title: Transcriptional regulatory network shapes the genome structure of Saccharomyces cerevisiae.
abstract: Among cellular processes gene transcription is central. More and more evidence is mounting that transcription is tightly connected with the spatial organization of the chromosomes. Spatial proximity of genes sharing transcriptional machinery is one of the consequences of this organization. Motivated by information on the physical relationship among genes identified via chromosomal conformation capture methods, we complement the spatial organization with the idea that genes under similar transcription factor control, but possible scattered throughout the genome, might be in physically proximity to facilitate the access of their commonly used transcription factors. Unlike the transcription factory model, "interacting" genes in our "Gene Proximity Model" are not necessarily immediate physical neighbors but are in spatial proximity. Considering the stochastic nature of TF-promoter binding, this local condensation mechanism could serve as a tie to recruit co-regulated genes to guarantee the swiftness of biological reactions. We tested this idea with a simple eukaryotic organism, Saccharomyces cerevisiae. Chromosomal interaction patterns and folding behavior generated by our model re-construct those obtained from experiments. We show that the transcriptional regulatory network has a close linkage with the genome organization in budding yeast, which is fundamental and instrumental to later studies on other more complex eukaryotes.
authors.affiliation: Institute for Theoretical Physics, University of Heidelberg, Heidelberg, Germany.
authors.forename: Songling
authors.initials: S
authors.lastname: Li
authors.forename: Dieter W
authors.initials: DW
authors.lastname: Heermann
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping; D015825:Chromosomes, Fungal; D019295:Computational Biology; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D016681:Genome, Fungal; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors
keywords: Saccharomyces cerevisiae; gene proximity; three-dimensional genome architecture; transcription factor; transcriptional regulatory network