Table 1.
Escape genes and CH-hypermethylated genes
| Gene | Gene body, %mCH | Gene promoter, %mCG | Diallelic RNA abundance, FPKM | Allele-specific RNA abundance, SRPM | |||
| Xa | Xi | Xa | Xi | Xa | Xi | ||
| Escape genes with mCH on Xi | |||||||
| 5530601H04Rik | 0.19 | 2.40 | 3.7 | 2.1 | 6.49 | 36.9 | 12.3 |
| Ddx3x | 0.17 | 1.89 | 0.2 | 6.3 | 44.8 | 84.9 | 44.5 |
| Eif2s3x | 0.10 | 1.67 | 3.4 | 1.4 | 22.5 | 30.5 | 24.4 |
| Ftx | 0.42 | 2.47 | 11.6 | 10.1 | 6.05 | 67.0 | 7.65 |
| Kdm5c | 0.28 | 3.11 | 1.2 | 3.0 | 7.40 | 57.9 | 25.0 |
| Kdm6a | 0.39 | 2.22 | 0.4 | 0.02 | 5.43 | 22.7 | 8.25 |
| Xist | 1.79 | 0.79* | 86.0 | 0.5 | 24.9 | 5.74 | 546 |
| Firre | 0.94 | 1.16 | 7.8 | 73.6 | 6.25 | 64.2 | 1.91* |
| Pbdc1 | 0.52 | 3.27 | 3.7 | 2.1 | 4.40 | 17.2 | 4.02* |
| Tmem29 | 0.43 | 1.52 | 6.1 | 27.8 | 10.2 | 28.8 | 3.52* |
| Escape genes without mCH on Xi | |||||||
| Gpm6b | 0.57 | 0.04 | 13.7 | 79.1 | 121 | 252 | 27.2 |
| Gpr34 | 1.15 | 0.04 | 65.9 | 59.8 | 3.62 | 13.9 | 4.01 |
| Slc16a2 | 1.15 | 0.16 | 0.1 | 74.3 | 5.31 | 34.1 | 3.91 |
| Tceal5 | 0.00 | 0.12 | 33.2 | 67.9 | 16.7 | 23.5 | 9.93 |
| Other CH-hypermethylated genes | |||||||
| Gm38020† | 0.07 | 3.85 | 93.5 | 93.4 | 2.76 | 43.7 | 4.99 |
| Jpx† | 0.77 | 3.46 | 6.8 | 26.5 | 1.21 | 7.51 | 0.815 |
| 4933407K13Rik‡ | 0.25 | 1.05 | 5.9 | 51.2 | 0.565 | 8.40 | 0.10 |
Bold italic values indicate significant gene body mCH on Xi, significant CG promoter hypomethylation on Xi, or Xi RNA abundance (FDR < 0.05 in both replicates).
*
Genes significant in one replicate only.
†
Occurs within the XIC. Gm38020 overlaps the escape gene Ftx, and Jpx has previously been reported to escape (42).
‡
Located at the Dxz4 macrosatellite, which is involved in Xi chromosome topology.