ArticlePloS one2015
Nucleosome Organization in Human Embryonic Stem Cells.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 38 citations in OpenAlex.
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Structural analysis of OCT4 binding to human LIN28B nucleosomes.Scientific reports · 2026Article
- Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications.eLife · 2025Article
- Nucleosome reorganisation in breast cancer tissues.Clinical epigenetics · 2024Article
- NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality.Genome biology · 2021Article
- Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits.International journal of molecular sciences · 2021Review
- Enhancers predominantly regulate gene expression during differentiation via transcription initiation.Molecular cell · 2021Article
- A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer.Cancer cell · 2020Article
- Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors.Cell reports · 2019Article
- DNMT3B shapes the mCA landscape and regulates mCG for promoter bivalency in human embryonic stem cells.Nucleic acids research · 2019Article
- Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells.Scientific reports · 2019Article
- Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome.Nucleic acids research · 2019Article
- A Scaled Framework for CRISPR Editing of Human Pluripotent Stem Cells to Study Psychiatric Disease.Stem cell reports · 2017Article
- Article
- Exploring the Link between Nucleosome Occupancy and DNA Methylation.Frontiers in genetics · 2017Article
- Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species.BMC genomics · 2015Article
- Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
The fundamental repeating unit of eukaryotic chromatin is the nucleosome. Besides being involved in packaging DNA, nucleosome organization plays an important role in transcriptional regulation and cellular identity. Currently, there is much debate about the major determinants of the nucleosome architecture of a genome and its significance with little being known about its role in stem cells. To address these questions, we performed ultra-deep sequencing of nucleosomal DNA in two human embryonic stem cell lines and integrated our data with numerous epigenomic maps. Our analyses have revealed that the genome is a determinant of nucleosome organization with transcriptionally inactive regions characterized by a "ground state" of nucleosome profiles driven by underlying DNA sequences. DNA sequence preferences are associated with heterogeneous chromatin organization around transcription start sites. Transcription, histone modifications, and DNA methylation alter this "ground state" by having distinct effects on both nucleosome positioning and occupancy. As the transcriptional rate increases, nucleosomes become better positioned. Exons transcribed and included in the final spliced mRNA have distinct nucleosome profiles in comparison to exons not included at exon-exon junctions. Genes marked by the active modification H3K4m3 are characterized by lower nucleosome occupancy before the transcription start site compared to genes marked by the inactive modification H3K27m3, while bivalent domains, genes associated with both marks, lie exactly in the middle. Combinatorial patterns of epigenetic marks (chromatin states) are associated with unique nucleosome profiles. Nucleosome organization varies around transcription factor binding in enhancers versus promoters. DNA methylation is associated with increasing nucleosome occupancy and different types of methylations have distinct location preferences within the nucleosome core particle. Finally, computational analysis of nucleosome organization alone is sufficient to elucidate much of the circuitry of pluripotency. Our results, suggest that nucleosome organization is associated with numerous genomic and epigenomic processes and can be used to elucidate cellular identity.
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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.