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

Planello, Aline C; Ji, Junfeng; Sharma, Vivek; Singhania, Rajat; Mbabaali, Faridah; Müller, Fabian; Alfaro, Javier A; Bock, Christoph; De Carvalho, Daniel D; Batada, Nizar N

doi:10.1186/2045-9769-3-4

Cell Regeneration

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

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.

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