The Dnmt1 Intrinsically Disordered Domain Regulates Genomic Methylation During Development

Abstract

The DNMT1 cytosine methyltransferase enzyme contains a large 300-aa intrinsically disordered domain (IDD) that we previously showed regulated DNA methylation patterns in mouse ES cells. Here we generated seven mouse lines with different mutations in the IDD. Homozygous mutant mice of five lines developed normally, with normal levels of methylation on both imprinted and nonimprinted DNA sequences. The other two lines, however, had alterations in imprinted and/or nonimprinted (global) DNA methylation appearing during embryonic development. Embryos of one line expressing a DNMT1 variant containing a 6-aa rat orthologous sequence in the IDD maintained imprinted methylation, showed very reduced levels of global methylation and occasionally completed fetal development. These in vivo studies demonstrate that at least two DNMT1-dependent methylation processes can be distinguished during fetal development. One process maintains the bulk of genomic methylation on nonimprinted sequences. The other process maintains methylation on a much smaller class of sequences including but not limited to gametic differentially methylated domains (gDMDs) that transmit essential imprinted parent-specific methylation for embryonic development.KEYWORDS DNA methylation; Dnmt1; genomic imprinting; intrinsically disordered protein; methyltransferase P ROFOUND increases and decreases in genomic methylation are seen during the reproductive cycle (Li 2002). The genomes of female and male germ cells gain enormous methylation, including maternal and paternal gDMD methylation as they differentiate from unmethylated primordial germ cells (,1% of CpG dinucleotides methylated) into mature gametes ( 70% sperm and 30% egg CpG methylation) (Li 2002;Peters 2014). During preimplantation, the parental genomes lose most of their global methylation yet retain gDMD methylation, resulting in blastocysts with ,10% of their CpGs methylated. After implantation, genomic methylation climbs rapidly as cells differentiate, rising to 60% methylated CpGs in early postimplantation embryos and peaking at 75% methylated CpGs in adult somatic cells.Changes in methylation are uneven across the genome; for example, during preimplantation, gDMD methylation is retained while global methylation falls sharply depending on the type of sequence element (Smith and Meissner 2013). Thus, at different times in development there are very different methylomes, or unique patterns of DNA methylation across the genome. The coincidence of shifts in the methylome and key developmental events suggest that methylome changes promote development.The importance of DNA methylation for normal development was shown in genetic studies. Targeted mutations of the Dnmt1 maintenance methyltransferase gene in mice have detrimental effects on development; homozygous Dnmt1-null embryos die soon after implantation with major structural abnormalities, complete loss of gametic differentially methylated domain (gDMD) methylation and 85% loss of global methylation (Li et al. 1992). Lesser phenotypic effe...

DNA Methylation in Embryo Development: Epigenetic Impact of ART (Assisted Reproductive Technologies)

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