DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis

Abstract

Background Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear. Results We isolate a strong hypomorphic Arabidopsis thaliana mutant of the POL2A catalytic subunit of DNA polymerase epsilon and show that POL2A is required to stabilize heterochromatin silencing genome-wide, likely by preventing replicative stress. We reveal that POL2A inhibits DNA methylation and histone H3 lysine 9 methylation. Hence, the release of heterochromatin silencing in POL2A-deficient mutants paradoxically occurs in a chromatin context of increased levels of these two repressive epigenetic marks. At the nuclear level, the POL2A defect is associated with fragmentation of heterochromatin. Conclusion These results indicate that POL2A is critical to heterochromatin structure and function, and that unhindered replisome progression is required for the faithful propagation of DNA methylation throughout the cell cycle.

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

“…S4 ). Our observations are consistent with recent publications where an increase in H3K9me2 and H3K27Ac marks was observed in the atxr5/6 (W) mutant ( 17 , 18 ). Although we cannot rule out that other untested epigenetic marks may be involved, these data suggest that loss of H3K27me1 is the major contributor to the chromocenter decompaction phenotype observed in atxr5/6 (W) mutants.…”

“…In particular, it seems possible that some form of genome instability or replication stress occurs in atxr5/6 (W), causing induction of DNA damage response genes. Indeed, similar sets of DNA damage genes are also activated in mutants of genes involved in DNA replication, such as in FAS1 and FAS2 , both components of the chromatin assembly factor 1 (CAF-1) chaperone complex, as well as in BRU1 , RFC1 , and mutations in DNA polymerases, Pol alpha (α), delta (δ), and epsilon (ε) ( 17 , 26 – 31 ).…”

Comprehensive analysis of Arabidopsis thaliana DNA polymerase epsilon catalytic subunit A and B mutants – an insight into differentially expressed genes and protein-protein interactions

“…TEs found in the pericentromeric heterochromatin are heavily methylated. In a recent study, Bourguet and his colleagues have noted that the significant release of heterochromatin silencing in AtPOL2A gene mutants is due to increased levels of DNA methylation and histone H3 lysine 9 methylation, and thus AtPOL2A is important to maintain heterochromatin structure and function [29]. Consistent with previous studies, we also observed that the silencing of the majority of pericentromeric TEs are released in atpol2a-1 mutant.…”

“…Our PPI analysis also showed that uncharacterized AT3G49160 interacts with FER1; both of these genes are known to be expressed in response to hydrogen peroxide [26][27][28]. AtPOL2A is important to maintain heterochromatin structure and function [29].…”

Epigenetics: a catalyst of plant immunity against pathogens

“…Chromatin density is key to transcriptional activity as it determines access of the transcriptional machinery to DNA. Heterochromatic regions are tightly packed and transcriptionally silent regions that are typically associated with repetitive sequences and TEs, whereas euchromatin is less dense and enriched with transcriptionally active genes (Bourguet et al, 2020). Chromatin density is dependent on the distribution of nucleosomes, each of which consists of two copies of four histone proteins (H2A, H2B, H3, H4), wrapped by c. 147 bp of DNA (Luger et al, 1997) and connected by variable stretches of internucleosomal DNA associated with linker H1 histones (Rutowicz et al, 2019).…”