A comparative transcription map of the murine bare patches (Bpa) and striated (Str) critical regions and human Xq28.

Abstract

The X-linked developmental mouse mutations bare patches (Bpa) and striated {Str) may be homologous to human X-linked dominant chondrodysplasia punctata (CDPX2) and incontinentia pigmenti (IP2), respectively, based on their genetic mapping and clinical phenotypes. Bpa and Str have been localized to an overlapping critical region of 600 kb that demonstrates conserved gene order with loci in human Xq28 between DXSII04 and DXS52. As part of efforts to isolate the genes involved in these disorders, we have begun to develop a comparative transcription map spanning this region in both species. Using techniques of cross-species conservation and hybridization, exon trapping, and cDNA selection we have identified four known genes or members of gene families--caltractin, a member of the ~/-aminobutyric acid (GABAA) receptor gene family, a member of the melanoma antigen gene (MAGE) family, and several members of the murine-specific, X-linked lymphocyte regulated gene (Xlr3) family. Trapped exons and, in some cases, longer cDNAs have been isolated for potentially 7-9 additional genes. One cDNA demonstrates highly significant homology with members of the Kriippel family of zinc finger transcription factors. A second novel cDNA demonstrates homology at the 3' end of the predicted amino acid sequence to a LIM domain consensus. Gene order appears conserved among those cDNAs determined to be present in both human and mouse. Three of the murine transcripts appear to be present in multiple copies within the Bpa/Str critical region and could be associated with a predisposition to genomic rearrangements. Reverse trancriptase PCR (RT-PCR) and Northern analyses demonstrate that several of the transcripts are expressed in mid-gestation murine embryos and neonatal skin, making them candidates for the Bpa and Str mutations and their respective homologous human disorders.

Analysis of the Set of GABAA Receptor Genes in the Human Genome

“…The organization of the three GABR genes (⑀-␣3-) on the human X chromosome (Fig. 3E), plus their same order found on the mouse X chromosome (35,39), when compared with the other clusters would be consistent with ⑀ being derived from the ␥ line and from the ␤ line of GABR genes of an ancestral chordate. However, species specialization within the ␥3 subgroup might have occurred independently.…”

“…That band location is as found for GABRE (33), for ␣3 (10, 11), and for (34,35). We have derived the precise locations, separations, and sizes of the genes there (Fig.…”

Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man

“…The critical region containing these two mutations is flanked by the loci DXHXS1104 and DXHXS52 (Levin et al 1996). In addition, we have completed the sequencing of the homologous human region.…”

“…In addition, we have completed the sequencing of the homologous human region. In the mouse, cosmid contigs partially spanning the Bpa/Str critical region were already available (Chatterjee et al 1994;Levin et al 1996) and STS markers and previously identified genes were used to construct a BAC and PAC contig (see Methods). Thirteen markers were used to isolate clones and facilitate contig construction, resulting in 28 clones selected for further characterization.…”

Changes in gene expression associated with loss of function of the NSDHL sterol dehydrogenase in mouse embryonic fibroblasts

“…The quality and concentration of RNA samples were assayed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RT-PCR and DNA sequencing of cDNA to test for the monoallelic expression of Nsdhl in sorted cell populations were performed as described (21) using a forward primer from exon 2 (NsdhlE2F, 5 Ј -CCAGCTGAT-CATGGTGAATC-3 Ј ) and a reverse primer from exon 5 (NsdhlE5R, 5 Ј -TGGCACTGCTGGTTAAAATGAGTTT-3 Ј ), generating a 400 bp PCR product that spans the site of the Bpa 1H mutation in exon 4.…”