A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation

Epigenetic priming in the male germline

Epigenetic priming presets chromatin states that allow the rapid induction of gene expression programs in response to differentiation cues. In the germline, it provides the blueprint for sexually dimorphic unidirectional differentiation. In this review, we focus on epigenetic priming in the mammalian male germline and discuss how cellular memories are regulated and inherited to the next generation. During spermatogenesis, epigenetic priming predetermines cellular memories that ensure the lifelong maintenance of spermatogonial stem cells and their subsequent commitment to meiosis and to the production of haploid sperm. The paternal chromatin state is also essential for the recovery of totipotency after fertilization and contributes to paternal epigenetic inheritance. Thus, epigenetic priming establishes stable but reversible chromatin states during spermatogenesis and enables epigenetic inheritance and reprogramming in the next generation.

Bivalent chromatin: a developmental balancing act tipped in cancer

Bivalent chromatin is defined by the co-occurrence of otherwise opposing H3K4me3 and H3K27me3 modifications and is typically located at unmethylated promoters of lowly transcribed genes. In embryonic stem cells, bivalent chromatin has been proposed to poise developmental genes for future activation, silencing or stable repression upon lineage commitment. Normally, bivalent chromatin is kept in tight balance in cells, in part through the activity of the MLL/COMPASS-like and Polycomb repressive complexes that deposit the H3K4me3 and H3K27me3 modifications, respectively, but also emerging novel regulators including DPPA2/4, QSER1, BEND3, TET1 and METTL14. In cancers, both the deregulation of existing domains and the creation of de novo bivalent states is associated with either the activation or silencing of transcriptional programmes. This may facilitate diverse aspects of cancer pathology including epithelial-to-mesenchymal plasticity, chemoresistance and immune evasion. Here, we review current methods for detecting bivalent chromatin and discuss the factors involved in the formation and fine-tuning of bivalent domains. Finally, we examine how the deregulation of chromatin bivalency in the context of cancer could facilitate and/or reflect cancer cell adaptation. We propose a model in which bivalent chromatin represents a dynamic balance between otherwise opposing states, where the underlying DNA sequence is primed for the future activation or repression. Shifting this balance in any direction disrupts the tight equilibrium and tips cells into an altered epigenetic and phenotypic space, facilitating both developmental and cancer processes.

A low-input high resolution sequential chromatin immunoprecipitation method captures genome-wide dynamics of bivalent chromatin

BACKGROUND

Bivalent chromatin is an exemplar of epigenetic plasticity. This co-occurrence of active-associated H3K4me3 and inactive-associated H3K27me3 histone modifications on opposite tails of the same nucleosome occurs predominantly at promoters that are poised for future transcriptional upregulation or terminal silencing. We know little of the dynamics, resolution, and regulation of this chromatin state outside of embryonic stem cells where it was first described. This is partly due to the technical challenges distinguishing bone-fide bivalent chromatin, where both marks are on the same nucleosome, from allelic or sample heterogeneity where there is a mix of H3K4me3-only and H3K27me3-only mononucleosomes.

RESULTS

Here, we present a robust and sensitive method to accurately map bivalent chromatin genome-wide, along with controls, from as little as 2 million cells. We optimized and refined the sequential ChIP protocol which uses two sequential overnight immunoprecipitation reactions to robustly purify nucleosomes that are truly bivalent and contain both H3K4me3 and H3K27me3 modifications. Our method generates high quality genome-wide maps with strong peak enrichment and low background, which can be analyzed using standard bioinformatic packages. Using this method, we detect 8,789 bivalent regions in mouse embryonic stem cells corresponding to 3,918 predominantly CpG rich and developmentally regulated gene promoters. Furthermore, profiling Dppa2/4 knockout mouse embryonic stem cells, which lose both H3K4me3 and H3K27me3 at approximately 10% of bivalent promoters, demonstrated the ability of our method to capture bivalent chromatin dynamics.

CONCLUSIONS

Our optimized sequential reChIP method enables high-resolution genome-wide assessment of bivalent chromatin together with all required controls in as little as 2 million cells. We share a detailed protocol and guidelines that will enable bivalent chromatin landscapes to be generated in a range of cellular contexts, greatly enhancing our understanding of bivalent chromatin and epigenetic plasticity beyond embryonic stem cells.