Genome-wide 5-hydroxymethylcytosine (5hmC) emerges at early stage of in vitro hepatocyte differentiation

Abstract

How cells reach different fates despite using the same DNA template, is a basic question linked to differential patterns of gene expression. Since 5-hydroxymethylcytosine (5hmC) emerged as an intermediate metabolite in active DNA demethylation, there have been increasing efforts to elucidate its function as a stable modification of the genome, including a role in establishing such tissue-specific patterns of expression. Recently we described TET1-mediated enrichment of 5hmC on the promoter region of the master regulator of hepatocyte identity, HNF4A, which precedes differentiation of liver adult progenitor cells in vitro. Here we asked whether 5hmC is involved in hepatocyte differentiation. We found a genome-wide increase of 5hmC as well as a reduction of 5-methylcytosine at early hepatocyte differentiation, a time when the liver transcript program is already established. Furthermore, we suggest that modifying sadenosylmethionine (SAM) levels through an adenosine derivative could decrease 5hmC enrichment, triggering an impaired acquisition of hepatic identity markers. These results suggest that 5hmC is a regulator of differentiation as well as an imprint related with cell identity.Furthermore, 5hmC modulation could be a useful biomarker in conditions associated with cell de-differentiation such as liver malignancies. Abstract It has been suggested that 5hydroxymethylcytosine (5hmC) is an imprint of cell identity. Here we show that commitment to a hepatocyte transcriptional program is characterized by a demethylation process and emergence of 5hmC at multiple genomic locations. Cells exposed to an adenosine derivative during differentiation did not reach such 5hmC levels, and this was associated with a lower expression of hepatocytemarkers. These results suggest that 5hmC enrichment is an important step on the road to hepatocyte cell fate.

Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity after de novo assembly of native full-length hepatitis B virus genomes

“…That being said, the study of epigenetics is still in its infancy. Recently we found that levels of 5hmC in gene bodies in differentiating hepatocytes is highly correlated with the expression of those genes [ 33 ]. Thus, there is still a lot more to discover regarding the function of modified bases.…”