H3K9 Acetylatome and transcriptome profiles during flag leaf aging in rice (Oryza Sativa)

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetics information via gene expression and epigenetically modification, as well as protein modification, but their mechanism either in fine-tune level or in global level is still unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq) and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza Sativa). We found that genome-wide H3K9 acetylation levels were increased with age-dependent senescence in rice flag leaf, the density and breath of H3K9ac was positively correlated with gene expression and transcript elongation. A set of 1,249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac was observed during rice flag leaf aging. We produced a landscape of H3K9 acetylation modified targets gene expression during flag leaf aging that includes known senescence associated genes such as transcription factors, receptor-like kinase, hormone pathway genes and metabolism related enzyme genes such as carbon metabolism, nitrogen metabolism, and their allocation, as well as miRNA biosynthesis related genes such as AGO1, DICER1. Our findings reveal a complex regulatory network of metabolism and senescence mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.