There are several potential mechanisms by which sex chromosome genes can affect phenotype directly (Davies & Wilkinson, 2006). One is through male-specific genes present only on the Y chromosome. A second is through dosage differences of sex chromosome genes between XX and XY organisms. As the X chromosome contains many more genes than the Y chromosome, one avenue is through dosage differences between XX and XY organisms of X and Y chromosome genes. Parity is achieved for a majority of these genes by a process of inactivation of most genes on one of the X chromosomes combined with upregulation of the remaining X chromosome in both sexes (Payer & Lee, 2008). Although most of the genes that escape inactivation of the second X chromosome have functional homologues on the Y chromosome, several do not, raising the possibility of dosage effects. A third means by which X and Y chromosome genes may contribute directly to sex differences is through imprinting. Females receive X chromosomes imprinted by both mother and father, while males only receive a single maternally imprinted X chromosome.
