ArticleMolecular and cellular biology2003
Collaborative competition mechanism for gene activation in vivo.
Article in Molecular and cellular biology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 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
115 citing papers in PubMed, 181 citations in OpenAlex.
- Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context.Cell · 2026Article
- Blocking heterochromatin spreading constrains cohesin binding at a yeast heterochromatic locus.PloS one · 2026Article
- Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.Cell genomics · 2025Article
- Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery.Heliyon · 2024Article
- Transcriptional silencing in Saccharomyces cerevisiae: known unknowns.Epigenetics & chromatin · 2024Review
- PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape.Nature immunology · 2024Article
- Coordination of transcription factors and SWI-SNF complexes regulates chromatin priming in developing T cells.Nature immunology · 2024Article
- PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Circadian regulation of stereotypic chromatin conformations at enhancers.bioRxiv : the preprint server for biology · 2024Article
- Review
- HAND2 Assists MYCN Enhancer Invasion to Regulate a Noradrenergic Neuroblastoma Phenotype.Cancer research · 2023Article
- Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response.Genes · 2022Review
- Generating specificity in genome regulation through transcription factor sensitivity to chromatin.Nature reviews. Genetics · 2022Review
- A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1.Genome biology · 2022Article
- Characterization of sequence determinants of enhancer function using natural genetic variation.eLife · 2022Article
- Enhancer RNAs step forward: new insights into enhancer function.Development (Cambridge, England) · 2022Article
- Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.Cell reports · 2022Article
- Article
- Extracting multi-way chromatin contacts from Hi-C data.PLoS computational biology · 2021Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The mechanism by which gene regulatory proteins gain access to their DNA target sites is not known. In vitro, binding is inherently cooperative between arbitrary DNA binding proteins whose target sites are located within the same nucleosome. We refer to such competition-based cooperativity as collaborative competition. Here we show that arbitrarily chosen foreign DNA binding proteins, LexA and Tet repressor, cooperate with an adjacently binding endogenous activator protein, Gcn4, to coactivate expression of chromosomal reporter genes in Saccharomyces cerevisiae. Coactivation requires that the cooperating target sites be within a nucleosome-length distance; it leads to increased occupancy by Gcn4 at its binding site; and it requires both Gcn5 and Swi/Snf which, at an endogenous Gcn4-dependent promoter, act subsequent to Gcn4 binding. These results imply that collaborative competition contributes to gene regulation in vivo. They further imply that, even in the presence of the cell's full wild-type complement of chromatin remodeling factors, competition of regulatory proteins with histone octamer for access to regulatory target sites remains a quantitative determinant of gene expression levels. We speculate that initial target site recognition and binding may occur via spontaneous nucleosomal site exposure, with remodeling factor action required downstream to lock in higher levels of regulatory protein occupancy.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.