ArticleNucleic acids research2016
Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 82 citations in OpenAlex.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- A Scalable MNase-seq Framework for Reproducible Nucleosome Profiling across Pluripotent Stem Cell and Cardiomyocyte Models.Computational and structural biotechnology journal · 2026Article
- IVF and Thermal Manipulation at the First Cleavage Stage Alter Offspring Circadian Phenotype, Sleep, and Brain Epigenetics.International journal of molecular sciences · 2025Article
- Cold-induced nucleosome dynamics linked to silencing of Arabidopsis FLC.Nature communications · 2025Article
- In vivo assembly of complete eukaryotic nucleosomes and (H3-H4)-only non-canonical nucleosomal particles in the model bacterium Escherichia coli.Communications biology · 2024Article
- nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome.Science advances · 2024Article
- Nucleosome reorganisation in breast cancer tissues.Clinical epigenetics · 2024Article
- Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns.The EMBO journal · 2023Article
- The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells.BMC genomics · 2023Article
- Mother-Fetus Immune Cross-Talk Coordinates "Extrinsic"/"Intrinsic" Embryo Gene Expression Noise and Growth Stability.International journal of molecular sciences · 2022Article
- A study of strong nucleosomes in the human genome.iScience · 2022Article
- NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA.Chromosoma · 2022Article
- GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency inGenome research · 2022Article
- Computational identification and experimental characterization of preferred downstream positions in human core promoters.PLoS computational biology · 2021Article
- Collaboration through chromatin: motors of transcription and chromatin structure.Journal of molecular biology · 2021Review
- Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer.International journal of molecular sciences · 2021Review
- Peculiarities ofInternational journal of molecular sciences · 2021Review
- Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes.International journal of molecular sciences · 2020Article
- Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters.Nature communications · 2020Article
- Beads on a string-nucleosome array arrangements and folding of the chromatin fiber.Nature structural & molecular biology · 2020Review
Corrections and comments
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Authors and funding
9 authors at 6 institutions in 3 countries.
Funding
Abstract
Nucleosomal DNA is thought to be generally inaccessible to DNA-binding factors, such as micrococcal nuclease (MNase). Here, we digest Drosophila chromatin with high and low concentrations of MNase to reveal two distinct nucleosome types: MNase-sensitive and MNase-resistant. MNase-resistant nucleosomes assemble on sequences depleted of A/T and enriched in G/C-containing dinucleotides, whereas MNase-sensitive nucleosomes form on A/T-rich sequences found at transcription start and termination sites, enhancers and DNase I hypersensitive sites. Estimates of nucleosome formation energies indicate that MNase-sensitive nucleosomes tend to be less stable than MNase-resistant ones. Strikingly, a decrease in cell growth temperature of about 10°C makes MNase-sensitive nucleosomes less accessible, suggesting that observed variations in MNase sensitivity are related to either thermal fluctuations of chromatin fibers or the activity of enzymatic machinery. In the vicinity of active genes and DNase I hypersensitive sites nucleosomes are organized into periodic arrays, likely due to 'phasing' off potential barriers formed by DNA-bound factors or by nucleosomes anchored to their positions through external interactions. The latter idea is substantiated by our biophysical model of nucleosome positioning and energetics, which predicts that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates nucleosome phasing at active genes significantly better than sequence-dependent models.
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