Nitrogen fixation in legumes requires the development of specialized organs called root nodules. Here we characterized the high-confidence transcriptome and genome-wide patterns of H3K4me3 marks in soybean roots and mature nodules symbiotic with Sinorhizobium fredii. Changes in H3K4me3 levels were positively associated with the transcription levels of functional genes in the nodules. The up-regulation of H3K4me3 levels was not only present in leghaemoglobin and nodulin-related genes, but also in genes involved in nitrogen and carbon metabolic pathways. In addition, genes regulating the transmembrane transport of metal ions, phosphates, sulphates, peptides, and sugars were differentially modified. On the contrary, a loss of H3K4me3 marks was found in several key transcription factor genes and was correlated with the down-regulation of the defense-related network in nodules, which could contribute to nodule maintenance. All these findings demonstrate massive reprogramming of gene expressions via alterations in H3K4me3 levels in the genes in mature soybean nodules.

豆类中的固氮需要发育称为根瘤的特殊器官。在这里，我们表征了大豆根和成熟根瘤中 H3K4me3 标记的高可信度转录组和全基因组模式与中华根瘤菌共生. H3K4me3 水平的变化与结节中功能基因的转录水平呈正相关。H3K4me3 水平的上调不仅存在于豆血红蛋白和结节素相关基因中，而且存在于参与氮和碳代谢途径的基因中。此外，调节金属离子、磷酸盐、硫酸盐、肽和糖类跨膜转运的基因被差异修饰。相反，在几个关键转录因子基因中发现了 H3K4me3 标记的丢失，这与结节中防御相关网络的下调有关，这可能有助于结节的维持。所有这些发现都证明了通过改变成熟大豆根瘤基因中 H3K4me3 水平的改变，基因表达的大规模重编程。