Nuclear Chaperone ASF1 is Required for Gametogenesis in Arabidopsis thaliana

H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana

BACKGROUND

H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction.

RESULTS

H2A.X is encoded by two genes in Arabidopsis genome, HTA3 and HTA5. We generated h2a.x double mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However, h2a.x mutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under the H2A.X promoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation in h2a.x developing seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide in h2a.x mutant endosperm. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling. h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA.

CONCLUSIONS

Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Overall, our data suggest that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.

H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana

Background

H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction.

Results

H2A.X is encoded by two genes in Arabidopsis genome, HTA3 and HTA5. We generated h2a.x double mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However, h2a.x mutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under the H2A.X promoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation in h2a.x developing seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide in h2a.x mutant seeds. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling. h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA.

Conclusions

Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Alternatively, H2A.X may be involved in recruiting methyltransferases to those sites. Overall, our data suggest that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.

Safeguarding genome integrity under heat stress in plants

Heat stress adversely affects an array of molecular and cellular events in plant cells, such as denaturation of protein and lipid molecules and malformation of cellular membranes and cytoskeleton networks. Genome organization and DNA integrity are also disturbed under heat stress, and accordingly, plants have evolved sophisticated adaptive mechanisms that either protect their genomes from deleterious heat-induced damages or stimulate genome restoration responses. In particular, it is emerging that DNA damage responses are a critical defense process that underlies the acquirement of thermotolerance in plants, during which molecular players constituting the DNA repair machinery are rapidly activated. In recent years, thermotolerance genes that mediate the maintenance of genome integrity or trigger DNA repair responses have been functionally characterized in various plant species. Furthermore, accumulating evidence supports that genome integrity is safeguarded through multiple layers of thermoinduced protection routes in plant cells, including transcriptome adjustment, orchestration of RNA metabolism, protein homeostasis, and chromatin reorganization. In this review, we summarize topical progresses and research trends in understanding how plants cope with heat stress to secure genome intactness. We focus on molecular regulatory mechanisms by which plant genomes are secured against the DNA-damaging effects of heat stress and DNA damages are effectively repaired. We will also explore the practical interface between heat stress response and securing genome integrity in view of developing biotechnological ways of improving thermotolerance in crop species under global climate changes, a worldwide ecological concern in agriculture.

Chromatin dynamics during DNA damage and repair in plants: new roles for old players

The genome of plants is organized into chromatin. The chromatin structure regulates the rates of DNA metabolic processes such as replication, transcription, DNA recombination, and repair. Different aspects of plant growth and development are regulated by changes in chromatin status by the action of chromatin-remodeling activities. Recent data have also shown that many of these chromatin-associated proteins participate in different aspects of the DNA damage response, regulating DNA damage and repair, cell cycle progression, programmed cell death, and entry into the endocycle. In this review, we present different examples of proteins and chromatin-modifying enzymes with roles during DNA damage responses, demonstrating that rapid changes in chromatin structure are essential to maintain genome stability.

Similar yet critically different: the distribution, dynamics and function of histone variants

Organization of the genetic information into chromatin plays an important role in the regulation of all DNA template-based reactions. The incorporation of different variant versions of the core histones H3, H2A, and H2B, or the linker histone H1 results in nucleosomes with unique properties. Histone variants can differ by only a few amino acids or larger protein domains and their incorporation may directly affect nucleosome stability and higher order chromatin organization or indirectly influence chromatin function through histone variant-specific binding partners. Histone variants employ dedicated histone deposition machinery for their timely and locus-specific incorporation into chromatin. Plants have evolved specific histone variants with unique expression patterns and features. In this review, we discuss our current knowledge on histone variants in Arabidopsis, their mode of deposition, variant-specific post-translational modifications, and genome-wide distribution, as well as their role in defining different chromatin states.

Gametophytic Abortion in Heterozygotes but Not in Homozygotes: Implied Chromosome Rearrangement during T-DNA Insertion at the ASF1 Locus in Arabidopsis

T-DNA insertional mutations in Arabidopsis genes have conferred huge benefits to the research community, greatly facilitating gene function analyses. However, the insertion process can cause chromosomal rearrangements. Here, we show an example of a likely rearrangement following T-DNA insertion in the Anti-Silencing Function 1B (ASF1B) gene locus on Arabidopsis chromosome 5, so that the phenotype was not relevant to the gene of interest, ASF1B. ASF1 is a histone H3/H4 chaperone involved in chromatin remodeling in the sporophyte and during reproduction. Plants that were homozygous for mutant alleles asf1a or asf1b were developmentally normal. However, following self-fertilization of double heterozygotes (ASF1A/asf1a ASF1B/asf1b, hereafter AaBb), defects were visible in both male and female gametes. Half of the AaBb and aaBb ovules displayed arrested embryo sacs with functional megaspore identity. Similarly, half of the AaBb and aaBb pollen grains showed centromere defects, resulting in pollen abortion at the bi-cellular stage of the male gametophyte. However, inheritance of the mutant allele in a given gamete did not solely determine the abortion phenotype. Introducing functional ASF1B failed to rescue the AaBb- and aaBb- mediated abortion, suggesting that heterozygosity in the ASF1B gene causes gametophytic defects, rather than the loss of ASF1. The presence of reproductive defects in heterozygous mutants but not in homozygotes, and the characteristic all-or-nothing pollen viability within tetrads, were both indicative of commonly-observed T-DNA-mediated translocation activity for this allele. Our observations reinforce the importance of complementation tests in assigning gene function using reverse genetics.