International Mammalian Genome Society


The 13th International Mouse Genome Conference
October 31-November 3, 1999

Table of Contents * Structure * Bioinformatics * Sequence * Mapping * New Tools * Gene Discovery * Developmental * Mutagenesis * Functional Genomics

D2 Integration of Physical, Radiation Hybrid and Deletion Maps on Proximal and Central Mouse Chromosome 5

Lengeling, A.1, Wiltshire, T.1, Tarantino, L.M.1, Alavizadeh, A.1, Otmani, C.1, Libby, B.2, Schimenti, J.2 and Bucan, M.1. 1Center of Neurobiology and Behavior, University of Pennsylvania, Philadelphia, PA 19104; 2The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609

Mouse Chromosome 5 (MMU 5) spans 98 cM and includes regions of conserved synteny with human chromosomes (HSA) 1, 4, 7, 12, 13, 18 and 22. We have initiated a physical mapping effort for a region that encompasses the proximal half of MMU 5 (45 cM/90 Mb). This region includes several gene clusters, such as four GABAA receptor subunit genes (Gabrg1-Gabra2-Gabrb1, Garba4) and five members of the tyrosine kinase gene superfamily (Pdgfra-Kit-Kdr, Tec-Txk). A high-resolution map is being developed for the central portion of the chromosome.

RH map: To generate an integrated map of MMU 5 we are using the mouse-hamster T31 Radiation Hybrid mapping panel. So far 96 MMU 5 loci (80 genes and 16 STSs) have been mapped on this panel and have been incorporated into the MIT RH framework map to give a total of 205 markers and an average density of 1 marker / 440 kb. In the course of the RH mapping effort we developed Rhbase (http://rhbase.med.upenn.edu/rh/), an RH data managment program that provides data storage and an interface to the RHMAP program and public databases

Physical map: We have started to develop a high resolution BAC clone contig for a 5 Mb region which includes the genomic region deleted in W19H. Hybridization and overgo probes constructed from BAC end-sequence, Mit markers and genes were used to screen a C57BL/6J BAC library. From 270 BACs analysed from this screen, 198 have been placed in contigs. In total, 19 expressed sequences including transcripts of several gene families, 79 STSs and 7 SSRs have been mapped, giving an average marker density of 1 marker / 48 kb and average 7X coverage. Approximately 1 Mb of this region, covering the GABAA receptor subunit gene cluster has been completed and a minimal tiling path of BACs has been already selected for sequencing.

Deletion complexes: In parallel, we have started to produce deletion complexes in this region. Targeting vectors for the Dpp6, Hdh, Qdpr, Gabrb1 and Clock loci have been constructed and are being used to generate sets of nested deletions through irradiation of ES cells. A set of 5-7 large deletions spanning the proximal half of MMU 5 are being used in region-specific mutagenesis. This screen involves a search for a wide range of visible and developmental mutations as well as anomalies in behavioral traits.

The integrated, high-resolution map will allow for molecular characterization and selection of deletion complexes for functional studies as well as selection of BAC clones for sequencing.

 


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