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Cell Rep. 2013 Jul 11;4(1):205-19. doi: 10.1016/j.celrep.2013.06.004. Epub 2013 Jun 27.

De novo DNA methylation in the male germ line occurs by default but is excluded at sites of H3K4 methylation.

Author information

1
Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA.

Abstract

To understand what dictates the emerging patterns of de novo DNA methylation in the male germline, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells by using methylated CpG island recovery assay (MIRA)-chip, chromatin immunoprecipitation (ChIP)-chip, and strand-specific RNA deep sequencing, respectively. Global de novo methylation occurred by default in prospermatogonia without any apparent trigger from preexisting repressive chromatin marks but was preceded by broad, low-level transcription along the chromosomes, including the four known paternally imprinted differentially methylated regions (DMRs). Default methylation was excluded only at precisely aligned constitutive or emerging peaks of H3K4me2, including most CpG islands and some intracisternal A particles (IAPs). Similarly, each maternally imprinted DMR was protected from default DNA methylation among highly methylated DNA by an H3K4me2 peak and transcription initiation at least in one strand. Our results suggest that the pattern of de novo DNA methylation in prospermatogonia is dictated by opposing actions of broad, low-level transcription and dynamic patterns of active chromatin.

PMID:
23810559
PMCID:
PMC3740941
DOI:
10.1016/j.celrep.2013.06.004
[Indexed for MEDLINE]
Free PMC Article

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