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Integrating Genomics into the Biology Curriculum
Summary: Sarah Elgin's research focuses on the role of chromatin structure in gene regulation in fruit flies. Her HHMI project involves developing curricula and multimedia materials that bring the concepts of genomics to the undergraduate and high school settings and help students become comfortable in using large data sets as a research tool in biology.
HHMI PROJECT SUMMARY
Original Project (2002 grant)
The 2002 grant supported several initiatives to bring the tools and concepts of genomics into the undergraduate and high school biology curricula. The idea is that students' experiences can be broadened if they move beyond examining one gene to considering the functions of the genome as a whole. We created a one-semester, upper-level laboratory course, Research Explorations in Genomics (Bio 4342), that provides up to 12 juniors and seniors with an opportunity to work as a team on a large-scale sequencing project, beginning with sample preparation and data collection at Washington University's (WU) Genome Sequencing Center (GSC) through sequence finishing and analysis. The goal of the course is to enable students to become comfortable in thinking about large data sets—how to generate them, how to analyze them, and how to use them—as a research tool in biology. Students in the course worked on sequencing and annotating the dot chromosome of D. virilis and a student-authored paper describing the results has been published. The course is now an established offering at WU.
We also added genomic investigations to the university's introductory offerings for biology students. In a short bioinformatics laboratory (Bio 3055), students work in teams, using Web-based bioinformatics tools to explore the impact of a particular mutation on protein structure and metabolic function, connecting a change in genotype with a change in phenotype (human genetic disability). Another initiative, the Summer Research Fellowships Program, enables middle school and high school science teachers to conduct research in the labs of WU faculty, learning first-hand about genomics research methods and developing genomics materials for their classrooms.
To give non-WU students the experience of touring the GSC, we developed a video that offers a guided tour of the facility and provides an up-close look at the equipment used in high-throughput sequencing. The video also includes animations of the processes used to sequence DNA.
Project Update (2006 grant)
A Genomics Education Partnership will enable students enrolled at other colleges and universities to work on a large-scale genome sequencing project, using data available through Web-based repositories. Students will be organized into teams and, using these online resources and the wet lab resources of the GSC, will finish and annotate a segment of a genome. We will bring their faculty to WU for a summer workshop and provide students with training exercises via the Web. Each year one to two projects will be undertaken in collaboration with the GSC and appropriate lead scientists. Initial projects of interest include the dot chromosomes of D.pseudoobscura and D. mojavensis, the genomes of selected human gut bacteria, regions of the maize genome as this becomes available, and targeted gene clusters from selected primate genomes. In addition to learning about genes and genomes and developing skills in using computers and accessing large databases, students will have a real sense of contributing to the body of scientific knowledge. Faculty involved in this project will gain an opportunity to work with a diverse group of students and the field as a whole will gain improved databases and additional analysis of the sequencing data being generated. We will also create opportunities for students at these and other schools to solve sample problems using already existing data and to obtain single-read sequencing data from the DNA samples they generate.
RESEARCH SUMMARY
My work at Washington University has led to a detailed picture of the chromatin structure of hsp26, a heat shock gene, demonstrating that formation of HS sites is necessary for gene activation and requires both GAGA factor binding and subsequent recruitment of RNA polymerase II. Immunofluorescent staining of polytene chromosomes led to the identification of heterochromatin protein 1 (HP1), located predominantly in the pericentric heterochromatin and small fourth chromosome, later shown by genetic analysis to play a key role in heterochromatin formation and gene silencing. My lab is currently studying an HP1-interacting protein, HP2. Investigations of heterochromatin structure and function have used a P-element carrying reporter genes to detect a visible phenotype (variegation of white, seen in the eye) and to analyze the altered nucleosome array, found to be more uniform in heterochromatic domains. These studies have shown that the fourth chromosome is made up of interspersed heterochromatic and euchromatic domains, providing unique opportunities for studying such domains and their boundaries.
Last updated March 2007
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