Shelterin components mediate genome reorganization in response to replication stress

Abstract

The dynamic nature of genome organization impacts critical nuclear functions including the regulation of gene expression, replication, and DNA damage repair. Despite significant progress, the mechanisms responsible for reorganization of the genome in response to cellular stress, such as aberrant DNA replication, are poorly understood. Here, we show that fission yeast cells carrying a mutation in the DNA-binding protein Sap1 show defects in DNA replication progression and genome stability and display extensive changes in genome organization. Chromosomal regions such as subtelomeres that show defects in replication progression associate with the nuclear envelope in sap1 mutant cells. Moreover, highresolution, genome-wide chromosome conformation capture (Hi-C) analysis revealed prominent contacts between telomeres and chromosomal arm regions containing replication origins proximal to binding sites for Taz1, a component of the Shelterin telomere protection complex. Strikingly, we find that Shelterin components are required for interactions between Taz1-associated chromosomal arm regions and telomeres. These analyses reveal an unexpected role for Shelterin components in genome reorganization in cells experiencing replication stress, with important implications for understanding the mechanisms governing replication and genome stability.T he 3D organization of the eukaryotic genome creates specialized microenvironments that play important roles in various nuclear processes (1). In addition to regulation of gene expression, proper execution of the DNA replication program and DNA damage repair also involve dynamic organization of the genome (2, 3). Indeed, computational analyses indicate spatial segregation of replication origins based on their timing of firing during S-phase (4), suggesting that besides local chromatin structure, the 3D organization of chromosomes is an important contributing factor in the spatiotemporal control of replication (5, 6). Despite important advances, understanding the connections between diverse chromosomal events and genome organization remains an important challenge.The complexities of genome organization have been studied in several model organisms, including the fission yeast Schizosaccharomyces pombe, for which the 3D organization has been explored at high resolution (7,8). This simple eukaryote contains the basic chromosomal elements of more complex systems, including partitioning of the genome into euchromatin and heterochromatin domains. The S. pombe genome conforms to a Rabl organization pattern in which centromere clusters and telomere clusters are anchored at opposing sides of the nuclear periphery (9, 10). In addition, two key elements shape genome architecture: cohesin-dependent locally crumpled 50-to 100-kb repeating elements called "globules" on chromosome arms and the constraints imposed by the compaction of the chromatin fiber by heterochromatin domains such as at pericentromeric regions (8). The relatively small size of the S. pombe genome combined with the conserved genome...

A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi

“…SHREC directly interacts with the shelterin component Ccq1, linking Taz1, RITS, and HP1-containing silencing complexes. These analyses have now come full circle, as there is accumulating evidence for the role of shelterin components Taz1 and Ccq1 in heterochromatin formation at late replicating origins that are sites for double-strand break formation during meiosis and genome organization in general [114, 115]. Data obtained from high resolution three-dimensional structured illumination fluorescence microscopy (3DSIM) suggested that the “condensed” heterochromatin at subtelomeres in S. pombe is less condensed than nearby “knobs” that were eliminated by ablation of H3K36me3 [116], a histone mark correlated with gene expression and enriched in the 3′ regions of genes but actually repressing transcription from cryptic promoters and controlling transcript elongation [117, 118].…”

A Matter of Scale and Dimensions: Chromatin of Chromosome Landmarks in the Fungi

“…SHREC directly interacts with the shelterin component Ccq1, linking Taz1, RITS, and HP1containing silencing complexes. These analyses have now come full circle, as there is accumulating evidence for the role of shelterin components Taz1 and Ccq1 in heterochromatin formation at late replicating origins that are sites for double-strand break formation during meiosis and genome organization in general [114,115]. Data obtained from high resolution three-dimensional structured illumination fluorescence microscopy (3DSIM) suggested that the "condensed" heterochromatin at subtelomeres in S. pombe is less condensed than nearby "knobs" that were eliminated by ablation of H3K36me3 [116], a histone mark correlated with gene expression and enriched in the 3′ regions of genes but actually repressing transcription from cryptic promoters and controlling transcript elongation [117,118].…”

Shelterin promotes tethering of late replication origins to telomeres for replication‐timing control

“…During G1/S phase, telomeres are anchored to the nuclear membrane, and Taz1-dependent origins tethered around the telomeres are suppressed by PP1. detected in the mutant cells of a chromatin-associated protein Sap1 (Mizuguchi et al, 2017). This was probably due to a transient interaction between internal late origins and telomeres during G1/S phase.…”

“…It is possible that this type of TAD contributes to formation of facultative heterochromatin around Taz1‐dependent late origins, although deletion of heterochromatin protein HP1 only marginally affected replication‐timing control (Zofall et al , ). The actual topological association between the chromosome arm regions and telomeres was not detected in wild‐type cells, but was detected in the mutant cells of a chromatin‐associated protein Sap1 (Mizuguchi et al , ). This was probably due to a transient interaction between internal late origins and telomeres during G1/S phase.…”