| Epigenetic regulation, including DNA mehylation, histone modification and chromatin remodeling, participates in various biological process, especially gene regulation during development, which makes it to be the forefront of bioscience. Rice is one of the most important food in the world, also the classic model of monocot organisms. But the study of epigenetic mechanisms is rarely reported in rice. Therefore, it is of great significance to study the epigenetic modification in rice.The dynamic structure of chromatin is essential for genome activities in higher eukaryotes. Chromatin remodeling factors are major factors to regulate chromatin structure through recognizing specific chromatin modification marks and altering nucleosome position or composition. Here we study two chromatin remodeling factors DDM1and CHR729in rice, which belong to the SNF2family. Our data demonstrated that DDM1could maintain the genome DNA methylation and stability. Nevertheless, CHR729was a plant-special CHD (Chromodomain, Helicase/ATPase and DNA-binding domain) protein gene which could maintain the histone methyaltion H3K4me3and H3K27me3levels and affect multiple aspects in rice development. At the same time, we could understand the relationship of epigenetic modifications.1. The rice DDM1had two homologous genes DDM1a and DDM1b which also had similar expression profile. The DNA methylation of many repeats, transposons and retrotranspsons had reduced in ddm1b. Loss of DDMlb might lead to plant shorter and pollen sterility, the phonotype might be caused by transposon activation. The over-expression DDM1b lines might grow better compared with the control lines. The ddm1b was hypersensitive to5-aza compared to wild type. Down-regulation of DDM1could be induced by5-aza treatment. DDM1might be involved in5-Aza inhibition of DNA methylation pathway in rice. Finally, the DDM1b protein could interact with the MSI1and ZIM genes in yeast, it suggested that DDM1b gene may be involved in the process of adversity as well as gametogenesis.2. A mutation or down-regulation of the CHR729caused a number of aberrant morphological phenotypes, including short and narrow leaves, reduced stemelongation, longer flowering time, and less secondary panicle branches and so on. The CHR729was found to bind to H3K27me3and H3K4me2in vitro by the single plant homeodomain (PHD) finger and the chromodomains, respectively. The expression of auxin biosynthesize genes YUCCA were reduced in chr729compared with wild-type, but the auxin response genes IAA and GH3were not effect when they responsed to the IAA. At the same time, the early induction of cytokinin responsive genes RR were reduced and solwed when they responed to the6-BA, and cytokinin oxidase genes CKX were up-regulated in chr729compared with wild-type. Then, we tested the H3K4m3and H3K27me3levels of YUCCA7, RRs before and after the treatment of6-BA, we found that the increase of H3K4me3in the wild-type but not in the chr729leaded to expression of these genes down regulated. The flowering pathway genes RID1and RFT1were down-regulated in chr729compared with wild-type under long day conditions that was the reason of the longer flowering time in chr729.3. Loss of CHR729leaded to decrease of overall H3K27me3and H3K4me3in rice seedling by western blot. Therefore, Genome-wide analysis by CHIP-seq revealed that H3K27me3and H3K4me3were lost from about56%and23%of marked loci, respectively, which correspond mostly to under-expressed or repressed genes. In addition, analysis of the CHIP-seq data compared with the Microarray data, a higher-than-expected proportion of down-regulated genes lost H3K4me3, among which many encode DNA-binding transcription factors in chr729. These results suggested that the rice CHR729protein was a bifunctional chromatin regulator able to recognize and modulate H3K4and H3K27methylation over repressed or tissue-specific genes, which may be associated with regulation of plant development. |
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