We asked whether DMRs that distinguish B-iPSC from fESC might allow us to identify their hematopoietic lineage of origin. In a separate CHARM experiment 25, we examined genome-wide methylation in highly purified multipotent and lineage-specific hematopoietic progenitors. Comparing DMRs in B-iPSC to those that define hematopoietic progenitors, we observed that B-iPSC cluster alongside Common Myeloid Progenitors (CMP) and distant from Common Lymphoid Progenitors (CLP; Supplementary Fig. 4a and Supplementary Table 4), which is notable given that B-iPSC were derived from Kit+, lineage-negative myeloid marrow precursors. Next, we asked whether the tissue of origin (bone marrow vs fibroblast) could be identified by the methylation state of tissue specific DMRs in F-iPSC, B-iPSC, and Bl-iPSC (a B lymphocyte-derived iPSC line described below). Using DMRs that distinguish fibroblast and bone marrow, and examining methylation in iPSCs and somatic cells from two different genetic backgrounds (B6CBA and B6129), we found that F-iPSC cluster alongside fibroblasts, and distant from bone marrow (Supplementary Fig. 4b). Similarly, the hematopoietic-derived B-iPSC and Bl-iPSC grouped with somatic cells from bone marrow. Thus, residual methylation indicates the tissue of origin of iPSC, and for blood-derivatives even their precise lineage, further supporting the phenomenon of epigenetic memory in iPSC.
