Abstract
The spatial organization of eukaryotic genomes is thought to play an important role in regulating gene expression. The recent advances in experimental methods including chromatin capture techniques, as well as the large amounts of accumulated gene expression data allow studying the relationship between spatial organization of the genome and co-expression of protein-coding genes. To analyse this genome-wide relationship at a single gene resolution, we combined the interchromosomal DNA contacts in the yeast genome measured by Duan et al. with a comprehensive collection of 1,496 gene expression datasets. We find significant enhancement of co-expression among genes with contact links. The co-expression is most prominent when two gene loci fall within 1,000 base pairs from the observed contact. We also demonstrate an enrichment of inter-chromosomal links between functionally related genes, which suggests that the non random nature of the genome organization serves to facilitate coordinated transcription in groups of genes.
Highlights
The regulation of transcription in eukaryotes is a complex process that involves several levels of coordination
Janga et al [19] addressed the distribution of different transcription factors (TFs) in yeast among different chromosomes and showed that the targets of a TF tend to cluster on specific chromosomes. the existence of highly prevalent chromosomal territories in the budding yeast has been disputed [6,23,24]
We restrict the analysis to links between loci on different chromosomes, which allows focusing on the interchromosomal interactions, and eliminating the influence of any cis- effects
Summary
The regulation of transcription in eukaryotes is a complex process that involves several levels of coordination This regulation relies on cis-elements (such as transcription factor binding sites) and on the genome organization at different scales, including the distribution of the nucleosomes, the folding of chromatin, as well as the chromosomal conformation and chromosomal territories [1,2,3,4,5,6]. Many aspects of nuclear organization have been observed in spite of its small genome These include the placement [7] and folding [8] of chromosomes, clustering of telomeres [8,9,10,11,12,13], the role of radial position within the nucleus [14], or the interactions between DNA and the nuclear envelope and association with the nuclear pores; for a comprehensive review see [15,16,17,18]. Janga et al [19] addressed the distribution of different transcription factors (TFs) in yeast among different chromosomes and showed that the targets of a TF tend to cluster on specific chromosomes. the existence of highly prevalent chromosomal territories in the budding yeast has been disputed [6,23,24]
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