H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

Abstract

Establishing and maintaining cell identity depends on the proper regulation of gene expression, as specified by transcription factors and reinforced by epigenetic mechanisms. Among the epigenetic mechanisms, heterochromatin formation is crucial for the preservation of genome stability and the cell type-specific silencing of genes. The heterochromatin-associated histone mark H3K9me3, although traditionally associated with the noncoding portions of the genome, has emerged as a key player in repressing lineage-inappropriate genes and shielding them from activation by transcription factors. Here we describe the role of H3K9me3 heterochromatin in impeding the reprogramming of cell identity and the mechanisms by which H3K9me3 is reorganized during development and cell fate determination.

Keywords: H3K9me3; cell identity; development; heterochromatin; reprogramming.

Figure 1. Megabase-scale domains of H3K9me3 vary by cell type and match regions resistant to reprogramming factor binding

Shown is a 25-Mb segment of human chromosome 16, visualized in the UCSC Genome Browser. The purple tracks show H3K9me3 signals by chromatin immunoprecipitation and sequencing (ChIP-seq), normalized by input-subtraction, for the selected cell/tissue-types. All ChIP-seq data come from the Roadmap Epigenomics Mapping Consortium (GSE16368). Note the close correspondence between the H3K9me3-enriched domains in foreskin fibroblasts (red arrows) and the fibroblast Differentially Bound Regions (DBRs, black bars), which are regions that fail to be targeted by iPS reprogramming factors in fibroblasts but are bound in ES cells [32]. Each of these regions lack H3K9me3 enrichment in ES cells, as well as in select other tissues (blue asterisks). Green arrows indicate representative H3K9me3 domains in other tissues that are absent in fibroblasts.

Figure 2. H3K9me2/3 heterochromatin domains impede diverse forms of cellular reprogramming

The diagram shows major cell fate transitions (black arrows) that occur during differentiation and reprogramming and the role of H3K9me2/3 in these transitions. The leftmost black arrow indicates conversion of differentiated cells to pluripotency, which can be carried out by nuclear transfer to an enucleated egg or by overexpression of pluripotency transcription factors. In both cases, pluripotency genes inside H3K9me3 domains are more resistant to activation, and the success rate is reprogramming is improved when H3K9me3 levels are reduced [32,52,72,74]. Thus, H3K9me3 domains impede reprogramming to pluripotency (red inhibitory arrows). When ES-derived differentiated cells are returned into ES culture conditions, thereby encouraging de-differentiation (dashed black arrow), the loss of a H3K9me2 methyltransferase increases the appearance of undifferentiated colonies and the expression of pluripotency genes [86]. In contrast to reprogramming, the differentiation of pluripotent cells in culture (upper black arrows) is promoted by increases in H3K9me2/3 [69,85]. Although H3K9me2/3 domains form in a tissue-specific fashion over the course of development (rightmost black arrows), the role of these domains in the directed conversion of cells across developmental lineages (bottom black arrow) remains to be investigated.