We compared DMRs in iPSCs with high hematopotietic potential (B-NP-iPSC and NP-iPSC-TSA-AZA) to those with low hematopoietic potential (NP-iPSC and NSC-NP-iPSC), and found that B-NP-iPSC and NP-iPSC-TSA-AZA harbored higher gene-body methylation of Wnt3 (Supplementary Fig. 12), a gene which along with its homologue Wnt3a plays a major role in blood development from fESC36. The blood-deficient NP-iPSC and NSC-NP-iPSC lines lacked gene body methylation. While promoter methylation is repressive, gene body methylation is seen in active genes37. When iPSC were differentiated into embryoid bodies, the blood-prone NP-iPSC-TSA-AZA showed higher levels of Wnt3/3a expression than the blood-deficient NP-iPSC (Supplementary Fig. 13a). Interestingly, supplementation of the culture media with Wnt3a during embryoid body differentiation restored blood-forming potential in the blood-deficient NP-iPSC and NSC-NP-iPSC lines, but had little effect on the already robust hematopoietic potential of B-NP-iPSC (Supplementary Fig. 13b). Albeit preliminary, these data correlate differential gene body methylation and expression of the Wnt3 locus with enhanced blood-forming potential in iPSC lines.
