RIG: Comparative Genomics of Indels in Primate Lineages

University Of Puerto Rico Mayaguez, Mayaguez PR

Investigators

Abstract

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.