Genomics Education Partnership: Bringing Genomics Research into Undergraduate Biology
Summary: Sarah Elgin's Genomics Education Partnership is a collaboration of faculty from primarily undergraduate institutions nationwide with the biology and computer science departments, and Genome Center of Washington University in St. Louis. The aim is to provide students with an opportunity to participate in a large-scale genome sequencing and annotation research project and contribute to scientific discovery.
Our initiatives bring the tools and concepts of genomics into the undergraduate and high school biology curricula. Students learn more and are more excited about science if they move beyond examining one gene to considering the function of genes as part of the whole genome.
With our 2002 grant we added genomic investigations to several biology courses at Washington University in St. Louis (WU). The first, a short bioinformatics laboratory, introduces students to a suite of Web-based informatics tools to explore the impact of a particular mutation on protein structure, metabolic function, and human health gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/bio3055/. The bioinformatics laboratory, or similar experiences, prepares students for a second course, Research Explorations in Genomics, which provides juniors and seniors with an opportunity to work as a team on a large-scale sequencing project. They begin by analyzing and refining raw sequence data at the WU Genome Sequencing Center, then they annotate and analyze the data in collaboration with WU computer science faculty. The course enables students to become comfortable thinking about large data sets as a research tool in biology—how to generate them, how to analyze them, and how to use them. The work has led to publication of two student-authored papers. Our current project is a comparative genomics analysis of the dot chromosomes of Drosophila, the fruit fly.
To give non-WU students insight into the university's Genome Sequencing Center, we developed a video, available at www.nslc.wustl.edu/elgin/genomics/gsc.html, that offers a guided tour of the facility and provides an up-close look at the people and equipment involved in large-scale sequencing. Animations show the processes used to sequence DNA and explain the complex molecular interactions that occur during sequencing. Supplemental materials include hands-on activities that further illustrate the process (This material was developed by WU’s Science Outreach initiative into a curriculum called “Significant Sequences.”). We have recently updated our materials by adding a video explaining “next generation” sequencing machines. All materials are freely available at our website (www.nslc.wustl.edu/elgin/genomics/index.html) and through WU Science Outreach (WUSO) (www.so.wustl.edu/biology.html).
Another initiative, the Summer Research Fellowship Program, enabled middle and high school science teachers to conduct research in the labs of WU faculty. The teachers then developed new lab curricula for high school students, including one on herbicide-resistant crop technology that was later developed by WUSO initiative into a “Building Food” curriculum, which is also available at their website. We continue to work with high school teachers, in collaboration with WUSO, on a course for high school teachers called the Molecular Basis of Heredity, funded by the National Science Foundation.
With our 2006 HHMI professors grant, we created the Genomics Education Partnership (GEP) to bring genomics research to students beyond WU by working with faculty from primarily undergraduate institutions. GEP is designed for undergraduate institutions that may not have ready access to DNA sequencing technology. Participation requires only access to the Web and computers for student use. Students enrolled at partner schools are able to work on a large-scale genome sequencing project using data available through Web-based repositories on the GEP Website. In addition to learning about genes and genomes and developing skills in using genomics databases, students contribute to scientific knowledge (currently through an analysis of the dot chromosomes of Drosophila), their work is deposited in public databases, and has led to two publications in peer-reviewed journals.
Interested faculty join GEP by participating in a 3- to 5-day workshop at WU, and return subsequent summers to work jointly on publications and curriculum development, including genomics course materials, assessment resources, and research projects that are made available on GEP's Web site, gep.wustl.edu. Currently, more than 60 faculty have implemented the curriculum materials and approaches in a variety of course formats, including as a lab component in a genetics course, as a stand-alone course, and as independent research for a small group of students.
The program is flourishing in diverse educational settings, including small and large schools, commuter and residential schools, schools with a high proportion of first-generation students and/or a high proportion of underrepresented minority students. Blending an introduction to genomics with a research experience appears to be cost-effective and pedagogically successful. Assessment data show that GEP students (more than 400 in 2008 alone) improve their understanding of genes and genomes, gain skill with genomics tools, and exhibit gains in attitude and learning that equal those gains attributed to summer undergraduate research experiences. The GEP faculty have published two papers in the science education literature on using genomics research as a teaching strategy.
With our new grant, we plan to expand GEP, using the basic organization and protocols worked out in previous years. We will recruit new schools throughout the country through nominations by the current faculty and foster local partnerships by holding St. Louis-based workshops. We plan to expand assessment to include the impact of the GEP on faculty careers, on institutional curriculum change, and on research opportunities for undergraduates. We will continue to focus on the comparative genomics of Drosophila, but we will broaden our efforts to different research topics and species comparison, which will provide students with a wider array of data and tools to address questions of their own or those posed by the group. We also plan to adapt our genome annotation workflow to generate a Web-based version that GEP faculty can use to build their own custom genome browsers and work on target genes and species of their own choosing.
Related HHMI Project Publications
Bednarksi, A.E., S.C.R. Elgin, and H.B. Pakrasi. "An Inquiry into Protein Structure and Genetic Disease: Introducing Undergraduates to Bioinformatics in a Large Introductory Course." Cell Biol. Edu. 4 (2005): 207-220. http://www.lifescied.org/cgi/content/full/4/3/207
Flowers, S.K., et al. "Genome Science: A Video Tour of the Washington University Genome Sequencing Center for High School and Undergraduate Students." Cell Biol. Edu. 4 (2005): 291-297. http://www.lifescied.org/cgi/content/full/4/4/291
Slawson, E.E., et al. "Comparison of Dot Chromosome Sequences from D. melanogaster and D. virilis Reveals an Enrichment of DNA Transposon Sequences in Heterochromatic Domains." Genome Biology 7 (2005): R15. http://genomebiology.com/2006/7/2/R15
Lopatto, D., et al. "Genomics Education Partnership." Science 322 (2005): 684-685. http://www.sciencemag.org/cgi/content/full/322/5902/684
Shaffer, C., et al. "The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions." CBE-Life Sci Educ. 9 (Spring 2010): 55-69. http://www.lifescied.org/cgi/reprint/9/1/55
I’m interested in the role that chromatin structure plays in gene regulation, both the effects from packaging large domains and local effects of the nucleosome array. My work at Washington University using the fruit fly Drosophila has led to a detailed picture of the chromatin structure of hsp26, a heat shock gene, demonstrating that formation of 5’ DNase hypersensitive sites is necessary for gene activation and requires both GAGA factor and 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. Using genetic analysis, we have shown that HP1 plays a key role in heterochromatin formation and gene silencing. We have mapped heterochromatin domains using a transposable element carrying reporter genes (showing variegation of white, indicating gene silencing) and have analyzed the nucleosome array, found to be more uniform in heterochromatic domains. We find that the fourth chromosome is primarily heterochromatic, even though it contains 80 genes. How these genes function and evolve in this domain is under study. Mapping experiments indicate that heterochromatin formation can be targeted by the presence of repetitious element,1360, and perhaps others. Work is ongoing to determine the targeting mechanism, and to analyze the role of critical heterochromatin-associated proteins, including HP1 and its partners.