Proteins in the Chromodomain-Helicase/ATPase-DNA-binding domain (CHD) family are divided into three groups. The function of group I CHD proteins in nucleosome positioning is well established, while that of group II members (represented by CHD3/Mi2) remains unclear. Using high-throughput approaches, we investigated the function of the group II rice (Oryza sativa) CHD protein CHR729 in nucleosome positioning, gene expression, histone methylation, and binding. Our data revealed that the chr729 mutation led to increased nucleosome occupancy in the rice genome and altered the expression and histone H3K4me3 modification of many, mainly underexpressed, genes. Further analysis showed that the mutation affected both the deposition and depletion of H3K4me3 in distinct chromatin regions, with concomitant changes in H3K27me3 modification. Genetic and genomic analyses revealed that CHR729 and JMJ703, an H3K4 demethylase, had agonistic, antagonistic, and independent functions in modulating H3K4me3 and the expression of subsets of genes. In addition, CHR729 binding was enriched in H3K4me3-marked genic and H3K27me3-marked intergenic regions. The results indicate that CHR729 has distinct functions in regulating H3K4me3 and H3K27me3 modifications and gene expression at different chromatin domains and provide insight into chromatin regulation of bivalent genes marked by both H3K4me3 and H3K27me3.

Chromodomain-Helicase / ATPase-DNA-binding domain（CHD）家族中的蛋白质分为三类。I组CHD蛋白在核小体定位中的功能已得到充分确立，而II组成员（由CHD3 / Mi2代表）的功能仍不清楚。使用高通量方法，我们研究组II稻（的函数稻在核小体定位，基因表达，组蛋白甲基化，并结合）CHD蛋白CHR729。我们的数据显示，该chr729突变导致水稻基因组中核小体占用增加，并改变了许多主要是表达不足的基因的表达和组蛋白H3K4me3修饰。进一步的分析表明，该突变影响了染色质区域中H3K4me3的沉积和消耗，同时伴随着H3K27me3修饰的变化。遗传和基因组分析表明，H3K4脱甲基酶CHR729和JMJ703在调节H3K4me3和基因子集的表达中具有激动，拮抗和独立的功能。此外，CHR729绑定丰富了H3K4me3标记的基因和H3K27me3标记的基因间区域。