Replication stress affects the fidelity of nucleosome-mediated epigenetic inheritance

Abstract

The fidelity of epigenetic inheritance or, the precision by which epigenetic information is passed along, is an essential parameter for measuring the effectiveness of the process. How the precision of the process is achieved or modulated, however, remains largely elusive. We have performed quantitative measurement of epigenetic fidelity, using position effect variegation (PEV) in Schizosaccharomyces pombe as readout, to explore whether replication perturbation affects nucleosome-mediated epigenetic inheritance. We show that replication stresses, due to either hydroxyurea treatment or various forms of genetic lesions of the replication machinery, reduce the inheritance accuracy of CENP-A/Cnp1 nucleosome positioning within centromere. Mechanistically, we demonstrate that excessive formation of single-stranded DNA, a common molecular abnormality under these conditions, might have correlation with the reduction in fidelity of centromeric chromatin duplication. Furthermore, we show that replication stress broadly changes chromatin structure at various loci in the genome, such as telomere heterochromatin expanding and mating type locus heterochromatin spreading out of the boundaries. Interestingly, the levels of inheritable expanding at sub-telomeric heterochromatin regions are highly variable among independent cell populations. Finally, we show that HU treatment of the multi-cellular organisms C. elegans and D. melanogaster affects epigenetically programmed development and PEV, illustrating the evolutionary conservation of the phenomenon. Replication stress, in addition to its demonstrated role in genetic instability, promotes variable epigenetic instability throughout the epigenome.

Ccp1 modulates epigenetic stability at centromeres and affects heterochromatin distribution in Schizosaccharomyces pombe

“…Given the prominent role of CAF-1 in the process of replication-coupled nucleosome assembly, this indicates that the fidelity of chromatin duplication is a major determinant of epigenetic stability. This is in agreement with our recent finding that replication stresses elevate the variability of CEN-PEV (31). Also noticeable, among three subunits of the histone chaperone CAF-1, only pcf1⌬ enhanced cnt2::ade6 variability, whereas pcf2⌬ or pcf3⌬ exhibited WT level variability, suggesting that epigenetic stability modulation is a unique function of Pcf1 instead of the CAF-1 complex as an integral entity.…”

“…An established CEN-PEV system was used as the readout for the genetic screen in which a reporter gene, ade6, was inserted at the central core of CEN2. Previous studies indicated that the occupancy of Cnp1 on ade6 correlates with transcriptional silencing (15,27,28,31). We reason that, using centromeric PEV of ade6 inserted in cnt2 (designated as cnt2::ade6 thereafter in this work) as the readout, switching between the ON and OFF states of ade6 reflects the changes of Cnp1 occupancy on the ade6 reporter gene through mitotic cell generations.…”

Polymerase pausing induced by sequence-specific RNA binding protein drives heterochromatin assembly

“…cerevisiae where tight protein-DNA interactions are sufficient to trigger recruitment of the SIR complex 46 . Consistent with this hypothesis, such transcription-replication conflicts are limited by Paf1-C 47 which inhibits heterochromatin assembly, while slowing of replisome progression enhances heterochromatin spread 48,49 . It has also been proposed that the 5'à3' RNA exonuclease Dhp1 (related to S. cerevisiae Rat1/Xrn2), which is required for RNAi-independent heterochromatin assembly, recruits the silencing machinery via a physical interaction with CLR-C 50,51 .…”

Transgenerational phenotype aggravation in CAF‐1 mutants reveals parent‐of‐origin specific epigenetic inheritance

“…Second, lack of CAF-1 shifts the ratio of histone variants H3.1 and H3.3 in chromatin, because only CAF-1-dependent chromatin assembly strongly prefers H3.1 over H3.3, whereas CAF-1-independent chromatin assembly, which can partially substitute for CAF-1 function in CAF-1 mutants, works well with H3.3 (Duc et al, 2015(Duc et al, , 2017. Third, CAF-1 locates to the site of the replication fork through its interaction with PROLIFERATING CELL NUCLEAR ANTIGEN (Shibahara & Stillman, 1999;Jiang & Berger, 2017) and lack of CAF-1 causes S-phase defects and replication stress, which impairs nucleosome-mediated epigenetic inheritance (Li et al, 2017). Most histone modifications are re-established immediately after S-phase (Alabert et al, 2015), often mediated by CAF-1 interacting with other chromatin proteins such as the mammalian methyl CpG binding protein that recruits a H3K9 methyltransferase (Sarraf & Stancheva, 2004) and HETEROCHROMATIN PROTEIN 1 (Quivy et al, 2004).…”