Spatial organization of the transcriptional regulatory network of Saccharomyces cerevisiae

Abstract

Transcriptional regulatory network (TRN) is a directed complex network composed of all regulatory interactions between transcription factors and corresponding target genes. Recently, the three-dimensional (3D) genomics studies have shown that the 3D structure of the genome makes a difference to the regulation of gene transcription, which provides us with a novel perspective. In this study, we constructed the TRN of the budding yeast Saccharomyces cerevisiae and placed it in the context of 3D genome model. We analyzed the spatial organization of the yeast TRN on four levels: global feature, central nodes, hierarchical structure and network motifs. Our results suggested that the TRN of S. cerevisiae presents an optimized structure in space to adapt to functional requirement.

The Spatial Organization of Bacterial Transcriptional Regulatory Networks

“…Similar analysis may be extended to other prokaryotes and eukaryotes when data are available, to examine if these features are general among organisms. Actually, our previous work in yeast has found opposite overall trend as compared with the current bacterial results [35], possibly due to the obvious difference between eukaryotes and prokaryotes (namely, the existence of karyotheca), but more species should be studied to obtain general conclusion. Meanwhile, our findings suggest that the spatial arrangement of genes has important effects on their regulation relationships and thus their biological functions, and the spatial effect may be exploited in practice to modulate gene expression based on 3D distance through gene editing approaches such as TALEN or CRISPR [36, 37], which lays a foundation for the spatial-distance-based gene circuit design in synthetic biology [38].…”