X inactivation analysis and DNA methylation studies of the ubiquitin activating enzyme E1 and PCTAIRE-1 genes in human and mouse

Escape from X inactivation of two new genes associated with DXS6974E and DXS7020E

Most genes on the X chromosome undergo "inactivation," being transcribed from only one copy in female somatic cells, but several human genes have been shown to be expressed from both the active and the otherwise inactivated homologue. To assess further the fraction and location of genes that escape inactivation, we have analyzed the inactivation status of a set of 73 expressed sequence tags that were derived from the sequencing of cDNA collections and mapped to the X chromosome. Of 33 that were expressed in cultured cells, as assessed by reverse transcription and PCR, 4 (about 12%) were transcribed from both the active and the inactive X chromosome. Two, RPS4 and PCTAIRE1, are already known to escape inactivation; the other 2, of unknown function, include a short cDNA with a full open reading frame and a transcript with no detectable open reading frame. They map, respectively, to Xp11.3-p11.4 and Xp22.2; both regions were previously reported to encode sequences transcribed from the inactive X. Neither transcript has a corresponding sequence on the Y. Thus, they exhibit double dosage in females compared to males, and inactivation status may be inconsequential for these transcribed sequences.

Expression of genes from the human active and inactive X chromosomes

X-chromosome inactivation results in the cis-limited inactivation of many, but not all, of the genes on one of the pair of X chromosomes in mammalian females. In addition to the genes from the pseudoautosomal region, which have long been anticipated to escape inactivation, genes from several other regions of the human X chromosome have now been shown to escape inactivation and to be expressed from both the active and inactive X chromosomes. The growing number of genes escaping inactivation emphasizes the need for a reliable system for assessing the inactivation status of X-linked genes. Since many features of the active or inactive X chromosome, including transcriptional activity, are maintained in rodent/human somatic-cell hybrids, such hybrids have been used to study the inactivation process and to determine the inactivation status of human X-linked genes. In order to assess the fidelity of inactivation status in such hybrids, we have examined the expression of 33 X-linked genes in eight mouse/human somatic-cell hybrids that contain either the human active (three hybrids) or inactive X (five hybrids) chromosome. Inactivation of nine of these genes had previously been demonstrated biochemically in human cells, and the expression of these genes only in hybrids retaining an active X, but not in those retaining an inactive X, confirms that expression in hybrids reflects expression in human cells. Although the majority of genes tested showed consistent patterns of expression among the active X hybrids or inactive X hybrids, surprisingly, 5 of the 33 genes showed heterogeneous expression among the hybrids, demonstrating a significantly higher rate of variability than previously reported for other genes in either human somatic cells or mouse/human somatic-cell hybrids. These data suggest that at least some X-linked genes may be under additional levels of epigenetic regulation not previously recognized and that somatic-cell hybrids may provide a useful approach for studying these chromosomal phenomena.

Mapping of 59 EST gene markers in 31 intervals spanning the human X chromosome

The positioning of Expressed Sequence Tags (ESTs) constitutes an important step towards a functional map of the human genome, including candidate genes for human genetic disorders that have been localized by linkage analysis. We localized 59 ESTs on the human X chromosome, including 44 derived from infant brain and 15 from adult muscle cDNA libraries. Localizations by a somatic cell hybrid panel were refined for five cDNAs by mapping them in yeast artificial chromosome (YAC) contigs.

Mapping the RP2 locus for X-linked retinitis pigmentosa on proximal Xp: a genetically defined 5-cM critical region and exclusion of candidate genes by physical mapping

Genetic linkage studies have implicated at least two loci for X-linked retinitis pigmentosa (XLRP) on proximal Xp. We now report a defined genetic localization for the RP2 locus to a 5-cM interval in Xp11.3-11.23. Haplotype analysis of polymorphic markers in recombinant individuals from two XLRP families has enabled us to identify DXS8083 and DXS6616 as the new distal and proximal flanking markers for RP2. Using STS-content and YAC end-clone mapping, an approximately 1.2 Mb YAC contig has been established encompassing the proximal RP2 boundary and extending from T1MP1 to DXS1240 in Xp11.23. Several ESTs have been positioned and ordered on this contig, one of which is novel to the region, identified by sequence data-base match to a physically mapped YAC insert terminal STS. Integration of the genetic and physical data has placed four retinally expressed genes proximal to DXS6616, and thereby excluded them from a causitive role in RP2. This work now provides a much needed focus for positional cloning approaches to isolation of the defective gene.