Regulation of Liver Regeneration by UHRF1

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Project Summary The remarkable regenerative potential of the liver in young mammals is due to the ability of quiescent hepatocytes to nimbly respond to mitogenic signals. This relies on a well-coordinated gene regulatory program, which we propose is embedded in the hepatic epigenome. The epigenome serves dual roles in regulating gene expression and in protecting cells from the threat of transposable elements (TEs), which if unleashed can cause DNA damage and genomic instability. A complex combination of epigenetic marks organizes the genome into regions (i.e. chromatin states) which dictate which regions stay open and which stay closed. Closed chromatin states encompass silenced genes and most TEs. Open chromatin states contain actively transcribed genes as well as genes held in a poised configuration in anticipation of signals that alter their expression to change cellular function or identity. We discovered that genes that promote liver regeneration are poised in quiescent livers, with repressive (H3K27me3) and activating (H3K4me3) marks. Since H3K27me3 was lost on these genes during regeneration, we conclude this is a key element of the epigenetic code that confers regenerative potential to young livers. We uncovered a surprising flexibility in this code through studying the epigenetic regulator, UHRF1, which is essential for maintaining DNA methylation during DNA replication. We found that Uhrf1 loss in hepatocytes (Uhrf1HepKO) resulted in global DNA hypomethylation, but did not activate TEs. We attributed this to epigenetic compensation by H3K27me3, which became enriched on hypomethylated TEs and depleted from promoters in Uhrf1HepKO mice, with a concomitant premature activation of pro-regenerative genes and accelerated liver regeneration in these mice. Our central hypothesis is that the youthful epigenetic code permits transcription factor access to pro-regenerative genes while restricting access to TEs, and that this code is rewritten during aging, resulting in TE activation and regenerative decline. We further hypothesize that UHRF1 and H3K27me3 are key elements of this code. To test this, we will identify the molecular mechanisms of epigenetic compensation in young Uhrf1HepKO livers and will examine the role of H3K27me3 in pro- regenerative genes regulation in wild type livers (Aim 1). By Integrating epigenomic and transcriptomic profiling of aged mouse and human livers compared to chromatin states in young livers, we will establish how aging repatterns the hepatic epigenome to repress pro-regenerative genes and activate TEs (Aim 2). In Aim 3, we explore whether depleting H3K27me3 can rejuvenate the liver. Together, the outcomes of this work will uncover how the dual roles of the epigenome – gene regulation and suppression of transposon threat – are integrated in regulating liver regeneration in young mice and will provide a foundation to manipulate the epigenome to augment regenerative potential in the elderly and those suffering from liver failure.