ArticleEpigenetics & chromatin2019
Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing.
Article in Epigenetics & chromatin, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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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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Who cites it
14 citing papers in PubMed, 15 citations in OpenAlex.
- A KDM5 variant outside the catalytic Jumonji C domain disrupts demethylase activity and alters the proximity interactome.G3 (Bethesda, Md.) · 2026Article
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- A Scalable MNase-seq Framework for Reproducible Nucleosome Profiling across Pluripotent Stem Cell and Cardiomyocyte Models.Computational and structural biotechnology journal · 2026Article
- Local chromatin context informs transcriptional outcomes for the histone demethylase KDM5.Epigenetics & chromatin · 2025Article
- Symmetric adenine methylation is an essential DNA modification in the early-diverging fungus Rhizopus microsporus.Nature communications · 2025Article
- Design and characterization of G-quadruplex RNA aptamers reveal RNA-binding by KDM5 lysine demethylases.Computational and structural biotechnology journal · 2025Article
- The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes.Nucleic acids research · 2024Article
- Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice.Genome research · 2024Article
- Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice.bioRxiv : the preprint server for biology · 2023Article
- M-DATA: A statistical approach to jointly analyzing de novo mutations for multiple traits.PLoS genetics · 2021Article
- Epigenetic Landscape of Liquid Biopsy in Colorectal Cancer.Frontiers in cell and developmental biology · 2021Review
- Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases.Nucleic acids research · 2020Article
- Diverse DNA Sequence Motifs Activate Meiotic Recombination Hotspots Through a Common Chromatin Remodeling Pathway.Genetics · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundPositioning of nucleosomes along DNA is an integral regulator of chromatin accessibility and gene expression in diverse cell types. However, the precise nature of how histone demethylases including the histone 3 lysine 4 (H3K4) demethylase, KDM5B, impacts nucleosome positioning around transcriptional start sites (TSS) of active genes is poorly understood.
resultsHere, we report that KDM5B is a critical regulator of nucleosome positioning in embryonic stem (ES) cells. Micrococcal nuclease sequencing (MNase-Seq) revealed increased enrichment of nucleosomes around TSS regions and DNase I hypersensitive sites in KDM5B-depleted ES cells. Moreover, depletion of KDM5B resulted in a widespread redistribution and disorganization of nucleosomes in a sequence-dependent manner. Dysregulated nucleosome phasing was also evident in KDM5B-depleted ES cells, including asynchronous nucleosome spacing surrounding TSS regions, where nucleosome variance was positively correlated with the degree of asynchronous phasing. The redistribution of nucleosomes around TSS regions in KDM5B-depleted ES cells is correlated with dysregulated gene expression, and altered H3K4me3 and RNA polymerase II occupancy. In addition, we found that DNA shape features varied significantly at regions with shifted nucleosomes.
conclusionAltogether, our data support a role for KDM5B in regulating nucleosome positioning in ES cells.
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