Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability

Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces chromatin compaction by accumulating the repressive modifications, H3K9me1/me2/me3, in the vicinity of stressed replication forks. This closed conformation is also favoured by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering single-stranded DNA gap formation and sensitizing cells towards chemotherapeutic drugs. These findings may help in explaining chemotherapy resistance and poor prognosis observed in patients with cancer displaying elevated levels of G9a/H3K9me3.</p

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

Eukaryotic genomes are folded into three-dimensional structures, such as self-associating topological domains, the borders of which are enriched in cohesin and CCCTC-binding factor (CTCF) required for long-range interactions1-7. How local chromatin interactions govern higher-order folding of chromatin fibers and the function of cohesin in this process remain poorly understood. Here we perform genome-wide chromatin conformation capture (Hi-C) analysis8 to explore the high-resolution organization of the Schizosaccharomyces pombe genome, which despite its small size exhibits fundamental features found in other eukaryotes9. Our analyses of wild type and mutant strains reveal key elements of chromosome architecture and genome organization. On chromosome arms, small regions of chromatin locally interact to form “globules”. This feature requires a function of cohesin distinct from its role in sister chromatid cohesion. Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structures and global chromosome territories. By contrast, heterochromatin, which loads cohesin at specific sites including pericentromeric and subtelomeric domains9-11, is dispensable for globule formation but nevertheless affects genome organization. We show that heterochromatin mediates chromatin fiber compaction at centromeres and promotes prominent interarm interactions within centromere-proximal regions, providing structural constraints crucial for proper genome organization. Loss of heterochromatin relaxes constraints on chromosomes, causing an increase in intra- and inter-chromosomal interactions. Together, our analyses uncover fundamental genome folding principles that drive higher-order chromosome organization crucial for coordinating nuclear functions

R\xe2\x80\x90loops and its chro\xe2\x80\x90mates

Since their discovery, R\xe2\x80\x90loops have been associated with both physiological and pathological functions that are conserved across species. R\xe2\x80\x90loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R\xe2\x80\x90loop accumulation as well as to resolve them. A growing body of evidence correlates R\xe2\x80\x90loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R\xe2\x80\x90loops homeostasis remains unclear. This review covers various mechanisms precluding R\xe2\x80\x90loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R\xe2\x80\x90loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication\xe2\x80\x90transcription conflicts. Finally, we discuss the potential role of several Chro\xe2\x80\x90 Mates (chromatin modifiers and remodelers) in the likely differentiation between persistent/detri-mental R\xe2\x80\x90loops and transient/benign R\xe2\x80\x90loops that assist in various physiological processes relevant for therapeutic interventions.</p

R‐loops and its chro‐mates

Since their discovery, R‐loops have been associated with both physiological and pathological functions that are conserved across species. R‐loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R‐loop accumulation as well as to resolve them. A growing body of evidence correlates R‐loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R‐loops homeostasis remains unclear. This review covers various mechanisms precluding R‐loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R‐loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication‐transc