Allele-Specific Expression Analysis Does Not Support Sex Chromosome Inactivation on the Chicken Z Chromosome

Heterogametic sex chromosomes have evolved many times independently, and in many cases, the loss of functional genes from the sex-limited Y or W chromosome leaves only one functional gene copy on the corresponding X or Z chromosome in the heterogametic sex. Because gene dose often correlates with gene expression level, this difference in gene dose between males and females for X- or Z-linked genes in some cases has selected for chromosome-wide transcriptional dosage compensation mechanisms to counteract any reduction in expression in the heterogametic sex. These mechanisms are thought to restore the balance between sex-linked loci and the autosomal genes they interact with, and this also typically results in equal expression between the sexes. However, dosage compensation in many other species is incomplete, and in the case of birds average expression from males (ZZ) remains higher than in females (ZW). Interestingly, recent reports in chickens and related species have shown that the Z chromosome is expressed less in males than would be expected from two copies of the chromosome, and recent data from cell-based approaches on 11 loci in chicken have suggested that one Z chromosome is partially inactivated in males, in a mechanism thought to be homologous to X inactivation in therian mammals. In the present study, we use controlled crosses in three tissues to test for the presence of Z inactivation in males, which would be expected to bias transcription to the active gene copy (allele-specific expression). We show that for the vast majority of genes on the chicken Z chromosome, males express both parental alleles at statistically similar levels, indicating no Z chromosome inactivation. For those Z chromosome loci with detectable ASE in males, we show that the most likely cause is cis-regulatory variation, rather than Z chromosome inactivation. Taken together, our results indicate that unlike the X chromosome in mammals, Z inactivation does not affect an appreciable number of loci in chicken.