Accumulation and loss of asymmetric non-CpG methylation during male germ-cell development

Abstract

DNA methylation is a well-characterized epigenetic modification involved in gene regulation and transposon silencing in mammals. It mainly occurs on cytosines at CpG sites but methylation at non-CpG sites is frequently observed in embryonic stem cells, induced pluriotent stem cells, oocytes and the brain. The biological significance of non-CpG methylation is unknown. Here, we show that non-CpG methylation is also present in male germ cells, within and around B1 retrotransposon sequences interspersed in the mouse genome. It accumulates in mitotically arrested fetal prospermatogonia and reaches the highest level by birth in a Dnmt3l-dependent manner. The preferential site of non-CpG methylation is CpA, especially CpApG and CpApC. Although CpApG (and CpTpG) sites contain cytosines at symmetrical positions, hairpin-bisulfite sequencing reveals that they are hemimethylated, suggesting the absence of a template-dependent copying mechanism. Indeed, the level of non-CpG methylation decreases after the resumption of mitosis in the neonatal period, whereas that of CpG methylation does not. The cells eventually lose non-CpG methylation by the time they become spermatogonia. Our results show that non-CpG methylation accumulates in non-replicating, arrested cells but is not maintained in mitotically dividing cells during male germ-cell development.

Epigenetics and developmental programming of welfare and production traits in farm animals

“…Prior to high-throughput sequencing, prevalent non-CpG methylation of cytosines had been detected in mouse embryonic stem cells at cytosine-phosphorous-adenine (CpA) and, to a lesser extent, at cytosine-phosphorous-thymine (CpT) sites (Ramsahoye et al 2000). More recent data confirm and extend this finding, demonstrating that non-CpG methylation is also present during male germ cell development (Ichiyanagi et al 2013), in oocytes (Shirane et al 2013) and is enriched within gene bodies of highly transcribed genes in both fetal and adult mouse brain (Lister et al 2013). Because mammals appear to lack enzymes that copy asymmetric non-CpG marks, it is currently not clear how this type of modification could contribute to the propagation of epigenetic states established as a result of fetal programming events.…”

The evidence for functional non-CpG methylation in mammalian cells

“…35 Loss of Dnmt3l in mice reduced CpA methylation in prospermatogonia from 15.2% to 2.8% of total methylation levels. 36 Barres et al found that DNMT3B depletion caused reduced non-CpG hypermethylation at the PGC-1α promoter in human primary muscle cells. 30 Mouse GVOs lacking Dnmt3a or Dnmt3l show global reductions in both CpG and non-CpG methylation.…”

Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency

“…DNMT3L lacks catalytic activity but acts as a co-factor for the establishment of CG methylation and non-CG methylation (Ichiyanagi et al 2013, Shirane et al 2013, Vlachogiannis et al 2015. DNMT3L can interact with histone H3 tail when its lysine 4 is unmethylated and induce de novo DNA methylation , Ooi et al 2007).…”