Table 2 Identification of TF motifs present in gametic DMRs of paternally hypomethylated nonimprinted genes
DMRMotif IDOccurrencesTF NameTF Expression in Primordial Germ Cells, Spermatogonia, and OogoniaMotifs Shared with Promoters Active in Male Germ Cells (for TFs Not Detected)Motifs Shared with Imprinted Gametic DMRs
Shank2MA0513.11Smad2+
MA0092.11Hand1++
MA0139.11Ctcf++
MA0024.21E2f1++
MA0145.21Tcfcp2l1
MA0598.11Ehf+
MA0506.11Nrf1++
MA0048.12Nhlh1++
Ankrd36MA0513.11Smad2+
MA0040.11Foxq1
MA0066.11Pparg+
MA0024.21E2f1++
MA0041.11Foxd3
MA0163.11Plag1++
MA0500.12Myog+
MA0048.11Nhlh1++
MA0524.11Tfap2c
MA0146.21Zfx++
MA0521.12Tcf12++
MA0484.11Hnf4g
MA0030.11Foxf2
MA0114.21Hnf4a
MA0525.13Tp63+
MA0106.21Tp53+
Arid1bMA0469.11E2f3++
MA0599.11Klf5++
MA0506.11Nrf1++
MA0024.21E2f1++
MA0495.11Maff+
MA0470.11E2f4++
MA0039.21Klf4++
MA0154.21Ebf1+
MA0146.22Zfx++
MA0471.11E2f6++
MA0048.12Nhlh1++
MA0496.11Mafk
MA0493.11Klf1
MA0079.31Sp1++
  • Many nonimprinted regions are methylated specifically in oocytes, but not in sperm, thus qualifying as gametic DMRs (Smallwood et al. 2011; Wang et al. 2014). In contrast to imprinted DMRs, they lose their methylation after fertilization. We selected DMRs associated with three nonimprinted genes, Shank2, Ankrd36, and Arid1b (sequences analyzed in Table S6). We identified 33 motifs in these regions, 17 (51%) of which are shared with motifs present in imprinted DMRs. This suggests that imprinted and nonimprinted DMRs may be protected from methylation by some of the same TFs.