| Transcriptional regulatory network(TRN)is a biomolecular network composed of transcription factors and their regulated target genes,which plays an important role in the process of organism adaptation to the environment.It is found that there are topological features in the transcriptional regulatory network,such as hierarchical structure,key nodes and network motifs.As an important component of TRN,the dynamic function of TRN motifs in vivo has been extensively studied.However,previous studies mainly considered the time variable and ignored the influence of the spatial distance between transcription factors and target genes on the expression level of target genes.Therefore,the spatial dynamic characteristics of TRN motifs remain unclear.In this study,the TRN of Escherichia coli was constructed,and the global and local spatial organization features of this TRN under heat stress were analyzed by integrating 3D genomic and transcriptome data,and compared with the corresponding features under normal temperature.Combined with gene function annotation,the heat-adaptive feedforward loop(FFL)motif was identified and screened in the E.coli TRN,and the spatial dynamic model of this motif was established,which was verified by genome editing experiments.In this study,it was found that the global and local spatial organization features of E.coli TRN changed significantly under heat stress,and the spatial distance between genes in the FFL motifs was specifically associated with the change of gene expression level:(1)At the global level,the gene interaction frequency of E.coli TRN increased significantly under heat shock.In heat shock condition,the short-range interactions in the E.coli TRN were significantly reduced,while the remote interactions were significantly enhanced.There was a positive correlation between gene interaction frequency and target gene expression in positive regulation(activation)relationship,and a negative correlation between gene interaction frequency and target gene expression in negative regulation(inhibition)relationship.(2)At the local level,the Middle layer and its interaction with other layers are enhanced under heat shock and heat stress,while the Bottom layer is the opposite.Under heat shock and heat stress,the interaction intensity of Out-hub and Bottleneck nodes of the TRN is higher than that of control group,while In-hub and Center nodes show an opposite trend.(3)At the network motif level,the sum of interaction frequencies of X-Y genes and Y-Z genes in the heat-adaptive Coherent type 1 FFL(C1-FFL)motifs decreased significantly,while the change trend of interaction frequencies in the Incoherent type 1 FFL(I1-FFL)was opposite.Under heat shock and heat stress,the expression of Z gene is directly proportional to the spatial distance of the directly regulated edges in the heatadaptive C1-FFL,while the indirect regulated edges of I1-FFL show an opposite trend.This study revealed the spatial organization features of TRN under heat stress and the spatial dynamic characteristics of the FFL motifs,which provided a theoretical basis for systematic understanding of the TRN function in the process of biological adaptation to environment. |
