ArticlePLoS genetics2017
Three distinct mechanisms of long-distance modulation of gene expression in yeast.
Article in PLoS genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 28 citations in OpenAlex.
- Epigenome regulators imbue a single eukaryotic promoter with diverse gene expression dynamics.iScience · 2026Article
- Condensin accelerates long-range intra-chromosomal interactions.Nature communications · 2026Article
- Condensin Accelerates Long-Range Intra-Chromosomal Interactions.bioRxiv : the preprint server for biology · 2025Article
- Article
- Article
- Transcriptional silencing in Saccharomyces cerevisiae: known unknowns.Epigenetics & chromatin · 2024Review
- Heat Shock Factor 1 forms nuclear condensates and restructures the yeast genome before activating target genes.bioRxiv : the preprint server for biology · 2024Article
- Transcription Factor Condensates Mediate Clustering ofbioRxiv : the preprint server for biology · 2024Article
- DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions.Nature communications · 2024Article
- Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles.Nature communications · 2022Article
- Capture Hi-C reveals the influence on dynamic three-dimensional chromosome organization perturbed by genetic variation or vanillin stress inFrontiers in microbiology · 2022Article
- Primordial super-enhancers: heat shock-induced chromatin organization in yeast.Trends in cell biology · 2021Review
- Existence, Transition, and Propagation of Intermediate Silencing States in Ribosomal DNA.Molecular and cellular biology · 2019Article
- Enhancement of LacI binding in vivo.Nucleic acids research · 2019Article
- Heat Shock Factor 1 Drives Intergenic Association of Its Target Gene Loci upon Heat Shock.Cell reports · 2019Article
- 3D clustering of co-regulated genes and its effect on gene expression.Current genetics · 2017Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Recent Hi-C measurements have revealed numerous intra- and inter-chromosomal interactions in various eukaryotic cells. To what extent these interactions regulate gene expression is not clear. This question is particularly intriguing in budding yeast because it has extensive long-distance chromosomal interactions but few cases of gene regulation over-a-distance. Here, we developed a medium-throughput assay to screen for functional long-distance interactions that affect the average expression level of a reporter gene as well as its cell-to-cell variability (noise). We ectopically inserted an insulated MET3 promoter (MET3pr) flanked by ~1kb invariable sequences into thousands of genomic loci, allowing it to make contacts with different parts of the genome, and assayed the MET3pr activity in single cells. Changes of MET3pr activity in this case necessarily involve mechanisms that function over a distance. MET3pr has similar activities at most locations. However, at some locations, they deviate from the norm and exhibit three distinct patterns including low expression / high noise, low expression / low noise, and high expression / low noise. We provided evidence that these three patterns of MET3pr expression are caused by Sir2-mediated silencing, transcriptional interference, and 3D clustering. The clustering also occurs in the native genome and enhances the transcription of endogenous Met4-targeted genes. Overall, our results demonstrate that a small fraction of long-distance chromosomal interactions can affect gene expression in yeast.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.