ArticleNature communications2020
Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 51 citations in OpenAlex.
- A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation.bioRxiv : the preprint server for biology · 2026Article
- Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing.Epigenetics & chromatin · 2026Article
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- Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA polymerase II productive elongation.Cell reports · 2024Article
- Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals.Molecular biology and evolution · 2024Article
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- Deep learning with a small dataset predicts chromatin remodelling contribution to winter dormancy of apple axillary buds.Tree physiology · 2024Article
- Detection and characterization of pancreatic and biliary tract cancers using cell-free DNA fragmentomics.Journal of experimental & clinical cancer research : CR · 2024Article
- Evolutionary innovation in conserved regulatory elements across the mammalian tree of life.bioRxiv : the preprint server for biology · 2024Article
- Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes.Cancer discovery · 2023Article
- Clustered PHD domains in KMT2/MLL proteins are attracted by H3K4me3 and H3 acetylation-rich active promoters and enhancers.Cellular and molecular life sciences : CMLS · 2023Article
- Epigenetic liquid biopsies for minimal residual disease, what's around the corner?Frontiers in oncology · 2023Review
- Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.Nature structural & molecular biology · 2022Article
- Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer.NPJ genomic medicine · 2022Article
- Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes.Nature communications · 2022Article
- The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes.Nature communications · 2022Article
- The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo.International journal of molecular sciences · 2021Review
- Chromatin dynamics: Nucleosome occupancy and sensitivity as determinants of gene expression and cell fate.Journal of cancer biology · 2021Article
- A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions.Methods in molecular biology (Clifton, N.J.) · 2021Review
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The organization of nucleosomes across functional genomic elements represents a critical layer of control. Here, we present a strategy for high-resolution nucleosome profiling at selected genomic features, and use this to analyse dynamic nucleosome positioning at inducible and cell-type-specific mammalian promoters. We find that nucleosome patterning at inducible promoters frequently resembles that at active promoters, even before stimulus-driven activation. Accordingly, the nucleosome profile at many inactive inducible promoters is sufficient to predict cell-type-specific responsiveness. Induction of gene expression is generally not associated with major changes to nucleosome patterning, and a subset of inducible promoters can be activated without stable nucleosome depletion from their transcription start sites. These promoters are generally dependent on remodelling enzymes for their inducible activation, and exhibit transient nucleosome depletion only at alleles undergoing transcription initiation. Together, these data reveal how the responsiveness of inducible promoters to activating stimuli is linked to cell-type-specific nucleosome patterning.
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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.