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The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Identification, organization and analysis of mammalian repetitive DNA

Jerzy Jurka
Linus Pauling Institute of Science and Medicine, 440 Page Mill Rd, Palo Alto, CA 94306.

There are three major components of this project: organization of databases of mammalian repetitive elements; development of specialized software for analysis of repetitive DNA and discovery and comparative studies of mammalian repeats. Our project has been advanced in all the three areas.

We have expanded previously published reference collection of human repeats. We have also compiled and analyzed a collection of the most abundant simple repeats from primates [1]. Both collections are available electronically via the NCBI server. Reference collections for other mammals continue to be developed and we will review their current status during the workshop.

Identification, elimination and basic studies of repetitive DNA at the sequence level may be very labor-intensive without specialized computer software. We have developed a software called 'CENSOR' [2], based on recently described principles for identification and analysis of repetitive DNA [3]. This software will be communicated and released to the public domain during the Human Genome Workshop.

We have discovered several new families of MER repeats from primates and other mammels. We will update this ongoing work during the workshop. Some of the previously reported MER repeats led us to discovery of unusual subfamilies in the L1 family of repeats [4]. We have also characterized the oldest known and one of the largest families of repeats in mammals (MIR family) [5]. Furthermore, we have discovered the youngest known subfamily of human Alu sequences [6]. These findings will be reported and discussed in the context of genomic studies.

This work was supported by the U.S. Department of Energy, Office of Health and Environmental Research, Grant No. DE-FG03-91ER61152.

[1] Jurka, J., and Pethiyagoda, C. (1994) Simple repetitive DNA sequences from primates: compilation and analysis. J. Mol. Evol. (in press).
[2] Jurka, J., Klonowski, P., Dagman, V., and Pelton, P. (1994) CENSOR - a program for identification and elimination of repetitive elements from DNA sequences. Submitted manuscript.
[3] Jurka, J. (1994) Approaches to identification and analysis of interspersed repetitive DNA sequences. In: Automatcd DNA Scqucncing and Analysis (Adams, M.D., Fields, C. and Venter, J.C., eds), Academic Press, pp. 294-298
[4] Smit, A.F.A., Toth, G., Riggs, A.D., and Jurka, J. (1994) Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. Submitted manuscript.
[5] Jurka, J., and Batzer, M. (in preparation)