CTCF-Dependent Chromatin Bias Constitutes Transient Epigenetic Memory of the Mother at the H19-Igf2 Imprinting Control Region in Prospermatogonia

Abstract

Genomic imprints—parental allele-specific DNA methylation marks at the differentially methylated regions (DMRs) of imprinted genes—are erased and reestablished in germ cells according to the individual's sex. Imprint establishment at paternally methylated germ line DMRs occurs in fetal male germ cells. In prospermatogonia, the two unmethylated alleles exhibit different rates of de novo methylation at the H19/Igf2 imprinting control region (ICR) depending on parental origin. We investigated the nature of this epigenetic memory using bisulfite sequencing and allele-specific ChIP–SNuPE assays. We found that the chromatin composition in fetal germ cells was biased at the ICR between the two alleles with the maternally inherited allele exhibiting more H3K4me3 and less H3K9me3 than the paternally inherited allele. We determined genetically that the chromatin bias, and also the delayed methylation establishment in the maternal allele, depended on functional CTCF insulator binding sites in the ICR. Our data suggest that, in primordial germ cells, maternally inherited allele-specific CTCF binding sets up allele-specific chromatin differences at the ICR. The erasure of these allele-specific chromatin marks is not complete before the process of de novo methylation imprint establishment begins. CTCF–dependent allele-specific chromatin composition imposes a maternal allele-specific delay on de novo methylation imprint establishment at the H19/Igf2 ICR in prospermatogonia.

Humanized H19/Igf2 locus reveals diverged imprinting mechanism between mouse and human and reflects Silver–Russell syndrome phenotypes

“…Consequently, the establishment of DNA methylation at hIC1 is inhibited. This finding adds to the growing consensus that H3K4 methylation marks are inhibitory to de novo DNA methylation in the germ line, whereas repressive histone marks do not play major role in the establishment of methylation at ICRs (14,(16)(17)(18)20). However, it is equally possible that the hypomethylated state of DNA attracts H3K4me2 at hIC1 by an unknown mechanism.…”

“…To investigate factors that may inhibit complete establishment of DNA methylation at hIC1 during spermatogenesis, we examined histone posttranslational modifications at hIC1. Parental allelespecific histone modifications have been described at mIC1 in both somatic and germ cells (14)(15)(16)(17)(18). Several studies have suggested an antagonistic relationship between "activating marks," such as dimethylation and trimethylation of histone H3 at lysine 4 (H3K4me2 and H3K4me3, respectively), and DNA methylation (17)(18)(19)(20).…”

Cross-talk between Site-specific Transcription Factors and DNA Methylation States

“…CTCF has also been shown to block methylation of a bound region (27,28). CTCF binds the Igf2/H19 imprinting control region and acts as a boundary element for the control of imprinted expression of maternal and paternal copies of Igf2 and H19 genes (29,30). Schoenherr et al (27) showed that introducing mutations at the four CTCF-binding sites within the imprinting control region resulted in loss of CTCF binding and a substantial increase in methylation.…”

The Role of CCCTC-Binding Factor (CTCF) in Genomic Imprinting, Development, and Reproduction1

“…During mouse spermatogenesis, the paternal-specific methylation pattern is acquired by the maternal H19 allele concomitantly with activation of Boris, and this allele is largely unmethylated while interacting with BORIS [99]. Moreover, in the prospermatogonial stage, both unmethylated H19/Igf2 alleles show different rates of de novo methylation, with the maternal allele presenting a CTCF-dependent delay in gain of methylation [100]. Unlike oocyte chromatin, the haploid nucleosomal chromatin of sperm is repackaged, exchanging histones for small basic protamines, and thus generating highly compact toroidal chromatin essential to sperm function [101,102].…”