ArticleNature communications2014
Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline.PLoS computational biology · 2026Article
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- A Scalable MNase-seq Framework for Reproducible Nucleosome Profiling across Pluripotent Stem Cell and Cardiomyocyte Models.Computational and structural biotechnology journal · 2026Article
- Super-enhancers: drivers of cells' identities and cells' debacles.Epigenomics · 2024Review
- Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions.JACS Au · 2024Review
- Single-cell multiomics reveals the complexity of TGFβ signalling to chromatin in iPSC-derived kidney organoids.Communications biology · 2022Article
- Article
- Differential condensation of sister chromatids acts with Cdc6 to ensure asynchronous S-phase entry in Drosophila male germline stem cell lineage.Developmental cell · 2022Article
- Analysis of chromatin accessibility in p53 deficient spermatogonial stem cells for high frequency transformation into pluripotent state.Cell proliferation · 2022Article
- Pioneer factors in development and cancer.iScience · 2021Review
- What do Transcription Factors Interact With?Journal of molecular biology · 2021Review
- Epigenetic regulation of cancer stem cell formation and maintenance.International journal of cancer · 2021Review
- Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos.BMC bioinformatics · 2021Article
- NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.BMC bioinformatics · 2021Article
- Species-Specific Relationships between DNA and Chromatin Properties of CpG Islands in Embryonic Stem Cells and Differentiated Cells.Stem cell reports · 2021Article
- Chromatin accessibility profiling methods.Nature reviews. Methods primers · 2021Article
- A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer.Cancer cell · 2020Article
- SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability.Genes & development · 2020Article
- Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome.Nature communications · 2020Article
- Genomic methods in profiling DNA accessibility and factor localization.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Article
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Authors and funding
9 authors.
Funding
Abstract
Chromatin structure determines DNA accessibility. We compare nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs) and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach to identify regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. Surprisingly, most chromatin remains unchanged; a majority of rearrangements appear to affect a single nucleosome. RoDs are enriched at genes and regulatory elements, including enhancers associated with pluripotency and differentiation. RoDs co-localize with binding sites of key developmental regulators, including the reprogramming factors Klf4, Oct4/Sox2 and c-Myc. Nucleosomal landscapes in ESC enhancers are extensively altered, exhibiting lower nucleosome occupancy in pluripotent cells than in somatic cells. Most changes are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of cell differentiation and reprogramming and likely identify regulatory regions essential for these processes.
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