Have you ever thought of how the day-night cycle can epigenetically affect plants? Latest research from Zhang et al. has shown a possible mechanism of how histone variants can negatively regulate gene expression in day-night cycles of rice seedling tissues. This paves a way for an exciting area of research of how histone variants can be differentially deposited in a very short time span, in order to fine tune the transcription due to the environmental stimuli in plants.
Histones variants, termed as the chromatin “wrap-artists“, have come into the spotlight for their diverse, context dependent actions in species ranging from the humble yeast (S. cerevisiae) to mammals and plants. These replication-independent proteins are constitutively expressed, which are distinct from their canonical counterparts, being expressed during cellular replication. As we know, histones are proteins responsible for DNA packaging into nucleosomes, thereby forming chromatin. The function of histone variants has been found to be more than that.
H2A.Z, a variant of canonical H2A histone, has surprising functions in chromatin architectures. Typically, H2A.Z enrichment seems to be variable in different species and tissue types, most prominently at the promoters and gene bodies. Lately, it has also been found to regulate enhancer activity. Studies have shown that H2A.Z enrichment at the transcription start site (TSS) reduces the energy barrier for RNA polymerase II, which is responsible for transcribing mRNAs efficiently. On the contrary, its gene body incorporation has been demonstrated to be a targeted gene repression mechanism. Recently it has also been linked to mammalian memory formation. Surprisingly in plants, H2A.Z has been implicated as an “environmental thermo-sensor” in Arabidopsis, as elevated temperature resulted in eviction of H2A.Z from the promoters, although it had not been linked to transcription in this particular case.
In spite of its delusive nature in gene transcription in metazoans, emerging research has exhibited some astounding features of H2A.Z. Zhang et al. have reported a causal link of differential H2A.Z deposition due to a day-night cycle in rice seedling tissues. Although its function in regulating circadian rhythm has been characterized in mammals, it is still unknown if this occurs in a similar context for plants. The work published by Zhang et al. was by far the first direct evidence of histone variant turnover due to day-light cycle in plants.
Initially, the investigators measured diurnal gene expression for H2A.Z encoding genes and it was found to be highly expressed during night time. This facilitated the idea of generating H2A.Z ChIP-seq (chromatin immunoprecipitation followed by sequencing) data for comparing their binding regions in day and night conditions.
Genome-wide H2A.Z ChIP-seq profiling of rice seedlings harvested at day and night were done to find the overall peak distributions. It was annotated mostly at the promoter and exons, as well as to the 5’-UTR regions for both conditions. More in depth analysis revealed that H2A.Z was less deposited at the TSS (transcription start site) region for a subset of genes during daytime, which had up-regulated expression. But for the nighttime H2A.Z deposition, it was increased to some set of genes, which down-regulated their gene expression. This was done by dividing H2A.Z ChIP-seq profiles around TSS into quantiles, thereby separating increased H2A.Z occupancy for down-regulated genes and decreased H2A.Z occupancy for up-regulated genes in different conditions.
Further gene ontology analysis revealed that up-regulated genes with lower H2A.Z abundance during daytime harvested rice seedlings were linked to important daylight related biological events such as photosynthesis and energy metabolism. In a similar fashion, genes that were highly expressed with less H2A.Z deposition at night, were involved in nocturnal activities, such as cellular protein modification, macromolecule modification, and protein phosphorylation processes.
This new report of H2A.Z demonstrates how histone variant incorporation at the nucleosome can be an important regulator for plant adaptation in a diurnal resolution. It may be another fine-tuning mechanism which gives the advantage of selectively depositing H2A.Z in an oscillating manner, to repress genes related to pathways that are perhaps not economical energy-wise, for the survival of the rice seedlings. Given that thermal stress-regulated grain yield in purple false brome (Brachypodium distachyon) is controlled by H2A.Z nucleosomes, it will be interesting to find out what role H2A.Z plays in the aspect of rice yield by manipulating its levels.