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Table 1 Genes escaping XCI in any of the three NPC lines in comparison with other studies

From: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq

Gene S Mb start position *NPC_ 129-Xi NPC_ Cast-Xi NPC_ 129-Xi [37] [35] [33] [48] [49] Other [29] (human) Cluster
Kdm6a/Utxa + 17.7 −0.3 −0.4 −0.8 * * * * *   UTX/DUSP21 (9/9) 4
Utp14a + 45.6 −0.3 −1.7 −0.8    *   *   UTP14A (3/9) 4
Eda2r - 94.6 −1.9 −2.0 −2.3        XEDAR (4/9) 3
Ogt + 98.8 0.2 −0.9 0.4   *    *   OGT (0/9) 3
Xist - 100.7 8.7 6.5 10.2 * * * * *   XIST (9/9) 4
Ftx/ B230206F22Rik - 100.8 −1.7 −0.8 −1.3     * * * [32] NA 3
5530601H04Rik - 102.3 0.2 −0.2 −0.4     * * * [34] NA 2
2610029G23Rik + 102.3 −0.4 −0.6 −0.4 * * *   * * [34] NA 3
Kdm5c/Jarid1c + 148.7 −1.1 −0.7 −1.7 * * * * *   NA 3
Nkap + 34.7 −0.6 −0.3 −8.2   *    *   NKAP (1/9) 3
Hcfc1 - 71.2 −2.5 −2.9 -   *      HCFC (6/9) 3
Vbp1 + 72.8 −2.3 −3.0 -   *      VBP1 (1/9) 3
Jpx/2010000I03Rik/Enox + 100.7 −1.1 −1.3 NA b      * * [36] NA NA
Chm - 110.3 0.2 −2.9 −3.0   *      CHM (6/9) 4
Gpm6b + 162.8 −0.4 −0.9 −3.6     * *   GPM6B (8/9) NA
Ofd1 - 162.9 −3.2 −0.2 −7.5        OFD1 (6/6) 3
Mecp2 - 71.3 −1.8 - −2.3        MECP2 (0/9) 2
Ercc6l - 99.4 −0.4 - −0.6        FLJ20105 (2/9) 2
Ndufb11 - 20.2 −0.5 - -        P17.3 (0/9) NA
A230072C01Rik + 20.5 −2.9 - -        NA 2
6720401G13Rik - 48.0 −2.8 - −5.4 * *      NA 1
Fmr1 + 65.9 −2.4 - -   *      FMR1 (1/9) 3
Trmt2b - 130.8 −0.5 - −3.9        FLJ12687 (0/9) NA
Rbm41 - 136.5 −2.4 - −5.8        FLJ11016 (3/9) 1
Figf + 160.9 −2.2 −3.8 -        NA 4
Mmgt1 - 53.9 - −0.5 -        NA  
Siah1b - 160.5 - −1.6 −5.4      *   NA  
Mid1 + 166.3 −4.9 −0.4 −7.1 * *    *   MID1 (1/9)  
Sox3 - 58.1 -   0.3        NA  
Taf1 + 98.7 −1.1 −2.9 −0.6   *    *   TAF1 (0/5)  
Gm5643/Hnrnpa1l2 + 138.7 −1.2 2.6 −1.6        NA  
Zrsr2 - 160.4 - −5.9 −2.0      *   NA  
Region 1              
 Gpkowa + 7.27 −2.4 −1.2 −8.4        GPKOW (0/9) 4
 Wdr45 + 7.30 −3.0 0.0 -        WDRX1 (0/9)  
 Tcfe3 + 7.34 −1.9 −0.8 −6.7        TFE3 (0/9) 4
 Gripap1a + 7.37 −1.1 −1.5 −6.3      *   GRIPAP1 (1/9) 4
 Slc35a2 + 7.46 −1.6 1.3 -      *   SLC35A2 (0/9)  
 Timm17b + 7.48 −0.9 −1.1 -        TIMM17B (0/9) 4
 Ftsj1/LOC100044636a - 7.83 −0.3 −1.2 -        FTSJ1 (0/9) 4
 Hdac6 - 7.52 −7.5 −1.6 -      *   HDAC6 (0/5)  
 Wdr13a - 7.71 - −1.0 -        WDR13 (0/9)  
 Rbm3a - 7.72 −6.4 −1.7 −5.8        RBM3 (0/9)  
 2900002K06Rika + 7.72 - −0.2 -        NA  
 Ebp - 7.77 - −2.6 -        EBP (0/9)  
Region 2              
 Ddx3x/LOC100045923a + 12.86 −1.7 −0.9 −2.1 * * * *    DDX3X (9/9) 3
 Med14a - 12.34 −0.5 −1.4 −7.3        CRSP2 (6/6) 3
 Usp9xa + 12.65 −0.9 −1.3 −9.0   *      USP9X (9/9) 3
 1810030O07Rika - 12.25 1.3 −5.1 −5.9 * *      MGC39350 (8/9) 3
Region 3              
 Uba1a + 20.24 −0.4 −3.7 −0.9        UBE1 (9/9) 3
 Cdk16/Pctk1a + 20.27 −1.1 - −0.4   *      PCTK1 (7/7) 3
 Usp11a + 20.28 −0.5 −7.1 −8.2        USP11 (4/9) 3
 Araf + 20.43 −1.0 - -        ARAF1 (0/6) 3
  1. Data in the columns *NPC_129-Xi, NPC_ Cast-Xi, NPC_ 129-Xi are represented as ratio Xi/Xa (log2). The bold ratios indicate escape from the corresponding gene, the bold italic ratios indicate that too little polymorphic sites and/or reads from Xi were present to classify the gene as escaper. A dash or values < −3.32 in these columns indicate that the corresponding gene is subject to XCI. Genes that escape XCI in human fibroblasts are in bold in the second-last column, with the ratio indicating the number of clones showing escape as observed by Carrel and Willard [29]. For the study by Berletch et al. [48], we only included escape genes from the mouse brain, while spleen and ovary are not included in this table. Cluster numbers in the last column refer to Fig. 4a and are indicated for genes that escape XCI in *NPC_129-Xi. S strand. aEscape is validated by RT-PCR sequencing (Additional file 1: Figure S13). bOnly two tags from the Xi, no signal from Xa. *Identified as escaper in other studies