Exclusion of RAI2 as the causative gene for Nance-Horan syndrome.

Nance-Horan syndrome (NHS) is an X-linked condition characterised by congenital cataracts, microphthalmia and/or microcornea, unusual dental morphology, dysmorphic facial features, and developmental delay in some cases. Recent linkage studies have mapped the NHS disease gene to a 3.5-cM interval on Xp22.2 between DXS1053 and DXS443. We previously identified a human homologue of a mouse retinoic-acid-induced gene (RAI2) within the NHS critical flanking interval and have tested the gene as a candidate for Nance-Horan syndrome in nine NHS-affected families. Direct sequencing of the RAI2 gene and predicted promoter region has revealed no mutations in the families screened; RAI2 is therefore unlikely to be associated with NHS.

Identification and characterization of the human homologue (RAI2) of a mouse retinoic acid-induced gene in Xp22.

We have identified a novel human gene during studies of a 1.3-Mb region of Xp22 between DXS418 and DXS999. A PAC contig spanning the region was constructed, sequenced, and analyzed by gene and exon prediction programs and by homology searches. Further investigation of predicted exons from PAC clone 389A20 led to the identification of a single-exon gene, designated RAI2 (retinoic acid-induced 2). RAI2 mapped 28 kb centromeric to marker DXS7996, between DXS7996 and DXS7997, and was transcribed from centromere to telomere. Northern blot analysis and reverse transcription-polymerase chain reaction analysis revealed expression of a 2.5-kb transcript in four fetal tissues (brain, lung, kidney, and heart) and eight adult tissues (heart, brain, placenta, lung, skeletal muscle, kidney, pancreas, and retina) but not in fetal or adult liver. The 530-amino-acid protein (57 kDa predicted mass) displays 94% homology with a mouse retinoic acid-induced gene product and contains a novel proline-rich (39%) domain of 68 amino acids. Retinoic acid is involved in vertebrate anteroposterior axis formation and cellular differentiation and has been shown to modulate gene expression controlling early embryonal development, suggesting a developmental role for RAI2. RAI2 remains a candidate gene for diseases mapping to the Xp22 region.

Identification and characterization of a novel serine-threonine kinase gene from the Xp22 region.

Eukaryotic protein kinases are part of a large and expanding family of proteins. Through our transcriptional mapping effort in the Xp22 region, we have isolated and sequenced the full-length transcript of STK9, a novel cDNA highly homologous to serine-threonine kinases. A number of human genetic disorders have been mapped to the region where STK9 has been localized including Nance-Horan (NH) syndrome, oral-facial-digital syndrome type 1 (OFD1), and a novel locus for nonsyndromic sensorineural deafness (DFN6). To evaluate the possible involvement of STK9 in any of the above-mentioned disorders, a 2416-bp full-length cDNA was assembled. The entire genomic structure of the gene, which is composed of 20 coding exons, was determined. Northern analysis revealed a transcript larger than 9.5 kb in several tissues including brain, lung, and kidney. The mouse homologue (Stk9) was identified and mapped in the mouse in the region syntenic to human Xp. This location is compatible with the location of the Xcat mutant, which shows congenital cataracts very similar to those observed in NH patients. Sequence homologies, expression pattern, and mapping information in both human and mouse make STK9 a candidate gene for the above-mentioned disorders.

Characterization of SCML1, a new gene in Xp22, with homology to developmental polycomb genes.

Using exon trapping, we have identified a new human gene in Xp22 encoding a 3-kb mRNA. Expression of this RNA is detectable in a range of tissues but is most pronounced in skeletal muscle and heart. The gene, designated "sex comb on midleg-like-1" (SCML1), maps 14 kb centromeric of marker DXS418, between DXS418 and DXS7994, and is transcribed from telomere to centromere. SCML1 spans 18 kb of genomic DNA, consists of six exons, and has a 624-bp open reading frame. The predicted 27-kDa SCML1 protein contains two domains that each have a high homology to two Drosophila transcriptional repressors of the polycomb group (PcG) genes and their homologues in mouse and human. PcG genes are known to be involved in the regulation of homeotic genes, and the mammalian homologues of the PcG genes repress the expression of Hox genes. SCML1 appears to be a new human member of this gene group and may play an important role in the control of embryonal development.

High-resolution physical map of the X-linked retinoschisis interval in Xp22.

X-linked retinoschisis (RS) is the leading cause of macular degeneration in young males and has been mapped to Xp22 between DXS418 and DXS999. To facilitate identification of the RS gene, we have constructed a yeast artificial chromosome (YAC) contig across this region comprising 28 YACs and 32 sequence-tagged sites including seven novel end clone markers. To establish the definitive marker order, a PAC contig containing 50 clones was also constructed, and all clones were fingerprinted. The marker order is: Xpter-DXS1317-(AFM205yd12-DXS7175-DXS7992) -60N8-T7-DXS1195-DXS7993-DXS7174 -60N8-SP6-DXS418-DXS7994-DXS7995-DXS7996-+ ++HYAT2-25HA10R-HYAT1-DXS7997-DXS7998- DXS257-434E8R-3542R-DXS6762-DXS7999-DXS 6763-434E8L-DXS8000-DXS6760-DXS7176- DXS8001-DXS999-3176R-PHKA2-Xcen. A long-range restriction map was constructed, and the RS region is estimated to be 1300 kb, containing three putative CpG islands. An unstable region was identified between DXS6763 and 434E8L. These data will facilitate positional cloning of RS and other disease genes in Xp22.