ArticleCell reports2013
Decoupling epigenetic and genetic effects through systematic analysis of gene position.
Article in Cell reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 56 citations in OpenAlex.
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- Exploring chromosomal position effects for predictable tuning of metabolic pathways in yeast.Nucleic acids research · 2026Article
- Genome-Wide Landscape of Position Effect Variegation inJournal of fungi (Basel, Switzerland) · 2026Article
- Magnaporthe oryzae pathotype Triticum (MoT) can act as a heterologous expression system for fungal effectors with high transcript abundance in wheat.Scientific reports · 2023Article
- Expression of mammalian proteins for diagnostics and therapeutics: a review.Molecular biology reports · 2022Review
- Metabolic recycling of storage lipids promotes squalene biosynthesis in yeast.Biotechnology for biofuels and bioproducts · 2022Article
- Identification of genome integration sites for developing a CRISPR-based gene expression toolkit in Yarrowia lipolytica.Microbial biotechnology · 2022Article
- Genomic environments scale the activities of diverse core promoters.Genome research · 2022Article
- Incorporating, Quantifying, and Leveraging Noncanonical Amino Acids in Yeast.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Transcriptome Analysis in Yeast Reveals the Externality of Position Effects.Molecular biology and evolution · 2021Article
- Single-cell dynamics of chromatin activity during cell lineage differentiation in Caenorhabditis elegans embryos.Molecular systems biology · 2021Article
- Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network.PLoS genetics · 2021Article
- Identifying chromatin features that regulate gene expression distribution.Scientific reports · 2020Article
- Effect of H2A.Z deletion is rescued by compensatory mutations in Fusarium graminearum.PLoS genetics · 2020Article
- Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq.ACS synthetic biology · 2020Article
- Role ofJournal of fungi (Basel, Switzerland) · 2020Article
- Loci specific epigenetic drug sensitivity.Nucleic acids research · 2020Article
- Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes.Genome research · 2020Article
- Extracting novel hypotheses and findings from RNA-seq data.FEMS yeast research · 2020Review
- Genomic Considerations for the Modification ofMicroorganisms · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Classic "position-effect" experiments repositioned genes near telomeres to demonstrate that the epigenetic landscape can dramatically alter gene expression. Here, we show that systematic gene knockout collections provide an exceptional resource for interrogating position effects, not only near telomeres but at every genetic locus. Because a single reporter gene replaces each deleted gene, interrogating this reporter provides a sensitive probe into different chromatin environments while controlling for genetic context. Using this approach, we find that, whereas systematic replacement of yeast genes with the kanMX marker does not perturb the chromatin landscape, chromatin differences associated with gene position account for 35% of kanMX activity. We observe distinct chromatin influences, including a Set2/Rpd3-mediated antagonistic interaction between histone H3 lysine 36 trimethylation and the Rap1 transcriptional activation site in kanMX. This interaction explains why some yeast genes have been resistant to deletion and allows successful generation of these deletion strains through the use of a modified transformation procedure. These findings demonstrate that chromatin regulation is not governed by a uniform "histone code" but by specific interactions between chromatin and genetic factors.
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What Socratic holds
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 Socratic graph.