H3K9ac-marked three-dimensional genome dynamics in rice under drought stress [ChIP-Seq]
Drought stress response involves vigorous reprogramming of transcriptome while the mechanism modulating this process remains elusive. The role of 3D-genome in the regulation of rice development has recently been unveiled in rice, which exhibited characteristics distinct from that in mammals and other plants. However, the relationship between spatial chromosome organization and drought responsive gene reprogramming is still poorly understood. In this study, we identified H3K9ac as an efficient histone mark that response dynamically to drought stress in rice and re-constructed high-resolution 3D genome contact maps based on these sites under the normal, drought, and recovery conditions. We discovered significant decondensation of chromatin contacts with over 10000 chromatin loops lost upon drought stress treatment while the recovery of 3D genome was limited after 4-day's re-watering. We identified dominate promoter-promoter interacting (PPI) loops under each condition and identified their significant correlations to altered gene expressions in response to the corresponding condition. Based on the relative contact intensities of the PPI connections, we characterized super-promoter regions that integrate closer connections of genes with more vigorous inductions to condition shifts. Especially, about 75% of the drought stress-dominate PPI loops were associated to the binding by a well-defined drought stress-responsive transcription factor, OsbZIP23. The mutation of OsbZIP23 led to the diffuse of over 80% DS-dominate PPI loops and impaired the expression of the connected genes. As a case study, we showed how OsbZIP23 binding to a super-promoter region can integrate the PPI loop formation and transcriptional activation of four function-vital dehydrin genes upon drought stress. Our results shed light on the mechanisms of 3D genome dynamic in response to water supply variations in rice and highlight the role of OsbZIP23 in the regulation of chromatin loop formation under drought stress. Overall design: This study involves 8 ChIA-PET samples, 8 RNA-seq samples, and 13 ChIP-seq samples. All experiments in this study were carried out using two biological replicates. Each replicate involved at least 30 rice seedlings. All buckets were randomly placed in the growth chamber during the treatments.