Diverse heterochromatin states restricting cell identity and reprogramming

Abstract

Heterochromatin is defined as a chromosomal domain harboring repressive H3K9me2/3 or H3K27me3 histone modifications and relevant factors that physically compact the chromatin. Heterochromatin can restrict where transcription factors bind, providing a barrier to gene activation and changes in cell identity. While heterochromatin thus helps maintain cell differentiation, it presents a barrier to overcome during efforts to reprogram cells for biomedical purposes. Recent findings have revealed complexity in the composition and regulation of heterochromatin, and shown that transiently disrupting the machinery of heterochromatin can enhance reprogramming. Here, we discuss how heterochromatin is established and maintained during development, and how our growing understanding of the mechanisms regulating H3K9me3 heterochromatin can be leveraged to improve our ability to direct changes in cell identity.

Keywords: H3K27me3; H3K9me3; heterochromatin; pioneer factors; reprogramming.

Figure 1.

H3K9me3-heterochromatin as a barrier to cell fate change. Central to the functions of H3K9me3-heterochromatin is the “reader-writer” module, in which H3K9me3 mark deposited by H3K9me3 methyltransferases is recognized by reader proteins, including HP1α/β/γ, which further recruit methyltransferases to modify the neighboring nucleosomes. This leads to spreading of heterochromatin domains and stable maintenance of H3K9me3 domains over the cell cycle. Further enrichment of linker histone H1, HP1 proteins and other heterochromatin associated proteins lead to heterochromatin compaction and restricting the TFs from activating their targets. Building from this basic principle, we discussed how heterochromatin is established and maintained in development, different compositions of heterochromatin domains, how it molds the TF bindings and finally how to this knowledge to enhance cellular reprogramming.

Figure 2.

Heterochromatin is dynamic during development. (A) Heterochromatin remodeling accompanies developmental progression during early mouse development. In the zygote, the maternal genome possesses H3K9me3 heterochromatin marks at centromeric and pericentromeric regions, whereas paternal genome does not. (B) An ensuing heterochromatin remodeling creates an open chromatin environment, a hallmark of totipotent states and leads to activation of repeat regions, which recruit heterochromatin machinery to establish heterochromatin and promote the transition from totipotency to pluripotency. (C) Heterochromatin domains in pluripotent stem cells are decorated with H3K9me3 marks, compacted by linker histone H1 and recruit heterochromatin associated proteins, including HP1. (D) During lineage specifications in mouse development, transcription factors, including KRAB-ZNF proteins direct heterochromatin machinery to repress alternative lineage-specific genes to maintain the cell fate. (E) Genes are increasingly marked by H3K9me3 for repression during germ layer development, but this mark is removed from key functional genes upon lineage specification [13].

Figure 3.

Groups of heterochromatin proteins regulate distinct classes of heterochromatin and can be disrupted to facilitate gene activation. (A) Published results showing knockdowns/knockouts (blue) and overexpression (red) experiments that lead to de-repression of heterochromatin and enhanced reprogramming. (B) Regulation of H3K9me3 at genes and repeat classes by H3K9me3 HMTs, protein complexes and selected heterochromatin proteins. Green boxes indicate the indicated protein or complex has been experimentally demonstrated to regulate H3K9me3 at the designated gene or repeat class.