In eukaryotes, DNA is wrapped around histone octamers, which are composed of two copies each of histones H2A, H2B, H3 and H4. This structural arrangement of histones and DNA is known as chromatin. One of the main features of chromatin is that its structure can be altered to regulate the accessibility of the genome for diverse biological processes. The dynamic structure of chromatin is modulated mainly by the deposition of covalent modifications on DNA and histones. Different combinations of these modifications throughout the genome are responsible for the “epigenetic” level of information that controls many cellular processes. We are interested in understanding how these chromatin modifications participate in the cellular mechanisms responsible for eukaryotic biology, and how our knowledge of the epigenome can be used to improve human health and agriculture.
DNA and chromatin replication
Epigenetic mechanisms are known to play a critical role in regulating transcription in multicellular eukaryotes. In contrast, the interplay between epigenetics and DNA replication remains largely unexplored.
In plants, a lot of our knowledge regarding the interaction between chromatin and DNA replication has come from the study of the proteins ATXR5 and ATXR6. It was shown that ATXR5 and ATXR6 act redundantly in mono-methylating histone H3 lysine 27 (H3K27me1) in plants (1). The absence of H3K27me1 in atxr5 atxr6 double mutants results in the loss of transposon silencing, heterochromatin decondensation and more interestingly, heterochromatic over-replication (2). We also have shown that methylation by ATXR5 and ATXR6 is restricted to the conserved histone variant H3.1. This finding provides a model for the epigenetic inheritance of heterochromatin during DNA replication (Fig. 1) (3). In plants, animals and yeasts, heterochromatin and euchromatin are replicated at different times during S phase of the cell cycle, and defects in replication timing are associated with genome instability. Our work on ATXR5 and ATXR6 is helping us understand how the epigenetic regulation of DNA replication contributes to genome stability.
Genome engineering and chromatin
Basic research and crop improvement rely on our ability to induce genetic alterations. CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) has recently been shown to be a powerful method to induce targeted mutations in many eukaryotes, including plants. Although the archae/bacteria-derived CRISPR/Cas system has many advantages, it could still benefit from optimization for use in the chromatin-based environment found in eukaryotes. Similarly to other processes like transcription, replication and DNA repair, accessibility to DNA is likely critical for efficient CRISPR/Cas-induced modifications. This suggests that some genomic regions (e.g. heterochromatin) will be more challenging to edit with CRISPR/Cas than others, and this could be particularly important in plants. Most crops are flowering plants and genome size, complexity and organization varies greatly in this clade due to expansion of transposons and other repetitive sequences (e.g. 85% of the maize genome consists of transposons). Also, many crops are polyploid and require multiple editing events to alter a single trait, a situation that would also benefit from increased efficiency of CRISPR/Cas.
1. Y. Jacob, S. D. Michaels, H3K27me1 is E(z) in animals, but not in plants. Epigenetics 4, 366-369 (2009).
2. Y. Jacob et al., Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases.
Nature 466, 987-991 (2010).
3. Y. Jacob et al., Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication. Science
343, 1249-1253 (2014).