Periodic Epi-organization of the Yeast Genome Revealed by the Distribution of Promoter Sites

The organization of transcription within the eukaryotic nucleus may be expected to both depend on and determine the structure of the chromosomes. This study shows that, in yeast, genes that are controlled by the same sequence-specific transcription factor tend to be regularly spaced along the chromo...

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Bibliographic Details
Published in:Journal of molecular biology 2003-06, Vol.329 (5), p.859-865
Main Author: Kepes, F
Format: Article
Language:English
Subjects:
Cell Nucleus - genetics
Chromosome Mapping
Chromosomes, Fungal
DNA-binding proteins
Evolution, Molecular
Gene Expression Regulation, Fungal
Genome, Fungal
nuclear functional organization
Promoter Regions, Genetic
replication
Replication Origin
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae Proteins - genetics
Saccharomyces cerevisiae Proteins - metabolism
Telomere-Binding Proteins - genetics
Telomere-Binding Proteins - metabolism
transcription
Transcription Factors - genetics
Transcription Factors - metabolism
Transcription, Genetic
yeast
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Summary:The organization of transcription within the eukaryotic nucleus may be expected to both depend on and determine the structure of the chromosomes. This study shows that, in yeast, genes that are controlled by the same sequence-specific transcription factor tend to be regularly spaced along the chromosome arms; a similar period characterizes the spacing of origins of replication, although periodicity is less pronounced. The same period is found for most transcription factors within a chromosome arm. However, different periods are observed for different chromosome arms, making it unlikely that periodicity is caused by dedicated scaffolding proteins. Such regularities are consistent with a genome-wide loop model of chromosomes, in which coregulated genes tend to dynamically colocalize in 3D. This colocalization may also involve co-regulated genes belonging to different chromosomes, as suggested by partial conservation of the respective positioning of different transcription factors around the loops. Thus, binding at genuine regulatory sites on DNA would be optimized by locally increasing the concentration of multimeric transcription factors. In this model, self-organization of transcriptional initiation plays a major role in the functional nuclear architecture.
ISSN:0022-2836
1089-8638
DOI:10.1016/S0022-2836(03)00535-7