Mitotic inheritance of genetic and epigenetic information via the histone H3.1 variant

Abstract

The replication-dependent histone H3.1 variant, ubiquitous in multicellular eukaryotes, has been proposed to play key roles during chromatin replication due to its unique expression pattern restricted to the S phase of the cell cycle. Here, we describe recent discoveries in plants regarding molecular mechanisms and cellular pathways involving H3.1 that contribute to the maintenance of genomic and epigenomic information. First, we highlight new advances concerning the contribution of the histone chaperone CAF-1 and the TSK-H3.1 DNA repair pathway in preventing genomic instability during replication. We then summarize the evidence connecting H3.1 to specific roles required for the mitotic inheritance of epigenetic states. Finally, we discuss the recent identification of a specific interaction between H3.1 and DNA polymerase epsilon and its functional implications.

Keywords: Arabidopsis; Chromatin; DNA replication; Epigenetics; Histone modifications; Histone variants.

Figure 1.. Interplay between H3.1 and genome stability in different genetic contexts.

(a-d) Chromatin replication in heterochromatin is represented, where parental nucleosomes are mainly composed of the H3.1 variant, except in the CAF-1 mutant. (a) In a wild-type plant, newly synthesized H3.1-H4 tetramers are loaded by the CAF-1 complex during replication. TSK binds H3.1K27me0 and resolves broken or stalled replication forks, ensuring genomic integrity. Post-replicative maturation of chromatin involves mono-methylation of H3.1K27 by ATXR5/6, which prevents ectopic binding of TSK. (b) In CAF-1 mutants, predominance of the H3.3 variant in chromatin prevents TSK activity, resulting in DNA damage at replication forks. (c) In the atxr5/6 mutant, absence of H3.1K27me1 causes aberrant binding of TSK and genomic instability outside of replication forks. (d) In a tsk context, H3.1 is loaded and mono-methylated correctly, but TSK is not available to resolve stalled or broken replication forks. (e) Schematic depiction of known H3.1-dependent structural phenotypes in the Arabidopsis genome: genomic stability (wild-type), large tandem duplications (CAF-1 mutants), heterochromatin amplification (atxr5/6 mutants). PCH: pericentromeric heterochromatin; CA: chromosome arm.

Figure 2.. Interplay between H3.1 and DNA polymerases during replication.

In constitutive heterochromatin, parental nucleosomes are enriched in H3.1 mono-methylated at K27. At the replication fork, the CMG helicase, which includes MCM2–7, CDC45, and GINS, unwinds parental double stranded DNA. DNA polymerase epsilon (Pol ɛ) then synthesizes the leading strand, while DNA polymerases alpha (Pol α) and delta (Pol δ) synthesize the lagging strand, with their respective catalytic subunits POL2A, POLA1, and POLD1. The CAF-1 complex interacts with the PCNA clamp to load newly synthesized H3.1-H4 tetramers on both strands of the fork, after which ATXR5/6 deposit H3K27me1. Parental H3-H4 are recycled symmetrically to the leading and lagging strands. POL2A can bind H3.1 in its unmethylated (i.e., newly synthesized) and mono-methylated (i.e., parental) forms with potential implications for epigenetic inheritance. DPB3–4 are the plant homologs of mammalian POLE3–4, two non-catalytic subunits of Pol ɛ that were shown mediate recycling of parental H3-H4 to the leading strand. The MCM2-CTF4-Pol α axis is required for recycling of parental H3-H4 to the lagging strand in mammals, and may accomplish similar functions in plants.