The histone modification H3K4me3 marks functional genes in soybean nodules

• Published in: Genomics (San Diego, Calif.) Calif.), 2020-11, Vol.112 (6), p.5282-5294
• Main Authors: Wang, Qianwen, Yung, Wai-Shing, Wang, Zhili, Lam, Hon-Ming
• Format: Article
• Language: English
• Subjects: Carbon - metabolism; Chromatin Immunoprecipitation Sequencing; Epigenetic regulation; Gene Expression Regulation, Plant; Gene Regulatory Networks; Glycine max - genetics; Glycine max - metabolism; H3K4me3; Histone Code; Histone modification; Histones - metabolism; Mature nodules; Membrane Transport Proteins - genetics; Membrane Transport Proteins - metabolism; Nitrogen - metabolism; Nodule function; Plant Roots - metabolism; RNA-Seq; Soybean; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptome
• ISSN: 0888-7543; 1089-8646
• DOI: 10.1016/j.ygeno.2020.09.052

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. •H3K4me3 levels were positively correlated with transcription in nodules and remaining roots.•Genes closely related to nodule functions were marked with higher H3K4me3 levels in nodules.•Bidirectional regulation of H3K4me3 levels were found in different families of transmembrane transporters.•Loss of H3K4me3 in several transcription factor genes potentially repressed defense-related regulatory network in nodules.•The role of H3K4me3 in maintaining nodule functions was supported.