Papachristou, E. K. | bioRxiv Science

bioRxiv2021

GLP is critical for oogenesis exhibiting a G9A-independent role in transcriptional repression

GLP (EHMT1) is a multifunctional protein, best known for its role as an H3K9me1 and H3K9me2 methyltransferase through its reportedly obligatory dimerization with G9A (EHMT2). Here, we investigate the role of GLP in the oocyte in comparison to G9A using oocyte-specific conditional knockout mouse models (G9a cKO, Glp cKO, G9a-Glp cDKO). Loss of GLP in Glp cKO and G9a-Glp cDKO oocytes re-capitulated meiotic defects observed in the G9a cKO; however, there was a significant impairment in oocyte maturation and developmental competence in Glp cKO and G9a-Glp cDKO oocytes beyond that observed in the G9a cKO. Consequently, loss of GLP in oogenesis results upon fertilisation in mid-gestation embryonic lethality. To assess the molecular functions of GLP and G9A, we applied a multi-omics approach, supported by immunofluorescence, to identify changes in epigenomic, transcriptomic and proteomic signatures in cKO oocytes. H3K9me2 was equally depleted in all cKO oocytes, whereas H3K9me1 was decreased only upon loss of GLP. The transcriptome, DNA methylome and proteome were markedly more affected in G9a-Glp cDKO than G9a cKO oocytes, with transcriptional de-repression associated with increased protein abundance and gains in genic DNA methylation in G9a-Glp cDKO oocytes. Together, our findings suggest that GLP contributes to transcriptional repression in the oocyte, independent of G9A, and is critical for oogenesis and oocyte developmental competence.

developmental biology↗

bioRxiv2021

The distinct effects of MEK and GSK3 inhibition upon the methylome and transcriptome of mouse embryonic stem cells

Mouse embryonic stem cells (mESCs) were first cultured in vitro in serum-containing medium with leukaemia inhibitory factor, in which they exhibit heterogeneous expression of both pluripotency and some early differentiation markers. Over the last decade, however, it has become commonplace to grow mESCs with inhibitors of MEK and GSK3 signalling, which together elicit a more homogeneously naive state of pluripotency. Whilst 2i/L-cultured mESCs have been shown to be globally hypomethylated, a comprehensive understanding of the distinct effects of these signalling inhibitors upon the DNA methylome is still lacking. Here we carried out whole genome bisulphite and RNA sequencing of mESCs grown with MEK or GSK3 inhibition alone, including different time points and concentrations of MEK inhibitor treatment. This demonstrated that MEK inhibition causes a dose-dependent impairment of maintenance methylation via loss of UHRF1 protein, as well as rapid impairment of de novo methylation. In contrast, GSK3 inhibition triggers impairment of de novo methylation alone, and consequent hypomethylation is enriched at enhancers with a 2i/L-specific chromatin signature and coincides with upregulation of nearby genes. Our study provides detailed insights into the epigenetic and transcriptional impacts of inhibiting MEK or GSK3 signalling in mouse pluripotent cells. HighlightsO_LIMEK inhibition causes dose-dependent impairment of maintenance methylation via loss of UHRF1 protein, as well as impairment of de novo methylation. C_LIO_LIGSK3 inhibition triggers impairment of de novo methylation alone, which results in hypomethylation of enhancers and non-CGI promoters. C_LIO_LIEnhancers that are hypomethylated following GSK3 inhibition are enriched for 2i/L-specific pluripotency factor binding, TET2 and H3K4me1. C_LIO_LIEnhancer hypomethylation coincides with increased expression of nearby and Capture Hi-C linked genes. C_LI

developmental biology↗