Epigenetic fates of gene silencing established by heterochromatin spreading in cell identity and genome stability

Abstract

Heterochromatin spreading, the propagation of repressive chromatin along the chromosome, is a reaction critical to genome stability and defense, as well as maintenance of unique cell fates. Here, we discuss the intrinsic properties of the spreading reaction and circumstances under which its products, formed distal to DNA-encoded nucleation sites, can be epigenetically maintained. Finally, we speculate that the epigenetic properties of heterochromatin evolved together with the need to stabilize cellular identity.

Keywords: Cellular identity; Chromatin structure; DNA methylation; Epigenetic inheritance; Heterochromatin spreading; Histone 3 lysine 9 methylation; Histone turnover.

Figure 1:. Variegation and inheritance of heterochromatin spreading generate mixed or uniform cell states respectively.

Heterochromatin is formed by a sequential process whereby first small heterochromatin domains (red) are formed proximal to nucleation sites (blue) by short range spreading. Nucleation-distal genes remain expressed (purple state). Long-range spreading then propagates the repressed state along the chromosome, silencing information orthogonal to the cellular state (grey state). The resultant heterochromatin domain can be either inherited with high fidelity, leading to a robust recapitulation of the repressed state and a uniform population (right) or with low fidelity, leading to variegated expression across a population (left).

Figure 2:. Systems of memory retention for nucleation-distal heterochromatin regions.

Since heterochromatin PTMs and factors are at least partially lost during S-phase, epigenetic memory requires mechanisms to quickly and reliably regain the repressed state. These may include one or more of the following: (1) DNA methylation – methylation of DNA, which is mainly found in higher eukaryotes and is concurrent with heterochromatic histone PTMs, is linked to the high fidelity process of DNA replication. Following S-phase, hemi-methyl DNA is recognized by DNA methyltransferases (DNMT), which restore DNA methylation to both strands. This leads to the recruitment of heterochromatin writers and effectors by both DNMTs and DNAme reader proteins and restoration of the heterochromatin state (2) reduced histone turnover – compared to euchromatin, certain heterochromatin regions may experience less turnover of nucleosomes and/or histone proteins. This prevents loss of epigenetic information via the incorporation of un-marked nucleosomes and promotes the inheritance of the heterochromatic state by the retention of modified nucleosomes. (3) local chromatin structure – a higher order structure present at heterochromatin regions could be either directly maintained or quickly re-established post-replication. This structure either allows for the retention of epigenetic information or enhances the reformation of heterochromatin (shown), perhaps by facilitating a local environment favorable to spreading or by recruiting the enzyme complexes required for it.

Figure 3:. Different heterochromatin loci experience stochastic or stable inheritance of heterochromatin spreading.

Heterochromatin regions with different functions, and possibly different requirements for epigenetic memory, exist within the same genome. Pericentromeric heterochromatin (left) has a primarily structural role in centromere function and the suppression of repetitive elements. Multiple strong nucleators (blue) are present in these regions, likely facilitating the re-establishment of heterochromatic state and minimizing the requirement for long distance spreading following the weakening in S-phase. Subtelomeric heterochromatin (right) varies in its extent of spreading. At cell identity loci (middle), variability is not tolerated if the epigenetic state is to be maintained over many cell divisions. The presence of different classes of nucleators collaborating to regain the epigenetic state after S-phase, or the prevention of information loss in the first place, may ensure that cell identity information is robustly inherited.