Previous studies have shown differential regulation in the overall expression and, in some cases, the imprinting status of imprinted genes across body tissues and brain regions (Albrecht et al., 1997; Gregg et al., 2010; Prickett and Oakey, 2012).
With the sequence polymorphisms between the two parents, we were able to analyze the status of imprinted gene expression and observed that several imprinted genes lost imprinting or expression, along with the altered expression of two potential imprinting regulators, the PRC2 gene OsFIE2 and the MET1 ortholog OsMET1b in the parental genome unbalanced endosperm.
It has been demonstrated that epigenetic imprints are established during gametogenesis in a parent-specific manner [41] [43], and that the DNA methylation status of imprinted genes is erased and reset during PGC development [44], [45].
The somatic status of imprinted genes is progressively erased during PGC migration through the hindgut and dorsal mesentery in vivo [30], [44], [60], and in the mouse, imprinted genes are hypomethylated in germ cells by E13.5 [62], [62].
However, the methylation status of imprinted DMRs scattered through the human genome has yet to be analyzed comprehensively in hepatoblastoma.
Overall, our DNA methylation analyses indicate that macroH2A1 depletion did not cause any change in the DNA methylation status of imprinted domains.
We also note that the Methyl-Seq data recapitulated the methylation status of imprinted genes less precisely than the PBAT data (Fig. 2C).
Most studies that have examined the methylation status of imprinting genes in foetuses or placentas in animal models or in humans have associated epigenetic anomalies with adverse effects on embryonic development [ 65 ].
We inspected the methylation status of imprinted genes and found that the expected 50% methylation level was faithfully recapitulated, even in the library generated from 30 ng of DNA, but not in the library obtained from 10 ng of DNA (Fig. 2C).
Our aim was to determine associations between the imprinting status of both imprinting clusters (BWSIC1/2) and the tumor incidence and type.
