TOR represses stress responses through global regulation of H3K27 trimethylation in plants

Target of rapamycin (TOR) functions as a central sensory hub linking a wide range of external stimuli to gene expression. The mechanisms underlying stimulus-specific transcriptional reprogramming by TOR remain elusive. Here, we describe an in silico analysis in Arabidopsis demonstrating that TOR-repressed genes are associated with either bistable or silent chromatin states. Both states regulated by the TOR signaling pathway are associated with a high level of histone H3K27 trimethylation (H3K27me3) deposited by CURLY LEAF in a specific context with LIKE HETEROCHROMATIN PROTEIN1. The combination of the two epigenetic histone modifications H3K4me3 and H3K27me3 implicates a bistable feature that alternates between an 'on' and an 'off' state, allowing rapid transcriptional changes upon external stimuli. The chromatin remodeler SWI2/SNF2 ATPase BRAHMA activates TOR-repressed genes only at bistable chromatin domains to rapidly induce biotic stress responses. Here, we demonstrate both in silico and in vivo that TOR represses transcriptional stress responses through global maintenance of H3K27me3. TOR regulates gene expression upon environmental stimuli via two types of chromatin, namely the repressive chromatin marked by H3K27me3 and the bistable chromatin marked by both H3K27me3 and H3K4me3.

Automated summary

The target of rapamycin (TOR) acts as a central sensory hub connecting external stimuli to gene expression. The mechanism for stimulus-specific transcriptional reprogramming by TOR is not well understood. In this study, we analyzed Arabidopsis in silico and found that TOR-repressed genes are associated with bistable or silent chromatin states. These chromatin states are regulated by histone modifications, particularly H3K27me3, and the combination of H3K4me3 and H3K27me3 allows rapid transcriptional changes in response to stimuli.