Application of microarrays to the analysis of the inactivation status of human X-linked genes expressed in lymphocytes

Dosage compensation in mammalian females is achieved by the random inactivation of one X chromosome early in development; however, inactivation is not complete. In addition to a majority of pseudoautosomal loci, there are genes that are expressed from both the active and the inactive X chromosomes, and which are interspersed among other genes subject to regular dosage compensation. The patterns of X-linked gene expression in different tissues are of great significance for interpreting their impact on sex differences in development. We have examined the suitability and sensitivity of a microarray approach for determining the inactivation status of X-linked genes. Biotinylated cRNA from six female and six male lymphocyte samples were hybridised to Affymetrix HG-U133A microarrays. A total of 36 X-linked targets detected significantly higher levels of female transcripts, suggesting that these corresponded to sequences from loci that escaped, at least partly, from inactivation. These included genes for which previous experimental evidence, or circumstantial evidence, existed for their escape, and some novel candidates. Six of the targets were represented by more than one probe set, which gave independent support for the conclusions reached. © 2004 Nature Publishing Group All rights reserved