Skip to main content

Advertisement

Table 1 List of Genes with aberrant promoter DNA methylation

From: Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors

iPSC type Gene name Position relative to TSS (base pairs) Type of DNA methylation aberration Overlapping TF binding site Delta Beta (Y-iPSCs – T-iPSCs)
Y-iPS L1TD1 3887 failure to demethylate SOX2, NANOG 0.205552761
Y-iPS ZNF202 −849 failure to demethylate SOX2, NANOG 0.253028526
Y-iPS VRTN −7 failure to demethylate NANOG 0.204685702
Y-iPS ZNF281 −893 failure to demethylate NANOG 0.217824711
Y-iPS PCBP1-AS1 1655 failure to demethylate NANOG 0.260023778
Y-iPS CELF2 −602 failure to demethylate NANOG 0.201570322
Y-iPS GCLC 2741 failure to demethylate NANOG 0.209894956
Y-iPS CCDC85A −1483 failure to demethylate NANOG 0.231654822
Y-iPS GPC6 −1912 failure to demethylate NANOG 0.2007506
Y-iPS RNF175 1925 failure to demethylate NANOG 0.24800605
Y-iPS LAPTM4B 2519 failure to demethylate NANOG 0.231217277
Y-iPS DUSP5 2071 failure to demethylate NANOG 0.254193033
Y-iPS TDGF1 1259 failure to demethylate NANOG 0.250850333
Y-iPS ZFP36L1 −544 failure to demethylate KLF4 0.310706089
Y-iPS CDC16 −199, −212 spurious methylation OCT4 0.362236745, 0.417741778
Y-iPS ADAR −226 spurious methylation OCT4 0.201398056
Y-iPS RPS23 3852 failure to demethylate OCT4 0.234123761
Y-iPS ZBTB44 −1063, −1044 failure to demethylate OCT4 0.234429233, 0.308618094
Y-iPS KIF3C −433, −422 failure to demethylate OCT4 0.348975978, 0.365098844
Y-iPS HORMAD2 −354, −363 failure to demethylate OCT4 0.233920207, 0.252708599
Y-iPS PSMA8 23 failure to demethylate cMYC 0.238296222
Y-iPS PLEKHG6 −189 failure to demethylate cMYC 0.203390178
T-iPS TNFSF8 −1308 failure to methylate NANOG 0.387689344
T-iPS FLJ31485 3444 failure to demethylate NANOG −0.340429706
T-iPS KCNH2 53 failure to methylate KLF4 0.246395267
T-iPS TMEM132C −365, −905 spurious methylation KLF4, OCT4 −0.327425161,−0.3128155
T-iPS WDR45L −469, −500 failure to methylate OCT4 0.291398672, 0.308650794
T-iPS PABPC1L2A 1760 failure to methylate cMYC 0.272031639
  1. Genes within 5 kilobase window around TSS that were bound by cMYC, OCT4, SOX2, NANOG and KLF4 in human ESCs are shown. TF stands for transcription factor.