Beyond the Identification of Transcribed Sequences:
Functional, Evolutionary and Expression Analysis
12th International Workshop
October 25-28, 2002
Washington, DC

List of Abstracts * Speakers * Organizers * Authors * Original Announcement

Status of Application of Tiling Genomic Fragment Arrays to Molecular Biology of Mammalian Cells

C. Horak2,3, X-H Pan1, J. Rimm2,3, R. Goetsch2, P. Bertone2, P. Miller4, N. Luscombe3, P. Harrison3, M. Gerstein3, S.M. Weissman1, and M. Snyder2,3
1Department of Genetics; 2Department of Molecular, Cellular, and Developmental Biology; 3Department of Molecular Biophysics and Biochemistry; 4Department of Medical Anesthesiology, Yale University School of Medicine, P.O. Box 208103, New Haven, CT 06520-8103
Telephone: (203) 737-2282
Fax: (203) 737-2286

Recently the Yale Center for Excellence in Genomic Sciences has constructed microarrays consisting of PCR fragments of average length about 800 base pairs covering all the unique DNA sequences of chromosome 22. We have begun to use these arrays in several types of experiments intended to analyze globally various aspects of cellular molecular biology. One type of study is chip analysis of the results of chromatin immunoprecipitation in which antibodies against specific transcription factors are used to precipitate cross linked chromatin, and DNA from the resulting precipitates is analyzed by hybridization to the genomic arrays. Our results with the beta globin locus and other results with E2F indicate the promise of this approach but also show its difficulties in cells of higher organisms. Current work is focused both on extending the results to additional transcription factors, and on refining the approach technically.

A second area that we and others have investigated is the use of these chips to define the transcribed regions of genomic DNA. There is qualitative agreement that the amount of transcriptional activity detected exceeds that predicted from known and suggested genes, although the significance of these additional transcripts remains to be determined. A third area in which the genomic arrays may be useful is in combination with global methods for detection of sequence variation. We have been engaged for some time in developing the use of immobilized enzymes for capturing DNA duplexes that contain internal mismatches. This approach has been applied to cDNA from a diploid lymphoblastoid cell line, with promising results. Initial tests suggest that genomic arrays will be valuable here also for identifying polymorphic mRNA templates.

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