Zfp57 inactivation illustrates the relationship between DNA methylation and imprinted gene expression in mouse neural precursor cells

ZFP57 interacts with the germline-derived differentially methylated regions (DMRs) of imprinted genes, and is required to maintain DMR methylation in mouse embryonic stem cells (ESCs). Although DNA methylation has a key role in maintaining genomic imprinting, several imprinted genes are controlled by different mechanisms, and a comprehensive study of the relationship between DMR methylation and imprinted gene expression is lacking. To address this issue, we differentiated wild-type and Zfp57 -/- hybrid mouse ESCs into neural precursor cells (NPCs) and evaluated allelic expression of imprinted genes. In Zfp57-mutant NPCs, we observed loss of allelic bias of all the 35 genes that were imprinted in wild-type cells, demonstrating that Zfp57-dependent methylation is required to globally maintain gene expression imprinting. Analysis of bulk expression showed that most of the genes expressed from the non-methylated chromosome were up-regulated, and most of those expressed from the methylated chromosome were down-regulated in mutant cells, but also that several other imprinted genes acquiring biallelic expression were not significantly affected, suggesting the existence of compensatory mechanisms that control their RNA level. Since neuronal differentiation was impaired in Zfp57-mutant cells, this study also indicates that deregulation of imprinted genes and/or other ZFP57-target non-imprinted genes is incompatible with proper neurogenesis. RNA-Seq profiles of Neuronal Progenitor Cells differentiated from WT hybrid JB1 cells ( mESCs) and Zfp57-/- line using Illumina HiSeq 2500 platform in two replicates.The presence of SNPs allowed the analysis of allele specific expression genome-wide.