ArticleNucleic acids research2013
Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes.iScience · 2026Article
- Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D.Nature communications · 2025Article
- A Cyclic Permutation Approach to Removing Spatial Dependency between Clustered Gene Ontology Terms.Biology · 2024Article
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- Inference of 3D genome architecture by modeling overdispersion of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- Chromatin Hubs: A biological and computational outlook.Computational and structural biotechnology journal · 2022Review
- Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.Methods (San Diego, Calif.) · 2020Review
- Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution.BMC bioinformatics · 2020Article
- G1/S transcription factors assemble in increasing numbers of discrete clusters through G1 phase.The Journal of cell biology · 2020Article
- Assessing stationary distributions derived from chromatin contact maps.BMC bioinformatics · 2020Article
- The Functional 3D Organization of Unicellular Genomes.Scientific reports · 2019Article
- Inferring the three-dimensional structures of the X-chromosome during X-inactivation.Mathematical biosciences and engineering : MBE · 2019Article
- Article
- Large-scale 3D chromatin reconstruction from chromosomal contacts.BMC genomics · 2019Article
- An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data.Biological procedures online · 2019Review
- 3D clustering of co-regulated genes and its effect on gene expression.Current genetics · 2017Review
- Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence.Nucleic acids research · 2017Article
- Form and function of topologically associating genomic domains in budding yeast.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Three distinct mechanisms of long-distance modulation of gene expression in yeast.PLoS genetics · 2017Article
- Heterogeneous Spatial Distribution of Transcriptional Activity in Budding Yeast Nuclei.Biophysical journal · 2017Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
While it has been long recognized that genes are not randomly positioned along the genome, the degree to which its 3D structure influences the arrangement of genes has remained elusive. In particular, several lines of evidence suggest that actively transcribed genes are spatially co-localized, forming transcription factories; however, a generalized systematic test has hitherto not been described. Here we reveal transcription factories using a rigorous definition of genomic structure based on Saccharomyces cerevisiae chromosome conformation capture data, coupled with an experimental design controlling for the primary gene order. We develop a data-driven method for the interpolation and the embedding of such datasets and introduce statistics that enable the comparison of the spatial and genomic densities of genes. Combining these, we report evidence that co-regulated genes are clustered in space, beyond their observed clustering in the context of gene order along the genome and show this phenomenon is significant for 64 out of 117 transcription factors. Furthermore, we show that those transcription factors with high spatially co-localized targets are expressed higher than those whose targets are not spatially clustered. Collectively, our results support the notion that, at a given time, the physical density of genes is intimately related to regulatory activity.
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