ArticleProceedings of the National Academy of Sciences of the United States of America2014
Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed, 112 citations in OpenAlex.
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- Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an m6A detection efficiency and calling bias correcting pipeline.Nucleic acids research · 2024Article
- Examining chromatin heterogeneity through PacBio long-read sequencing of M.EcoGII methylated genomes: an mbioRxiv : the preprint server for biology · 2023Article
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- Old and newly synthesized histones are asymmetrically distributed in Drosophila intestinal stem cell divisions.EMBO reports · 2023Article
- Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting.Nature structural & molecular biology · 2023Article
- Transcription factor binding process is the primary driver of noise in gene expression.PLoS genetics · 2022Article
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
- Microbial metabolic noise.WIREs mechanisms of disease · 2021Review
- Interplay between genetic, epigenetic, and gene expression variability: Considering complexity in evolvability.Evolutionary applications · 2021Review
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- Coupled liquid biopsy and bioinformatics for pancreatic cancer early detection and precision prognostication.Molecular cancer · 2021Review
- The Epigenetics of Gametes and Early Embryos and Potential Long-Range Consequences in Livestock Species-Filling in the Picture With Epigenomic Analyses.Frontiers in genetics · 2021Review
- Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses.Frontiers in immunology · 2021Review
- A Comparative Overview of Epigenomic Profiling Methods.Frontiers in cell and developmental biology · 2021Review
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- Nucleosomal proofreading of activator-promoter interactions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Nucleosome positioning sequence patterns as packing or regulatory.PLoS computational biology · 2020Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Nucleosomes, the basic unit of chromatin, have a critical role in the control of gene expression. Nucleosome positions have generally been determined by examining bulk populations of cells and then correlated with overall gene expression. Here, we describe a technique to determine nucleosome positioning in single cells by virtue of the ability of the nucleosome to protect DNA from GpC methylation. In the acid phosphatase inducible PHO5 gene, we find that there is significant cell-to-cell variation in nucleosome positions and shifts in nucleosome positioning correlate with changes in gene expression. However, nucleosome positioning is not absolute, and even with major shifts in gene expression, some cells fail to change nucleosome configuration. Mutations of the PHO5 promoter that introduce a poly(dA:dT) tract-stimulated gene expression under nonpermissive conditions led to shifts of positioned nucleosomes similar to induction of PHO5. By contrast, mutations that altered AA/TT/AT periodicity reduced gene expression upon PHO5 induction and stabilized nucleosomes in most cells, suggesting that enhanced nucleosome affinity for DNA antagonizes chromatin remodelers. Finally, we determined nucleosome positioning in two regions described as "fuzzy" or nucleosome-free when examined in a bulk assay. These regions consisted of distinct nucleosomes with a larger footprint for potential location and an increase population of cells lacking a nucleosome altogether. These data indicate an underlying complexity of nucleosome positioning that may contribute to the flexibility and heterogeneity of gene expression.
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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.