Regional localization of 64 cosmid contigs, including 18 genes and 14 markers, to intervals on human chromosome 9q34

Chromosomal location, exon/intron organization and evolution of lipocalin genes

Lipocalins exhibit low sequence similarity that contrasts with a tightly conserved folding shared by all members of this superfamily. This conserved folding can be, at least partly, accounted for by a highly conserved gene structure. The array of lipocalin genes that have so far been studied mostly in mammals indicate a large conservation of a typical seven exon/six intron arrangement. Other conserved features include a partly coding exon 1 of variable size, fixed sizes of exons 2-5 that code for an array of lipocalin-specific beta-strands and a tendency of the last exons to either fuse or expand into further exons without major changes in the length of the resulting open reading frame. The conserved exon/intron arrangement as well as a clustering of most lipocalin genes in given chromosomes of human and mouse indicate that the lipocalin genes diverged from a shared ancestor by successive rounds of duplications followed by late changes in exon arrangements.

Isolation of novel cDNAs by subtractions between the anterior mesendoderm of single mouse gastrula stage embryos

The anterior mesendoderm of mid- to late primitive streak stage mouse embryos has the ability to induce anterior neuroectodermal fate in naive epiblast [S.-L. Ang and J. Rossant (1993) Development 118, 139-149]. A number of genes have been found to be expressed in this tissue, notably the transcription factor Lim1. Lim1-null mice have anterior mesendoderm defects that result in a lack of head formation. Thus, the anterior mesendoderm of gastrula stage mouse embryos should express Lim1-regulated genes that are essential for head development. To identify Lim1-regulated genes, a differential screen with subtraction was developed, using cDNA pools that were amplified from the anterior mesendoderm of single wild-type and Lim1-null gastrula stage embryos. This novel screen strategy has yielded 22 cDNAs that show differential expression between anterior mesendoderm cells of wild-type and Lim1-null embryos. The expression of one novel cDNA SII6 initially colocalizes with Lim1 in the anterior mesendoderm of gastrula stage embryos. Moreover, SII6 expression is undetectable in the anterior mesendoderm of Lim1-null embryos. This screen identifies a set of putative Lim1 target genes that may have important roles in vertebrate head formation. Furthermore, this differential screen strategy should provide a broadly applicable approach to identify differences in gene expression between embryonic tissues of limiting quantity.

Advances in fluorescent in situ hybridisation

Recent advances in fluorescent in situ hybridisation included the generation of allele-specific probes, bar-coded chromosomes, and the visualisation of chromosome territories and genes within the nucleus. One major advance has been our ability to visualise and make precise and reproducible measurements from stretched DNA molecules prepared directly from human cells.

A 1.7-megabase sequence-ready cosmid contig covering the TSC1 candidate region in 9q34

The disease gene TSC1 has been genetically mapped to human chromosome region 9q34, in a 4-cM interval between the markers D9S149 and D9S114. Within this interval there is conflicting genetic evidence as to the finer localization of the gene. We have used finger-printing methods and hybridization to produce a 1.7-Mb overlapping clone map covering the TSC1 candidate region, with a single gap of 20 kb. We have localized 12 previously cloned genes and 17 genetic markers on this map and have confirmed the order of the genetic map. This deep set of overlapping clones is now ready to be used for candidate gene isolation, for transcription studies, or for sequencing.