Integrated multi-omics analysis reveals poised chromatin and co-regulation of clustered immune receptor genes in soybean

This study is led by Professor Zhenhui Zhong (College of Life Sciences, Sichuan University, Chengdu, China).

The authors investigated global chromatin states and gene expression levels in soybean. The soybean genome was classified into eight chromatin states, with NLRs and PRRs significantly enriched in a ​​poised state​​ (co-marked by both active and repressive epigenetic modifications) compared to randomly selected background genes. Notably, these resistance genes exhibited lower expression levels.

To further dissect the transcription potential of R genes under ​​poised chromatin state​​, the authors integrated ​​RNA polymerase II (Pol II) ChIP-seq​​ and ​​ATAC-seq​​ data. While Pol II binding signals at NLRs and PRRs were generally weaker than background genes, NLRs showed Pol II enrichment near transcription start sites (TSS). But both gene types maintained high chromatin accessibility at TSS regions comparable to background genes, suggesting retained transcriptional potential despite low expression. ​​To dissect the repression mechanisms, the authors analyzed H3K27me3 profiles and uncovered distinct silencing patterns: NLRs showed sharp H3K27me3 peaks flanking the TSS, whereas PRRs displayed broad deposition across the entire gene body.

By incorporating ​​Hi-C​​ data, this study demonstrated that clustered R-genes preferentially localize within the same ​​topologically associating domains (TADs)​​. These TAD-associated clusters exhibited increased repressive marks, particularly in PRRs. Pearson correlation analysis of histone modifications revealed that R-genes within a TAD shared similar chromatin states. Given this epigenetic landscape, co-expression analysis under biotic stress further confirmed that these genes are subject to TAD-mediated co-regulation.

In summary, this multi-omics study (epigenomics, 3D genomics, and transcriptomics) deciphers the epigenetic regulation of soybean NLRs and PRRs. Key findings include:

1. A ​​poised chromatin state of both active and repressive marks​​ balancing low expression with high chromatin accessibility;
2. ​​TAD-dependent co-regulation​​ of clustered R-genes via shared chromatin states.

See the article:

Epigenetically poised chromatin states regulate PRR and NLR genes in soybean

https://link.springer.com/article/10.1007/s42994-025-00233-4