Differential deposition of H2A.Z in combination with histone modifications within related genes in Oryza sativa callus and seedling

Abstract

As a histone variant, H2A.Z is highly conserved among species and plays a significant role in diverse cellular processes. Here, we generated genome-wide maps of H2A.Z in Oryza sativa (rice) callus and seedling by combining chromatin immunoprecipitation using H2A.Z antibody and high-throughput sequencing. We found a significantly high peak and a small peak of H2A.Z distributed at the 5' and 3' ends of highly expressed genes, respectively. H2A.Z was also associated with inactive genes in both tissues. H3 lysine 4 trimethylation was associated with H2A.Z deposition at the 5' end of expressed genes, and H3 lysine 27 trimethylation peaks were partially associated with H2A.Z. In summary, our study provides global analysis data for the distribution of H2A.Z in the rice genome. Our results demonstrate that the differential deposition of H2A.Z might play important roles in gene transcription during rice development.

Differential deposition of H2A.Z in rice seedling tissue during the day-night cycle

“…S1B). All these results were consistent with the findings for callus and day seedling tissues 14 A heatmap based on the presence of H2A.Z at the TSSs was used to divide all the genes into 3 groups. These were genes without H2A.Z deposition genes, genes where H2A.Z was significantly enriched at the 5 0 end, and genes where H2A.Z was enriched at the 5 0 end and across the gene bodies (Fig.…”

“…2C and 2D). 14 The gene loci LOC_Os03g17570 (ortholog of Arabidopsis circadian gene PRR7) was highly expressed during the day and had a similar expression pattern to Arabidopsis, whereas H2A.Z deposition was opposite to its expression levels during the day-night cycle ( Fig. 2E).…”

“…17,18 In plants, such as Arabidopsis, H2A.Z also plays a central role in the regulation of flowering time. 19 In our recent study, we found that H2A.Z may play important roles in regulating gene transcription during rice development 14 However, the mechanism behind the deposition of H2A.Z during the day-night cycle in rice is unknown.…”

“…Z data for day seedling tissue was reported in our previous publication. 14 The night seedling data showed that 86.9% of total reads were mapped to the genome and 35,159 peaks were called through these mapped reads. Then we examined the distribution of H2A.Z-related nucleosomes in the promoter, the 5 0 untranslated region (UTR), and the 3 0 UTR, exon, intron, and intergenic regions.…”

Defining chromatin state transitions predicts a network that modulates cell wall remodeling in phosphate-starved rice shoots

“…H2A.Z is also abundant at the TSS of PCG, but appears to play roles in gene expression by localizing to gene bodies and the TES, as well (Coleman-Derr and Zilberman, 2012, Sura et al, 2017, Zahraeifard et al, 2018). In contrast to H3K4me3, TSS-localized H2A.Z is negatively correlated with basal expression (Figure 2; (Zilberman et al, 2008, Coleman-Derr and Zilberman, 2012, Yelagandula et al, 2014, Dai et al, 2017, Zhang et al, 2017, Zahraeifard et al, 2018). Interestingly, our data show that both H2A.Z and H3K4me3 localized downstream of the TSS region are negatively correlated with expression.…”