Enhancer-associated H3K4 methylation safeguards in vitro germline competence

Abstract

<jats:title>SUMMARY</jats:title><jats:p>Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast reactivate a naïve pluripotency expression program and differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain largely unknown.</jats:p><jats:p>Here we show that early germline genes that are active in the naïve pluripotent state become homogeneously dismantled in germline competent epiblast cells. In contrast, the enhancers controlling the expression of major PGC genes transiently and heterogeneously acquire a primed state characterized by intermediate DNA methylation, chromatin accessibility, and H3K4me1. This primed enhancer state is lost, together with germline competence, as epiblast cells develop further. Importantly, we demonstrate that priming by H3K4me1/2 enables the robust activation of PGC enhancers and is required for germline competence and specification. Our work suggests that H3K4me1/2 is directly involved in enhancer priming and the acquisition of competence.</jats:p>

Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus

“…Although they appeared mostly active in both cell lines at day 0, they lost activity in XO cells during differentiation. Concomitantly, a broad $16-kb-wide H3K9me3 domain, covering the Xist promoter region, appeared only in XO cells at days 2 and 4 (Figure 2H; Figure S2J) and was similarly observed in differentiating male ESCs in a published dataset (Figure S2K) (Bleckwehl et al, 2021). X chromosome dosage thus appears to control mainly the promoter-proximal region, where it counteracts active repression by H3K9me3 during differentiation.…”

The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conservedin vivo

“…The ChIP-seq data from mouse WT in vitro pluripotent cell types (i.e. serum+LIF ESC, 2i+LIF ESC and EpiLC) was obtained from Cruz-Molina et al 5 and Bleckwehl et al 79 . All publically available ChIP-seq and ATAC-seq datasets used in this work, including those generated by ENCODE 97 , are listed in Table S1.…”

“…PE sets were annotated using GREAT 3.0 79 , except for the chicken PE, which were annotated with ConsensusPathDb 80 . Zebrafish de novo PE had to be lifted to assembly danRer7 for annotation with GREAT.…”

“…(A) ATAC-seq and ChIP-seq data for p300, H3K27me3and H3K27ac were used to call PEs in three distinct in vitro pluripotent states (i.e. 2i ESC, S+L ESC and EpiLC)5,79 . PEs are characterized by high p300/ATAC signals, high H3K27me3 levels and low H3K27ac levels and located at least 5kb apart from a TSS (Methods).…”

Establishment and function of chromatin modification at enhancers

“…Based on both developmental and genetic studies, it is generally accepted that H3K4me1 is upstream of H3K27ac at enhancers. Many developmental enhancers show evidence of 'priming' or 'poising', in which the region is enriched with H3K4me1 but not H3K27ac in the absence of detectable transcription [97][98][99][100][101][102]. Further, H3K4me1 often appears prior to H3K27ac during differentiation [90,103,104] and inducible transcription [103,105].…”