Construction Of Gene Regulatory Network And Identification Of Transcription Enhancer Of Transcription Factor MYC2 In Tomato Jasmonate Signaling Pathway

The plant hormone Jasmonate(JA)regulates plant defense responses and growth by inducing transcriptional reprogramming.JA-induced gene transcription is regulated by its master transcription factor MYC2.In order to adapt to challenging environmental stress,plants need to balance growth and resistance responses,which depend on the fine regulation of gene transcription by JA.Transcription enhancers are cis-acting elements that control the spatiotemporal specificity and precise expression of gene transcription.When the cells are stimulated by the signal,the gene transcriptional regulatory complex is assembled on the transcription enhancer to achieve regulation of gene transcription.Our previous study on Arabidopsis found that MYC2 generates JA enhancer(JAEs)to control target gene transcription under JA stimulation.And the study on tomato found that MYC2 regulates resistance gene expression by secondary transcription factor using hierarchical transcriptional regulation module.However,how JAEs participates in the JA-induced gene transcriptional regulatory network and specifically regulates gene transcription remains unresolved.Construction of transcriptional regulatory networks and identification of JAEs in JA signaling are important for understanding JA-mediated defense responses in plants.To this end,this study constructed a JA-induced gene expression regulatory network and identified JAEs in tomato through RNA-seq and ChIP-seq analysis.The main results are summarrized as following:(1)In total 3,563 wound-induced genes were identified by transcriptome data abalysis.Among them,1,812 genes were up-regulated and 1,512 were down-regulated.Functional enrichment analysis showed that differentially expressed genes were mainly involved in jasmonate-mediated signaling pathway and wounding defense responses.(2)The co-expressed genes were divided into 11 clusters by time series clustering.Conservative motif analysis of the promoter region of genes in each cluster reveals that the motifs of different cluster are different.The most enriched motifs are the binding sites of MYB,NAC,TCP,AP2 and AUX/IAA transcription factors.The regulatory network of the wounding response genes was predicted by integrating transcription factors and the motifs of co-expressed gene.(3)Analysis of the ChIP-seq data of MYC2 revealed that MYC2 was not only enriched in the promoter of the target gene,but also significantly enriched in the non-promoter region.We defined the target of MYC2 in the non-promoter region as a JAEs of tomato.By this we identified 395 genes in the target gene of MYC2 with JAEs.Functional enrichment analysis showed that JAEs in tomato mainly controlled the expression of wounding response genes,JA synthesis and carbohydrate metabolism.