别差异并在特定适应和功能的背景下解释它们成为可能。在脊椎动物中，灵长类为比较基因组学研究提供了极好的模型，因为基因组序列、覆盖范围和基因注释的质量目前在其他哺乳动物群体中是无法比拟的。该项目利用这一资源，旨在识别、验证和评估大量插入和缺失(INDELs)的影响和历史，特别是那些位于已知功能元件中的插入和缺失，如调节元件和基因。具体地说，主要目标是使用四对比较：人与黑猩猩(HUCH)、人与大猩猩(Hugo)、人与猕猴(Huma)和人与猩猩(HuOr)，通过计算识别并在实验室验证那些具有自然选择特征的功能基因。为了完成该项目的主要目标，这些实验旨在达到四个具体目标：(1)在五个物种之间的配对比较中鉴定、表征和分析Indels；(2)鉴定Indels的功能元件；(3)估计Indels对基因结构和蛋白质产物的影响；(4)确定Indels的祖先状态和询问Indels的侧翼序列，以确定自然选择的特征。这项研究将集中在大Indels(10-1,000个碱基)上，因为它们更有可能产生巨大的影响，还因为它们很容易通过基本的分子技术，如聚合酶链式反应和电泳法进行鉴定。此外，该项目可以作为进一步研究其他哺乳动物和非哺乳动物物种的模型，以及对任何可获得基因组序列的脊椎动物物种的种群遗传学研究。这项研究将通过培训从事基础科学研究的拉美裔少数族裔的个人，扩大对科学的参与。在通过比较公布的基因组序列进行计算发现后，含有Indel的片段将通过基本的PCR技术进行扩增，并通过凝胶电泳进行验证，由于大小的巨大差异，不同的等位基因将可见，这一策略将允许该项目分成几个部分，并由本科生进行几项独立的比较基因组学研究。因此，许多参与的少数民族学生将接触到分子生物学的基本和高级技术，以及基因组分析的最新主题。

The main goal of comparative genomics is to identify functional elements by comparing sequences between organisms. Current rapid development of next generation technologies made it possible to compare entire genomes, identify differences, and interpret them in the context of specific adaptations and functions. Among vertebrates, the primates provide excellent models for comparative genomics studies because the quality of genome sequence, coverage, and annotation of genes is currently unmatched in other mammalian groups. This project takes advantage of this resource and aims to identify, verify, and assess the impact and history of large insertions and deletions (indels), especially those located within known functional elements, such as regulatory elements and genes. Specifically, the main objective is to use four pairs of comparisons: human to chimpanzee (HuCh), human to gorilla (HuGo), human to macaque (HuMa), and human to orangutan (HuOr), to identify computationally and validate in the laboratory those functional indels with signatures of natural selection. To accomplish the main objective of the project, the experiments are designed to reach four specific aims: (1) identification, characterization and analysis of indels in pair-wise comparison between the five species, (2) identification of indels in functional elements, (3) estimation of indel impact on gene structure and protein products, and (4) determination of ancestral states and interrogating flanking sequences of indels for the signatures of natural selection. The study will concentrate on large indels (10-1,000 bp) since they are more likely to have large impacts, and also because they are easily identified with only basic molecular techniques such as PCR and electrophoresis. In addition, the project can serve as a model for further investigations in other mammalian and non-mammalian species, as well as for population genetics studies in any vertebrate species for which the genome sequence is available.This study will broaden participation in science by training individuals from the underrepresented Hispanic minority who will conduct basic science research. Following their computational discovery by comparison of published genome sequences, the indel-containing fragments will be amplified by a basic PCR technique and validated by gel electrophoresis, where different alleles will be visible due to large differences in size, a strategy that will allow the project to be divided into parts, and generate development of several independent comparative genomics studies by undergraduate students. Thus, many participating minority students will be exposed to basic and advanced techniques in molecular biology, as well as to the most current topics in genome analysis.