International Mammalian Genome Society

The 16th International Mouse Genome Conference (2002)


POSTER 165 - DEFINING GAP SIZES BETWEEN CONTIGS IN THE MOUSE GENOME USING FIBRE FISH

R Banerjee
The Wellcome Trust Sanger Institute

Porter KM, Faulkner LM, Gribble SM, Gregory SM, Carter NP
The Wellcome Trust, Sanger Institute

To sequence the mouse it was essential to construct a comprehensive and integrated clone map. Mouse BAC clone fingerprints were overlapped at high stringency to generate 7,587 contigs which were aligned to the human sequence via BAC end sequence homology before further joins were made between adjacent contigs based on the original restriction fingerprint data. Contigs were then ordered relative to the mouse using mouse markers from existing genetic and radiation hybrid maps. The whole genome fingerprint database contains 296 contigs with an average length of 9.3Mb.The physical maps of chromosomes 4 and 11 consist of eight and seven contigs respectively. In our studies we have used metaphase FISH and DNA fibre FISH to size the gaps between these contigs. Initially, we FISH mapped pairs of mouse BAC clones from adjoining contig ends onto mouse metaphase chromosomes to confirm the chromosomal localisation and secondly to confirm their colocalisation thus mapping the BAC clones to within a 1-2Mb chromosome region. Clone pairs that colocalised on metaphase chromosomes were then hybridized onto mouse extended chromatin fibres for further refinement of gap sizes. Fibre FISH revealed relationships between two clone pairs suggesting that the gap size between contig ends in each case is less than 100 Kb. We have successfully estimated the gap sizes between all the contigs on mouse chromosomes 4 and 11.


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