Table 1.
Classification of X-linked protein-coding genes in relation to copy number, evolution, X upregulation and escape from XCI
| X-linked protein-coding genes | Copy number*
|
Evolutionary origin‡
|
Human–mouse comparison§
|
||||||
|---|---|---|---|---|---|---|---|---|---|
| Single | Multicopy | Ampliconic | ‘Old’ | ‘New’ | XCR | XAR | Shared | Independently acquired | |
| Human X-linked genes (n = 800) | 72% | 15% | 13% | 71% | 29% | 39% | 31% | 82% | 10% |
|
| |||||||||
| Mouse X-linked genes (n = 853) | 69% | 14% | 17% | 60% | 40% | 35% | 25% | 77% | 16% |
|
| |||||||||
| Percentage of genes per category | |||||||||
|
| |||||||||
| Human testis-specific genes|| | 11% | 38% | 84% | Low | High | Low | Low | 16% | 89% |
|
| |||||||||
| Mouse testis-specific genes|| | 16% | 23% | 69% | Low | High | Low | Low | 18% | 67% |
|
| |||||||||
| Genes upregulated by transcription initiation and/or RNA stability¶ | Yes | Yes | ND | Yes | Yes | Yes | Yes | Yes | ND |
|
| |||||||||
| Human escape genes (n = 518) | 15%# | ND | ND | 15%** | 12% | 5% | 27% | ND | 0% |
|
| |||||||||
| Mouse escape genes (n = 393) | 3%# | ND | ND | ND | ND | 2%** | 8% | ND | 0% |
ND, not determined; XAR, X added region; XCI, X chromosome inactivation; XCR, X conserved region.
Percentages of protein-coding X-linked genes that are classified as single-copy, multicopy or ampliconic in humans and in mice11.
Percentages of X-linked genes in each category based on evolutionary origin: old or new genes are those present or absent, respectively, on orthologous autosomes in chickens; genes in the XCR are subsets of old genes that are orthologous to genes on chicken autosome 1, whereas genes in the XAR are subsets of old genes that are orthologous to genes on chicken autosome 4. Percentages for human genes are obtained from REF. 13, and percentages for mouse genes are estimates on the basis of their human orthologues.
Percentages of X-linked genes that are shared between humans and mice or that are independently acquired after the human–mouse divergence11.
Percentages of genes predominantly expressed in the testes in each category of human and mouse X-linked genes11. If percentages were not available, ‘high’ and ‘low’ indicate the trend.
‘Yes’ indicates that the gene category is regulated by transcription initiation and/or RNA stability. Note that new genes are less affected by histone acetyltransferase KAT8 knockdown than old X-linked genes. However, transcripts of new genes have enhanced half-lives compared with transcripts of old genes27.
Percentage of X-linked genes that consistently escape XCI in human–rodent hybrid cell lines and in a mouse cell line69,76. The total number of genes assayed (n), excluding genes in the pseudoautosomal regions, is indicated in parentheses.
Percentage of escape genes in each category. Not all escape genes could be categorized as old, new, XCR, XAR or shared, as some escape genes were lost in mice. In humans, 336 genes could be categorized on the basis of REF. 13.