Local DNA Demethylation Defines HNF4A Promoter Choice During Hepatocyte Differentiation

Hector HERNANDEZ-VARGAS, International Agency for Research on Cancer (IARC), France
HERNANDEZ-VARGAS H. 1 , ANCEY P. 1 , ECSEDI S. 1 , LAMBERT M. 2 , CROS M. 1 , HERCEG Z. 1

1 Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
2 INSERM U1052, Centre de Recherche en CancÚrologie de Lyon, Lyon, France

​Background:
Hepatocellular carcinoma (HCC) is commonly preceded by a chronic disease leading to damage of the liver architecture. During liver injury, hepatic progenitor cells (HPCs) are essential for tissue regeneration through an activation process called “ductular reaction”. Interestingly, poorly differentiated hepatocytes are observed in inflammatory hepatitis and the degree of HPCs’ activation is correlated with the degree of inflammation. Because of its role in determining cellular fate, DNA methylation may have an important function during the process of HPC differentiation. 
Results:
To understand the role of DNA methylation during hepatocyte differentiation, we profiled approximately 450k methylation sites at different time points in the progression from progenitor to hepatocyte stages using the bipotent liver progenitor HepaRG cell line. The top most significant differentially methylated region (DMR) was the P1 promoter of HNF4A, a master transcription factor of hepatocyte differentiation. Progressive demethylation of HNF4A P1 was highly correlated with increased expression of P1-dependent isoforms of HNF4A. Gene expression of the TET1 and TET2 demethylases was increased during the early transition towards differentiation. Moreover, TET1 was significantly enriched during this transition at the HNF4A DMR locus, and proximal ligation assays revealed the colocalization of the pioneer hepatocyte transcription factor FOXA2 and TET1 demethylase during differentiation.
Conclusion:
These data supports a model where liver progenitors are poised for targeted demethylation at specific genomic locations involved in terminal stages of hepatocyte differentiation. In addition, intragenic methylation may have a role in controlling cellular programs through isoform switching with a potential role of TETs enzymes in this process.