Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

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.

Large-scale Sequencing of the Human and Mouse T Cell Receptor Loci

Leroy Hood[1], Lee Rowen[1], Kai Wang[1], Inyoul Lee[1], Cecilie Boysen[2], and Ben F. Koop[3].
[1]Department of Molecular Biotechnology, University of Washington, FJ-20, Seattle, Washington 98195. [2]Caltech, 391 South Holiston, #147-75, Pasadena, California 91125. [3]Department of Biology, University of Victoria, Victoria, British Colombia, V8W 2Y2.

T cell receptors play a major role in immunity and autoimmune diseases. For this reason, their genomic sequence has been chosen as a model system for the development of strategies and tools related to the human genome project. The complete genomic sequence of a multigene locus enables a delineation of genes and gene boundaries, and an assessment of the proportion of pseudogenes. Additionally, it provides PCR access to microsatellite markers and other possible sites of polymorphic variance and, therefore, will facilitate efforts to discover mutations related to disease susceptibility. Strong sequence homologies found in a cross-species comparison between human and mouse counterparts will assist in identifying regulatory regions, new genes and alterative functions for DNA sequence information The cross-species comparison will also conduce to an understanding of the evolutionary mechanisms that underlie overall gene organization.

Well over a megabase of the T cell receptor loci from human and mouse have been sequenced using the shotgun strategy. The preponderance of the data comes from the TCR beta loci (~95% complete in human, ~60% complete in mouse). Our current efforts are aimed at completing the beta loci and the human alpha locus.

Major new discoveries from the human and mouse T cell receptor loci sequence include the following:

A cross-species comparison of the human and mouse alpha-delta constant regions reveals ~70% homology across nearly 100 kb of sequence, suggesting that non-coding DNA may have heretofore undiscovered functions.

The T cell receptor beta locus is also the site of the human and mouse pancreatic trypsinogen multigene family, suggesting that genes with apparently unrelated functions can occupy the same genomic space.

Approximately half of the human T cell receptor beta locus is comprised of long homologous repeats in which members of multigene subfamilies are embedded. These repeats suggest a mechanism for the divergence of gene function. Indeed, a portion of the human TCR beta locus has even been translocated to another chromosome. The mouse locus, by way of contrast, contains far less repeated DNA. In this regard, the comparative genomic sequences have provided an explanation for why there are twice as many TCR beta variable gene segments in human as mouse, even though both species have about the same number of subfamilies.

We anticipate that the sequences of the human and mouse TCR alpha loci, when completed, will yield further insights into features of mammalian genomes. We also anticipate improvements in sequencing technology, data management, and organizational strategies will increase the ease and throughput of mammalian genomic sequencing.