In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

Abstract

SummaryThe maintenance of H3K9 and DNA methylation at imprinting control regions (ICRs) during early embryogenesis is key to the regulation of imprinted genes. Here, we reveal that ZFP57, its cofactor KAP1, and associated effectors bind selectively to the H3K9me3-bearing, DNA-methylated allele of ICRs in ES cells. KAP1 deletion induces a loss of heterochromatin marks at ICRs, whereas deleting ZFP57 or DNMTs leads to ICR DNA demethylation. Accordingly, we find that ZFP57 and KAP1 associated with DNMTs and hemimethylated DNA-binding NP95. Finally, we identify the methylated TGCCGC hexanucleotide as the motif that is recognized by ZFP57 in all ICRs and in several tens of additional loci, several of which are at least ZFP57-dependently methylated in ES cells. These results significantly advance our understanding of imprinting and suggest a general mechanism for the protection of specific loci against the wave of DNA demethylation that affects the mammalian genome during early embryogenesis.

The stem cell transcription factor ZFP57 induces IGF2 expression to promote anchorage-independent growth in cancer cells

“…Imprinting of IGF2 is 15 regulated at the IGF2-H19 ICR, and ZFP57 binds to this region in ES cells. 27 In this study, we also observed the binding of ZFP57 to the IGF2-H19 ICR in HT1080 cells.…”

“…26 Several reports have suggested that this transcription factor binds to KRAB-associated protein 1 (KAP1), a scaffold protein for various heterochromatin-inducing factors, through its KRAB domain, and is involved in genome imprinting by recruiting KAP1 to several ICRs. 26,27,33 In addition, mutations in the ZFP57 gene result in transient neonatal diabetes mellitus type 1, possibly through Plagl1 overexpression. 34,35 The role of ZFP57 in tumorigenesis has not been elucidated yet.…”

“…In embryo and ES cells, Zfp57 regulates the expression of a variety of imprinted genes. 26,27 Among imprinted genes, IGF2 is involved in tumorigenesis in various cancers. 28,29 We therefore explored the possibility that IGF2 may be a downstream gene of ZFP57 in HT1080 cells.…”

“…Based on previous reports showing binding of ZFP57 to the imprinting control region (ICR) of IGF2-H19 in ES cells, 27 we first examined whether the same was true in HT1080 cells. ChIP analysis revealed that ZFP57 binds to the region containing the ZFP57-binding motif within the IGF2-H19 ICR in HT1080 cells (Figure 3a).…”

Characterization of multi-locus imprinting disturbances and underlying genetic defects in patients with chromosome 11p15.5 related imprinting disorders

“…Mutations in genes encoding members of the zinc-finger protein family have been considered good candidates as causative defects of MLID, given the well-established role of ZFP57 mutation in patients with transient neonatal diabetes mellitus and MLID [26,27]. However, no mutations have been found to date in other members of the protein family in MLID patients.…”