ABSTRACT
Following erasure in the blastocyst, the entire genome undergoes de novo methylation at the time of implantation, with CpG islands being protected from this process. This bimodal pattern is then preserved throughout development and the lifetime of the organism. Using mouse embryonic stem cells as a model system, we demonstrate that the binding of an RNA polymerase complex on DNA before de novo methylation is predictive of it being protected from this modification, and tethering experiments demonstrate that the presence of this complex is, in fact, sufficient to prevent methylation at these sites. This protection is most likely mediated by the recruitment of enzyme complexes that methylate histone H3K4 over a local region and, in this way, prevent access to the de novo methylation complex. The topological pattern of H3K4me3 that is formed while the DNA is as yet unmethylated provides a strikingly accurate template for modeling the genome-wide basal methylation pattern of the organism. These results have far-reaching consequences for understanding the relationship between RNA transcription and DNA methylation.
Subject(s)
Blastocyst Inner Cell Mass/metabolism , DNA Methylation , Embryo, Mammalian/metabolism , Gene Expression Regulation, Developmental , Histones/metabolism , Transcription, Genetic , Animals , Blastocyst Inner Cell Mass/cytology , CpG Islands , DNA-Directed RNA Polymerases/metabolism , Embryo, Mammalian/cytology , Mice , Mice, Transgenic , Transcription Factors/metabolismABSTRACT
Fragile X syndrome is the most frequent cause of inherited intellectual disability. The primary molecular defect in this disease is the expansion of a CGG repeat in the 5' region of the fragile X mental retardation1 (FMR1) gene, leading to de novo methylation of the promoter and inactivation of this otherwise normal gene, but little is known about how these epigenetic changes occur during development. In order to gain insight into the nature of this process, we have used cell fusion technology to recapitulate the events that occur during early embryogenesis. These experiments suggest that the naturally occurring Fragile XFMR1 5' region undergoes inactivation post implantation in a Dicer/Ago-dependent targeted process which involves local SUV39H-mediated tri-methylation of histone H3K9. It thus appears that Fragile X syndrome may come about through inadvertent siRNA-mediated heterochromatinization.
Subject(s)
DNA Methylation , Epigenesis, Genetic , Fragile X Mental Retardation Protein/genetics , Fragile X Syndrome/genetics , Gene Expression Regulation, Developmental , 5' Untranslated Regions , Animals , Cell Differentiation , Embryonic Development , Embryonic Stem Cells/metabolism , Fibroblasts/metabolism , Heterochromatin/chemistry , Histones/metabolism , Humans , Mice , Nerve Tissue Proteins/genetics , Phenotype , Promoter Regions, Genetic , RNA/metabolism , RNA Interference , RNA, Small Interfering/metabolismABSTRACT
After erasure in the early animal embryo, a new bimodal DNA methylation pattern is regenerated at implantation. We have identified a demethylation pathway in mouse embryonic cells that uses hydroxymethylation (Tet1), deamination (Aid), glycosylation (Mbd4) and excision repair (Gadd45a) genes. Surprisingly, this demethylation system is not necessary for generating the overall bimodal methylation pattern but does appear to be involved in resetting methylation patterns during somatic-cell reprogramming.
Subject(s)
DNA Methylation , Embryonic Stem Cells/metabolism , Amination , Animals , DNA Repair/genetics , MiceABSTRACT
The human beta-globin genes constitute a large chromosomal domain that is developmentally regulated. In nonerythroid cells, these genes replicate late in S phase, while in erythroid cells, replication is early. The replication origin is packaged with acetylated histones in erythroid cells, yet is associated with deacetylated histones in nonerythroid cells. Recruitment of histone acetylases to this origin brings about a transcription-independent shift to early replication in lymphocytes. In contrast, tethering of a histone deacetylase in erythroblasts causes a shift to late replication. These results suggest that histone modification at the origin serves as a binary switch for controlling replication timing.