ArticleNucleic acids research2010
Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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142 citing papers in PubMed.
- Integrative modeling of the genome structure and dynamics in fission yeast.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- Easy Hi-C: A Low-Input Method for Capturing Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Inference of 3D genome architecture by modeling overdispersion of Hi-C data.Bioinformatics (Oxford, England) · 2023Article
- Hodge theory-based biomolecular data analysis.Scientific reports · 2022Article
- Article
- Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells.Biophysics and physicobiology · 2022Article
- Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection.Journal of fungi (Basel, Switzerland) · 2021Article
- Subtelomeric Chromatin in the Fission YeastMicroorganisms · 2021Review
- Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C.Epigenetics & chromatin · 2021Review
- Potential roles of condensin in genome organization and beyond in fission yeast.Journal of microbiology (Seoul, Korea) · 2021Review
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- 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
- Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases.Molecular cell · 2020Article
- Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.Briefings in functional genomics · 2020Article
- Computing 3D Chromatin Configurations from Contact Probability Maps by Inverse Brownian Dynamics.Biophysical journal · 2020Article
- Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation.Developmental cell · 2020Article
82 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
We have comprehensively mapped long-range associations between chromosomal regions throughout the fission yeast genome using the latest genomics approach that combines next generation sequencing and chromosome conformation capture (3C). Our relatively simple approach, referred to as enrichment of ligation products (ELP), involves digestion of the 3C sample with a 4 bp cutter and self-ligation, achieving a resolution of 20 kb. It recaptures previously characterized genome organizations and also identifies new and important interactions. We have modeled the 3D structure of the entire fission yeast genome and have explored the functional relationships between the global genome organization and transcriptional regulation. We find significant associations among highly transcribed genes. Moreover, we demonstrate that genes co-regulated during the cell cycle tend to associate with one another when activated. Remarkably, functionally defined genes derived from particular gene ontology groups tend to associate in a statistically significant manner. Those significantly associating genes frequently contain the same DNA motifs at their promoter regions, suggesting that potential transcription factors binding to these motifs are involved in defining the associations among those genes. Our study suggests the presence of a global genome organization in fission yeast that is functionally similar to the recently proposed mammalian transcription factory.
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