Table 4.

Table of differentially methylated genes regulating a stem cell phenotype and/or cell cycle regulation and proliferation in side-population compared to cytotrophoblasts or extravillous trophoblasts.

Gene	Location	Methylation difference in side-population trophoblasts compared to cytotrophoblasts	q. value	Methylation difference in side-population trophoblasts compared to extravillous trophoblasts	q. value	Function/ Biological Relevance
PRDM2	Chr1: 14109294	3.8	0.9690	−32.6	0.0004	Maintains muscle stem cells in a quiescent state. Aids stem cell self-renewal [56].
	Chr1: 14109300	4.2	0.9690	−28.9	0.0041
LRP5	Chr11: 68139919	0.5	0.9690	5.0	0.0006	Canonical Wnt signalling through LRP5 permits the regenerative capacity of mammary epithelial stem cells [57].
	Chr11: 68141102	0.1	0.9690	32.3	0.0094
	Chr11: 68141123	4.0	0.9690	36.7	0.0005
	Chr11: 68097308	6.2	0.9363	−33.4	0.0026
	Chr11: 68097314	3.9	0.9690	−31.6	0.0029
	Chr11: 68153864	20.8	0.7617	−37.6	0.0002
TPT1	Chr13: 45914874	34.1	<0.0001	35.4	<0.0001	Enhances Oct4 and Nanog expression in embryonic stem cells [42].
	Chr13: 45914880	34.7	<0.0001	35.5	<0.0001
RCC1	Chr1: 28845226	14.1	0.0039	14.1	0.0002	Critical cell cycle regulator involved in the S-phase of mitosis [58].
	Chr1: 28845238	14.1	0.0042	13.2	0.0028
PMF1	Chr1: 156186626	10.6	0.0003	8.3	0.0021	Regulates transcription of genes involved in cell growth and cell death [59].
	Chr1: 156186325	−5.0	<0.0001	8.3	0.0021
	Chr1: 156186433	−2.8	0.0004	−1.2	0.3362
	Chr1: 156186383	−0.1	0.9690	1.6	0.0070
	Chr1: 156186392	−0.7	0.9193	2.3	<0.0001
	Chr1: 156186393	−0.2	0.9690	1.6	0.0008
	Chr1: 156186496	−1.1	0.9193	3.1	0.00123
B4GALT6	Chr18: 29265352	11.3	0.0088	10.3	0.0220	Required for normal proliferation and differentiation of epithelial cells. Murine knockout models show growth retardation and premature fetal death [60].
MAPK11	Chr22: 50717438	−34.5	0.0086	9.7	0.7256	Required for cytotrophoblast differentiation to syncytiotrophoblast. Inhibition enhances cytotrophoblast proliferation [61].
DHX34	Chr19: 47852601	17.6	<0.0001	17.6	<0.0001	Involved in nonsense-mediated mRNA decay, a process important for stem cell differentiation [62].
	Chr19: 47852604	17.2	<0.0001	17.2	<0.0001
	Chr19: 47852629	18.2	<0.0001	18.2	<0.0001
MDM4	Chr1: 204537885	17.0	0.9193	−41.1	0.0010	Promotes cell proliferation though inhibition of the p53 pathway [63].
	Chr1: 204537886	0.7	0.9680	−57.2	<0.0001
	Chr1: 204537940	−1.9	0.9690	−30.5	0.0022
HOXB1	Chr17: 46570458	−0.6	0.9690	−28.6	0.0031	Mediates neural stem and progenitor proliferation and differentiation [64].
DCAF12L1	ChrX:125715240	−3.6	<0.0001	−1.2	0.3769	Expressed in murine TSC and is dcaf12L is down-regulated upon Elf5 depletion [34].
	ChrX:125715250	−3.7	<0.0001	−1.5	0.1722
	ChrX:125715261	−3.0	0.0002	−2.6	0.0003
	ChrX:125715276	−3.0	0.0002	−2.5	0.0007
	ChrX:125715286	−3.0	0.0004	−2.1	0.0011
	ChrX: 125715243	−2.1	0.0272	−2.7	<0.0001
	ChrX: 125715281	−1.0	0.9193	−2.1	0.0011
STAB1	Chr3: 52520822	4.9	0.9690	−35.1	0.0006	Required for rat TSC self-renewal and maintenance [35].