Lineage-Specific Gene Expression and DNA Methylation During in vitro Hepatogenesis

Hepatocytes differentiated from human embryonic stem cells have a great potential for the treatment of liver disease as well as drug testing. Moreover, in vitro hepatogenesis is a powerful tool for analyzing the molecular mechanisms underlying liver development. DNA methylation is an important epigenetic mechanism, which influences the differential gene expression during embryonic development. We profiled gene expression and DNA methylation of three states of in vitro hepatogenesis including human embryonic stem cells, endoderm progenitors, and mature hepatocytes using microarray analysis. Among 525 state specific expressed genes, 67 genes showed significant negative correlation between gene expression and DNA methylation. State specific expression and methylation of target genes were validated by quantitative reverse transcription–PCR and pyrosequencing, respectively. To elucidate genome-scale methylation change beyond promoter, we also performed methylated DNA enrichment sequencing. We found dynamic change of methylation in intergenic region of human genome during the differentiation. Our study allowed identification of methylation markers which can be applied to developing standardized protocols of in vitro hepatogenesis and should facilitate searching the molecular mechanisms underlying liver development.