ArticleNucleic acids research2012
Nuclear colocalization of transcription factor target genes strengthens coregulation in yeast.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 32 citations in OpenAlex.
- Dual control of liver regeneration by Nr1d1 homeostasis and Klf2 checkpoint.Cell death discovery · 2026Article
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- Polymer folding through active processes recreates features of genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genetic circuit design automation for yeast.Nature microbiology · 2020Article
- TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains.Frontiers in genetics · 2020Article
- The Functional 3D Organization of Unicellular Genomes.Scientific reports · 2019Article
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- Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance.Molecular biology and evolution · 2016Article
- Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- CCSI: a database providing chromatin-chromatin spatial interaction information.Database : the journal of biological databases and curation · 2016Article
- Analysis methods for studying the 3D architecture of the genome.Genome biology · 2015Review
- Coordinated Expression of Phosphoinositide Metabolic Genes during Development and Aging of Human Dorsolateral Prefrontal Cortex.PloS one · 2015Article
- Article
- Reproducibility of 3D chromatin configuration reconstructions.Biostatistics (Oxford, England) · 2014Article
- Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data.Quantitative biology (Beijing, China) · 2013Article
- Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements.Nucleic acids research · 2013Article
- Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome.Nucleic acids research · 2013Article
- Article
- A complex network framework for unbiased statistical analyses of DNA-DNA contact maps.Nucleic acids research · 2013Article
- On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic chromosomes are not randomly distributed in the interphase nucleus, but instead occupy distinct territories. Nonetheless, the genome-wide relationships of gene regulation to gene nuclear location remain poorly understood in yeast. In the three-dimensional view of gene regulation, we found that a considerable number of transcription factors (TFs) regulate genes that are colocalized in the nucleus. Colocalized TF target genes are more strongly coregulated compared with the other TF target genes. Target genes of chromatin regulators are also colocalized. These results demonstrate that colocalization of coregulated genes is a common process, and three-dimensional gene positioning is an important part of gene regulation. Our findings will have implications in understanding nuclear architecture and function.
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