Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA.
Cell (Impact Factor: 32.24). 02/2012; 148(4):816-31. DOI: 10.1016/j.cell.2011.12.035
Source: PubMed


Differential methylation of the two parental genomes in placental mammals is essential for genomic imprinting and embryogenesis. To systematically study this epigenetic process, we have generated a base-resolution, allele-specific DNA methylation (ASM) map in the mouse genome. We find parent-of-origin dependent (imprinted) ASM at 1,952 CG dinucleotides. These imprinted CGs form 55 discrete clusters including virtually all known germline differentially methylated regions (DMRs) and 23 previously unknown DMRs, with some occurring at microRNA genes. We also identify sequence-dependent ASM at 131,765 CGs. Interestingly, methylation at these sites exhibits a strong dependence on the immediate adjacent bases, allowing us to define a conserved sequence preference for the mammalian DNA methylation machinery. Finally, we report a surprising presence of non-CG methylation in the adult mouse brain, with some showing evidence of imprinting. Our results provide a resource for understanding the mechanisms of imprinting and allele-specific gene expression in mammalian cells.

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    • "DNA methylation is an epigenetic mark that has traditionally been regarded as a very stable modification of the genome. It occurs mainly at cytosines located on CpG dinucleotides although there is now evidence of significant amounts of cytosine methylation occurring in different contexts (mainly at CpA) in oocytes, embryonic stem cells and in neurons [46] [47] [63] [84]. DNA methylation is known to be involved in several cellular and molecular mechanisms such as control of gene transcription, establishment of cellular identity, silencing of transposon elements, parental imprinting, X-chromosome inactivation and carcinogenesis [3]. "
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    ABSTRACT: Epigenetic modifications of the genome play important roles in controlling gene transcription thus regulating several molecular and cellular processes. A novel epigenetic modification -5-hydroxymethylcytosine (5hmC) – has been recently described and attracted a lot of attention due to its possible involvement in the active DNA demethylation mechanism. TET enzymes are dioxygenases capable of oxidizing the methyl group of 5-methylcytosines (5mC) and thus converting 5mC into 5hmC. Although most of the work on TET enzymes and 5hmC has been carried out in embryonic stem (ES) cells, the highest levels of 5hmC occur in the brain and in neurons, pointing to a role for this epigenetic modification in the control of neuronal differentiation, neural plasticity and brain functions. Here we review the most recent advances on the role of TET enzymes and DNA hydroxymethylation in neuronal differentiation and function.
    Genomics 11/2014; 104(5). DOI:10.1016/j.ygeno.2014.08.018 · 2.28 Impact Factor
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    • "However, they did not directly examine active demethylation in one-cell stage pronuclei or look at the functional role of Tet3 or TDG in this process. Their raw data on the maternal genome also show low levels of overall methylation at maternally imprinted alleles relative to other reports (around 75% versus around 95% expected) (Kobayashi et al., 2012; Xie et al., 2012) and the existence of unexpectedly high levels of methylation at paternally imprinted alleles (15%–46% versus around 5%), raising the possibility that there was significant contamination of the oocyte and two-cell embryo samples used with a somatic DNA source such as cumulus cells. Crucially, we demonstrate an active demethylation process that requires Tet3-mediated oxidation and encompasses the conversion of 5mC to unmodified cytosine. "
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    ABSTRACT: The epigenomes of mammalian sperm and oocytes, characterized by gamete-specific 5-methylcytosine (5mC) patterns, are reprogrammed during early embryogenesis to establish full developmental potential. Previous studies have suggested that the paternal genome is actively demethylated in the zygote while the maternal genome undergoes subsequent passive demethylation via DNA replication during cleavage. Active demethylation is known to depend on 5mC oxidation by Tet dioxygenases and excision of oxidized bases by thymine DNA glycosylase (TDG). Here we show that both maternal and paternal genomes undergo widespread active and passive demethylation in zygotes before the first mitotic division. Passive demethylation was blocked by the replication inhibitor aphidicolin, and active demethylation was abrogated by deletion of Tet3 in both pronuclei. At actively demethylated loci, 5mCs were processed to unmodified cytosines. Surprisingly, the demethylation process was unaffected by the deletion of TDG from the zygote, suggesting the existence of other demethylation mechanisms downstream of Tet3-mediated oxidation.
    Cell Stem Cell 10/2014; 15(4):447-458. DOI:10.1016/j.stem.2014.08.003 · 22.27 Impact Factor
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    • "Using this recently developed computational procedure [13], we identified an average of 2,266 variable CpG sites per individual that exhibited significant difference in allelic methylation based on genomic factors (methylation difference >0.2). Consistent with previous observations [12], [13], [23], most ASM events were due to SNPs present directly at CpG sites, (69.7%–92.5%, average 86.4%), with non-SNP CpG sites representing a very small fraction of putative genome-methylome interaction (Figure S3a, S3b in File S1). "
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    ABSTRACT: Genetic polymorphisms can shape the global landscape of DNA methylation, by either changing substrates for DNA methyltransferases or altering the DNA binding affinity of cis-regulatory proteins. The interactions between CpG methylation and genetic polymorphisms have been previously investigated by methylation quantitative trait loci (mQTL) and allele-specific methylation (ASM) analysis. However, it remains unclear whether these approaches can effectively and comprehensively identify all genetic variants that contribute to the inter-individual variation of DNA methylation levels. Here we used three independent approaches to systematically investigate the influence of genetic polymorphisms on variability in DNA methylation by characterizing the methylation state of 96 whole blood samples in 52 parent-child trios from 22 nuclear pedigrees. We performed targeted bisulfite sequencing with padlock probes to quantify the absolute DNA methylation levels at a set of 411,800 CpG sites in the human genome. With mid-parent offspring analysis (MPO), we identified 10,593 CpG sites that exhibited heritable methylation patterns, among which 70.1% were SNPs directly present in methylated CpG dinucleotides. We determined the mQTL analysis identified 49.9% of heritable CpG sites for which regulation occurred in a distal cis-regulatory manner, and that ASM analysis was only able to identify 5%. Finally, we identified hundreds of clusters in the human genome for which the degree of variation of CpG methylation, as opposed to whether or not CpG sites were methylated, was associated with genetic polymorphisms, supporting a recent hypothesis on the genetic influence of phenotypic plasticity. These results show that cis-regulatory SNPs identified by mQTL do not comprise the full extent of heritable CpG methylation, and that ASM appears overall unreliable. Overall, the extent of genome-methylome interactions is well beyond what is detectible with the commonly used mQTL and ASM approaches, and is likely to include effects on plasticity.
    PLoS ONE 07/2014; 9(7):e99313. DOI:10.1371/journal.pone.0099313 · 3.23 Impact Factor
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