ArticlePLoS biology2011
Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output.
Article in PLoS biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 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
117 citing papers in PubMed, 204 citations in OpenAlex.
- High-mobility group N proteins are required for regulation of antigen-presentation genes in macrophages.Journal of immunology (Baltimore, Md. : 1950) · 2026Article
- NASP functions in the cytoplasm to prevent histone H3 aggregation during early embryogenesis.The Journal of cell biology · 2026Article
- Differential control of both cell cycle-regulated and quantitative histone mRNA expression bybioRxiv : the preprint server for biology · 2026Article
- HMGB1 regulates mitochondrial structure and reactive oxygen species balance during the transition from naïve to primed pluripotency.Frontiers in cell and developmental biology · 2026Article
- NASP functions in the cytoplasm to prevent histone H3 aggregation during early embryogenesis.bioRxiv : the preprint server for biology · 2025Article
- The DNA replication checkpoint targets the kinetochore to reposition DNA structure-induced replication damage to the nuclear periphery.Cell reports · 2025Article
- HMGB1 deforms nucleosomal DNA to generate a dynamic chromatin environment counteracting the effects of linker histone.Science advances · 2025Article
- HMGB1 Deficiency Occurs in a Broad Range of Human Cancers and Is Often Associated with Unfavorable Tumor Phenotype.Diagnostics (Basel, Switzerland) · 2025Article
- Multifaceted roles of H2B mono-ubiquitylation in D-loop metabolism during homologous recombination repair.Nucleic acids research · 2025Article
- The role of the dynamic epigenetic landscape in senescence: orchestrating SASP expression.npj aging · 2024Review
- Reversible Histone Modifications Contribute to the Frozen and Thawed Recovery States of Wood Frog Brains.Biomolecules · 2024Article
- Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility.Nature genetics · 2024Article
- Unraveling Histone Loss in Aging and Senescence.Cells · 2024Review
- The acidic intrinsically disordered region of the inflammatory mediator HMGB1 mediates fuzzy interactions with CXCL12.Nature communications · 2024Article
- A single fiber view of the nucleosome organization in eukaryotic chromatin.Nucleic acids research · 2024Article
- Use of Machine Learning for the Identification and Validation of Immunogenic Cell Death Biomarkers and Immunophenotypes in Coronary Artery Disease.Journal of inflammation research · 2024Article
- Regulation of DNA damage and transcriptional output in the vasculature through a cytoglobin-HMGB2 axis.Redox biology · 2023Article
- ATF3 induction prevents precocious activation of skeletal muscle stem cell by regulating H2B expression.Nature communications · 2023Article
- The histone chaperone NASP maintains H3-H4 reservoirs in the early Drosophila embryo.PLoS genetics · 2023Article
- The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response.Genes · 2022Review
57 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
17 authors at 8 institutions in 3 countries.
Funding
Abstract
The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. Nucleosome number in cells was considered fixed, but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker, and variant histones, and a correspondingly reduced number of nucleosomes, possibly because HMGB1 facilitates nucleosome assembly. Yeast nhp6 mutants lacking Nhp6a and -b proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and affects the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform and can be modelled assuming that different nucleosomal sites compete for available histones. Sites with a high propensity to occupation are almost always packaged into nucleosomes both in wild type and nucleosome-depleted cells; nucleosomes on sites with low propensity to occupation are disproportionately lost in nucleosome-depleted cells. We suggest that variation in nucleosome number, by affecting nucleosomal occupancy both genomewide and gene-specifically, constitutes a novel layer of epigenetic regulation.
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.