ArticleMolecular cell2011
Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter.
Article in Molecular cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
What it found
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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.
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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.
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Who cites it
76 citing papers in PubMed, 103 citations in OpenAlex.
- ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility.bioRxiv : the preprint server for biology · 2026Article
- Cohesin facilitates nucleosome invasion by transcription factors.Science advances · 2026Article
- Cohesin Facilitates Nucleosome Invasion by Transcription Factors.bioRxiv : the preprint server for biology · 2025Article
- Native nucleosome-positioning elements as alternatives to the 601 sequence for nucleosome repositioning studies.Nucleic acids research · 2025Article
- Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration.Cell reports · 2024Article
- Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility.NAR genomics and bioinformatics · 2023Article
- Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration.bioRxiv : the preprint server for biology · 2023Article
- Review
- Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions.Molecular cell · 2023Article
- Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient.Cell systems · 2023Article
- Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation.Cell research · 2022Article
- Partitioned usage of chromatin remodelers by nucleosome-displacing factors.Cell reports · 2022Article
- Reb1, Cbf1, and Pho4 Bias Histone Sliding and Deposition Away from Their Binding Sites.Molecular and cellular biology · 2022Article
- Measuring DNA mechanics on the genome scale.Nature · 2021Article
- Variation, Variegation and Heritable Gene Repression inFrontiers in genetics · 2021Review
- Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.PLoS computational biology · 2021Article
- FACT and Ash1 promote long-range and bidirectional nucleosome eviction at the HO promoter.Nucleic acids research · 2020Article
- Article
- Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters.PloS one · 2019Article
- Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome.Molecular biology of the cell · 2018Article
16 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
3 authors at 1 institution in 1 country.
Funding
Abstract
Nucleosome-depleted regions (NDRs) are ubiquitous on eukaryotic promoters. The formation of many NDRs cannot be readily explained by previously proposed mechanisms. Here, we carry out a focused study on a physiologically important NDR in the yeast CLN2 promoter (CLN2pr). We show that this NDR does not result from intrinsically unfavorable histone-DNA interaction. Instead, we identified eight conserved factor binding sites, including that of Reb1, Mcm1, and Rsc3, that cause the local nucleosome depletion. These nucleosome-depleting factors (NDFs) work redundantly, and simultaneously mutating all their binding sites eliminates CLN2pr NDR. The loss of the NDR induces unreliable "on/off" expression in individual cell cycles, but in the presence of the NDR, NDFs have little direct effect on transcription. We present bioinformatic evidence that the formation of many NDRs across the genome involves multiple NDFs. Our findings also provide significant insight into the composition and spatial organization of functional promoters.
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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.