In female mammals, most genes on one X chromosome are silenced as a result of X-chromosome inactivation. However, some genes escape X-inactivation and are expressed from both the active and inactive X chromosome. Such genes are potential contributors to sexually dimorphic traits, to phenotypic variability among females heterozygous for X-linked conditions, and to clinical abnormalities in patients with abnormal X chromosomes. Here, we present a comprehensive X-inactivation profile of the human X chromosome, representing an estimated 95% of assayable genes in fibroblast-based test systems. In total, about 15% of X-linked genes escape inactivation to some degree, and the proportion of genes escaping inactivation differs dramatically between different regions of the X chromosome, reflecting the evolutionary history of the sex chromosomes. An additional 10% of X-linked genes show variable patterns of inactivation and are expressed to different extents from some inactive X chromosomes. This suggests a remarkable and previously unsuspected degree of expression heterogeneity among females.

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

] that a nonrandom organization of long interspersed element (LINE) repetitive sequences on the X chromosome might be responsible for its facultative heterochromatization. In this paper, we present data indicating that the LINE-1 (L1) composition of the human X chromosome is fundamentally distinct from that of human autosomes. The X chromosome is enriched 2-fold for L1 repetitive elements, with the greatest enrichment observed for a restricted subset of LINE-1 elements that were active <100 million years ago. Regional analysis of the X chromosome reveals that the most significant clustering of these elements is in Xq13-Xq21 (the center of X inactivation). Genomic segments harboring genes that escape inactivation are significantly reduced in L1 content compared with X chromosome segments containing genes subject to X inactivation, providing further support for the association between X inactivation and L1 content. These nonrandom properties of L1 distribution on the X chromosome provide strong evidence that L1 elements may serve as DNA signals to propagate X inactivation along the chromosome. A mong placental mammals, the basic features of X chromosome inactivation are well established (1, 2). X inactivation is a chromosome-wide mechanism of gene regulation, transcriptionally silencing the majority of genes on the X chromosome during mammalian female embryogenesis. This process serves to maintain the correct dosage relationship of genes between females (XX) and males (XY). X inactivation is believed to involve three distinct steps: initiation of inactivation early in development, spreading of inactivation in cis along the length of the chromosome, and subsequent maintenance throughout all successive somatic cell divisions. XIST, a functional non-proteinencoding RNA, maps to the X inactivation center in human and mouse (3)(4)(5). Xist has been shown by transgenic and knockout experiments in mice to play a pivotal role in initiating X inactivation (6-9). Once inactivated, the chromosome acquires a number of features associated with transcriptionally inactive chromatin: the X becomes late-replicating, hypoacetylated, and hypermethylated at cytosine residues in CpG islands of housekeeping genes (1, 2). More recent studies have shown that the inactive X becomes coated with XIST RNA and that the chromatin structure incorporates at least one unique histone variant, . This has led to speculation that an XIST RNA-protein-DNA complex may be an important component in delineating the heterochromatic structure. All of these features indicate that a complex system has evolved to create and maintain the inactive state.Although genetic and molecular aspects of initiation and maintenance of X inactivation have been characterized, the propagation of the signal in cis remains unknown. In particular, it is unknown whether cis-acting DNA sequences participate in this process. Early studies of mice carrying X:autosome translocations and later autosomally integrated Xist yeast artificial chromosome transgenes indicate that inactivation...