Spatial organization of the transcriptional regulatory network of Saccharomyces cerevisiae

Abstract

A transcriptional regulatory network (TRN) is a complex network composed of all of the regulatory interactions between transcription factors and the corresponding target genes. Recently, three‐dimensional (3D) genomic studies have shown that the 3D structure of the genome may influence the regulation of gene transcription, which provides us with a novel perspective. In the present study, we constructed the TRN of the budding yeast Saccharomyces cerevisiae and placed it in the context of a 3D genome model. We analyzed the spatial organization of the yeast TRN on four levels: global features, central nodes, hierarchical structure and network motifs. The results obtained suggest that the TRN of S. cerevisiae presents an optimized structure in space to adapt to functional requirements.

Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology

“…A gene is not only modulated by one gene, TF, or regulatory element, it tends to be regulated by multiple components of them. Moreover, recent studies found that the chromatin architecture could profoundly affect the GRN [11] ( Fig. 1 ).…”

Additional insights into the organization of transcriptional regulatory modules based on a 3D model of the Saccharomyces cerevisiae genome

“…The second one is that of Sun et al . [ 15 ], published in 2019. The authors used the 3D model of S. cerevisiae genome proposed by Duan et al .…”

“…The TRMs were explored from a new perspective, which integrates functional and spatial information presently available, and addressed the following question: are target genes associated to a common TF (TRM) randomly disseminated within the nucleus, or are they preferentially co-localized? In the literature, this question was only partially answered, focusing essentially on spatial distances between genes coding for TFs and associated targets [ 15 ]. Our analysis represents an additional step in this context, reporting all distances between genes that belong to any TRM, as described in the latest release of the YEASTRACT database.…”