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

Abstract

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.

X-chromosome inactivation: molecular mechanisms from the human perspective

“…Assaying individual genes on the X is labor-intensive, and higher throughput genomic methodologies are also being utilized. Microarrays allow for the comparison of expression from many genes simultaneously, and several studies have compared X-linked expression levels between males and females (Craig et al 2004;Talebizadeh et al 2006;Johnston et al 2008). However, such an approach does ask an inherently diVerent question; so it is perhaps not surprising that microarraybased studies show inconsistent results with the hybrid data, detecting fewer escaping genes, for many possible reasons.…”

A Model Incorporating Potential Skewed X‐Inactivation in MZ Girls Suggests that X‐Linked QTLs Exist for Several Social Behaviours Including Autism Spectrum Disorder

“…Craig et al, 2004) -for the vast majority of X-linked alleles one parental set in each female cell may be expressed predominantly over the other set. This is a particularly important consideration when looking at monozygotic female (MZF) twins as the process of X-inactivation and the possibility of skewed inactivation may lead to 'identical' twins having nonidentical gene expression.…”

Inactivation status of PCDH11X: sexual dimorphisms in gene expression levels in brain

“…Other more indirect approaches focus on the epigenetic modifications that differentiate active and inactive X chromosomes, namely promoter DNA methylation and histone modifications (Carrel et al 1996;Jegalian and Page 1998;Matarazzo et al 2002). In recent reports, microarray technology was used to compare the expression of a high number of X-linked genes in female and in male lymphocytes (Craig et al 2004) and in lymphoblastoid cell lines from normal males, normal females and individuals with supernumerary X chromosomes (Sudbrak et al 2001).…”