Epigenetically poised chromatin states regulate PRR and NLR genes in soybean

In the plant innate immune system, pattern recognition receptor (PRR) and nucleotide-binding domain leucine-rich repeat (NLR) proteins recognize pathogens and activate defenses. To prevent excessive immune responses that could affect growth, plants regulate PRRs and NLRs at the transcriptional and post-transcriptional levels. Poised or bivalent chromatin states, marked by the simultaneous presence of active and repressive epigenetic modifications, maintain genes in a transcriptionally primed state, keeping their expression low while enabling their rapid activation in response to stress. Here, we investigated how poised chromatin states regulate PRR and NLR genes in soybean (Glycine max). Our integrative epigenomic and transcriptomic analysis revealed that although NLR and PRR genes both harbor abundant active and repressive histone modifications and exhibit high chromatin accessibility, their basal expression levels remain relatively low. Moreover, clustered NLR and PRR genes residing within the same topologically associating domains shared similar chromatin states and expression dynamics, suggesting coordinated control. These gene families had distinct epigenetic features: NLR genes displayed narrow H3K27me3 peaks together with strong pausing of RNA Polymerase II at their 5' ends, whereas PRR genes were characterized by broader H3K27me3 peaks. Together, our results shed light on the role of poised chromatin states in coordinating growth and defense responses in soybean.

The online version contains supplementary material available at 10.1007/s42994-025-00233-4.