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

• Published in: BMC research notes Vol. 15; no. 1; p. 67
• Main Authors: Poinsignon, Thibault, Gallopin, Mélina, Camadro, Jean-Michel, Poulain, Pierre, Lelandais, Gaëlle
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 19-02-2022; BioMed Central; BMC
• Subjects: 3D-Scere; Analysis; Brewer's yeast; Cell cycle; Chromosome conformation capture; Chromosomes; Gene expression; Gene Expression Regulation, Fungal; Gene Regulatory Networks; Genetic aspects; Genetic regulation; Genetic transcription; Genomes; Life Sciences; Localization; Research Note; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins; Saccharomyces cerevisiae Proteins - genetics; Transcription Factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcriptional regulations; Yeast; France; 3D-Scere; Chromosome conformation capture; Yeast; Transcriptional regulations
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-022-05940-5

Transcriptional regulatory modules are usually modelled via a network, in which nodes correspond to genes and edges correspond to regulatory associations between them. In the model yeast Saccharomyces cerevisiae, the topological properties of such a network are well-described (distribution of degrees, hierarchical levels, organization in network motifs, etc.). To go further on this, our aim was to search for additional information resulting from the new combination of classical representations of transcriptional regulatory networks with more realistic models of the spatial organization of S. cerevisiae genome in the nucleus.
Taking advantage of independent studies with high-quality datasets, i.e. lists of target genes for specific transcription factors and chromosome positions in a three dimensional space representing the nucleus, particular spatial co-localizations of genes that shared common regulatory mechanisms were searched. All transcriptional modules of S. cerevisiae, as described in the latest release of the YEASTRACT database were analyzed and significant biases toward co-localization for a few sets of target genes were observed. To help other researchers to reproduce such analysis with any list of genes of their interest, an interactive web tool called 3D-Scere ( https://3d-scere.ijm.fr/ ) is provided.