Linking replication stress with heterochromatin formation

Abstract

The eukaryotic genome can be roughly divided into euchromatin and heterochromatin domains that are structurally and functionally distinct. Heterochromatin is characterized by its high compaction that impedes DNA transactions such as gene transcription, replication, or recombination. Beyond its role in regulating DNA accessibility, heterochromatin plays essential roles in nuclear architecture, chromosome segregation, and genome stability. The formation of heterochromatin involves special histone modifications and the recruitment and spreading of silencing complexes that impact the higher-order structures of chromatin; however, its molecular nature varies between different chromosomal regions and between species. Although heterochromatin has been extensively characterized, its formation and maintenance throughout the cell cycle are not yet fully understood. The biggest challenge for the faithful transmission of chromatin domains is the destabilization of chromatin structures followed by their reassembly on a novel DNA template during genomic replication. This destabilizing event also provides a window of opportunity for the de novo establishment of heterochromatin. In recent years, it has become clear that different types of obstacles such as tight protein-DNA complexes, highly transcribed genes, and secondary DNA structures could impede the normal progression of the replisome and thus have the potential to endanger the integrity of the genome. Multiple studies carried out in different model organisms have demonstrated the capacity of such replisome impediments to favor the formation of heterochromatin. Our review summarizes these reports and discusses the potential role of replication stress in the formation and maintenance of heterochromatin and the role that silencing proteins could play at sites where the integrity of the genome is compromised.

Keywords: Epigenetics; Gene silencing; Heterochromatin; Replication stress.

Fig. 1

During S phase, the replisome encounters a number of impediments, which could interfere with its progression and have the potential to endanger the stability of the genome. When faced with such obstacles, in many cases, the cell triggers the S phase checkpoint and stabilizes the replication fork. In the event of replication fork breakdown or “collapse,” replication can restart by recruiting an alternative pathway requiring homology-directed repair (HDR), which could eventually result in loss of genetic and/or epigenetic information. If stalled forks fail to restart, persistent checkpoint activation can lead to apoptosis. As discussed in the text, silencing factors are also recruited to sites of replication stress. Possible roles of heterochromatin proteins at these loci could be in preserving the stability of the replisome or in modulating the cellular response to replication stress via largely unknown mechanism(s). Such events could also serve as an initial signal and potentially trigger the formation of heterochromatin