Comparison of DNA methylation profiles in human fetal and adult red blood cell progenitors

Table 1 Enrichment of transcription factor binding sites (TFBS) near differentially methylated CpGs

Motif name	Consensus	P value	q -value	Fold enrichment
TFBS enriched near CpGs hypomethylated in fetal erythroblasts
SOX2	BCCATTGTTC	1.0 × 10⁻¹³	0	1.5
TCF3	ASWTCAAAGG	1.0 × 10⁻⁸	0	1.8
REST-NRSF	GGMGCTGTCCATGGTGCTGA	1.0 × 10⁻⁸	0	5.5
SOX6	CCATTGTTNY	1.0 × 10⁻⁸	0	1.3
GATA1	AGATGKDGAGATAAG	1.0 × 10⁻⁵	0.0001	2.4
MAZ	GGGGGGGG	1.0 × 10⁻⁵	0.0002	1.1
TCF4	ASATCAAAGGVA	1.0 × 10⁻⁵	0.0002	1.4
FOXA1	WAAGTAAACA	1.0 × 10⁻⁵	0.0002	1.3
HNF6	NTATYGATCH	1.0 × 10⁻⁴	0.0004	1.4
TCFL2	ACWTCAAAGG	1.0 × 10⁻⁴	0.0005	1.9
TFBS enriched near CpGs hypomethylated in adult erythroblasts
NF1	CYTGGCABNSTGCCAR	1.0 × 10⁻²¹¹	0	3.9
IRF2	GAAASYGAAASY	1.0 × 10⁻⁷⁸	0	7.3
TLX/NR2E1	CTGGCAGSCTGCCA	1.0 × 10⁻⁷⁶	0	2.4
NF1-halfsite	YTGCCAAG	1.0 × 10⁻⁵⁶	0	1.4
ISRE	AGTTTCASTTTC	1.0 × 10⁻⁵⁴	0	7.5
BACH1	AWWNTGCTGAGTCAT	1.0 × 10⁻⁴²	0	6.4
RUNX1	AAACCACARM	1.0 × 10⁻³⁷	0	1.6
RUNX2	NWAACCACADNN	1.0 × 10⁻³⁶	0	1.7
NRF2	HTGCTGAGTCAT	1.0 × 10⁻³⁶	0	5.8
c-JUN	GATGASTCATCN	1.0 × 10⁻³³	0	2.3

For these analyses, we used the HOMER software and analyzed TFBS located near CpGs (±200 base pairs) that are hypomethylated in fetal or adult erythroblasts. The top 10 enriched motifs are shown here for each cell type; see Additional file 1: Tables S6-S7 for the complete list of significant TFBS. We calculated q-values using the Benjamini-Hochberg method. We calculated the fold enrichment by comparing the number of hypomethylated CpGs near a given TFBS in fetal and adult erythroblasts. The consensus motif follows the IUPAC nomenclature when more than one base is possible.

ISSN: 1756-994X