Non-germline Restoration of Genomic Imprinting for a Small Subset of Imprinted Genes in Ubiquitin-like PHD and RING Finger Domain-Containing 1 (Uhrf1) Null Mouse Embryonic Stem Cells [Gene Regulation]
April 21st, 2015 by Qi, S., Wang, Z., Li, P., Wu, Q., Shi, T., Li, J., Wong, J.
The underlying mechanism for the establishment and maintenance of differential DNA methylation in imprinted genes is largely unknown. Previous studies using Dnmt1 knockout ES cells demonstrated that, while re-expression of DNMT1 restored DNA methylation in the non-imprinted regions, the methylation patterns of imprinted genes could only be restored through germ-line passage. Knockout of Uhrf1, an accessory factor essential for DNMT1-mediated DNA methylation, in mouse ES cells also led to impaired global DNA methylation and loss of genomic imprinting. Here we demonstrated that, although re-expression of UHRF1 in Uhrf1-/- ES cells restored DNA methylation for the bulk genome but not for most of the imprinted genes, it did rescue DNA methylation for imprinted H19, Nnat and Dlk1 genes. Analysis of histone modifications at the differential methylated regions (DMRs) of the imprinting genes by chromatin immunoprecipitation (ChIP) assays revealed that for the imprinted genes whose DNA methylation could be restored upon re-expression of UHRF1, the active histone marks especially H3K4me3 were maintained at considerably low and maintained the low levels even in the Uhrf1-/- ES cells. In contrast, for the imprinted genes whose DNA methylation could not be restored upon UHRF1 re-expression, the active histone marks especially H3K4me3 were relatively high and became even higher in the Uhrf1-/- ES cells. Our study thus supports a role for histone modifications in determining the establishment of imprinting-related DNA methylation and demonstrates that mouse ES cells can be a valuable model for mechanistic study of establishment and maintenance of differential DNA methylation in imprinted genes.