Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence

In this work, we detected lysinebutyrylation (Kbu) and crotonylation(Kcr) sites in rice histone proteins by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells. Comparative analysis of genome-wide histone Kbu, Kcr, and H3K9ac in combination of RNA-sequencing revealed that a large number of rice genes are marked by both Kbu and Kcr, most of which overlap with H3K9ac and are active genes. Under starvation and submergence, Kbu andKcr appeared to be less dynamic than H3K9ac and the three marks displayed changes in different sets of genes. Kbu and Kcr seemed to have a function to poise stress-induced gene activation. The results suggest that histone Kbu and Kcr provide a platform for histone acetylation during gene activation and that the proportional mixture of distinct histone lysine acylations which are regulated by environmental cues and has functionally consequence in chromatin modification and gene expression in plants. RNA-seq and H3K9ac, Kbu, and Kcr ChIP-seq of rice seedlings under normal conditions and starvation and submergence treatments; RNA-seq and H3K9ac ChIP-seq of rice leaf in 4 diurnal times.