Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells
Open accessAbstract
Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) should provide a robust means to assess whether the genomes of these cells have similar pluripotent states. Recent studies have suggested that ESCs and iPSCs represent different pluripotent states with substantially different gene expression profiles. We describe here a comparison of global chromatin structure and gene expression data for a panel of human ESCs and iPSCs. Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ESCs and iPSCs with respect to these marks. Gene expression profiles confirm that the transcriptional programs of ESCs and iPSCs show very few consistent differences. Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ESCs from iPSCs.
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MAPT expression increases substantially during neuronal differentiation.
“MAPT is transcriptionally repressed in iPSCs by H3K27me3 rather than by DNA methylation and H3K9me3 and its expression increases substantially during neuronal differentiation (Guenther et al., 2010).”
From Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing (2021) · cites this paper as Guenther et al., 2010
The Introduction and Discussion describe chromatin marks and gene-expression comparisons between ESCs and iPSCs, but do not report MAPT expression during neuronal differentiation. Searches for MAPT, tau, and neuronal differentiation found no passage addressing the claimed increase. (LLM, conf=0.76)
Experimental — accuracy not yet measuredMAPT is transcriptionally repressed in iPSCs by H3K27me3 rather than by DNA methylation and H3K9me3.
“MAPT is transcriptionally repressed in iPSCs by H3K27me3 rather than by DNA methylation and H3K9me3 and its expression increases substantially during neuronal differentiation (Guenther et al., 2010).”
From Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing (2021) · cites this paper as Guenther et al., 2010
The Results and Discussion section reports that H3K27me3 occurs at promoters of many repressed genes in iPSCs, but does not identify MAPT among them. Searches for MAPT and for the proposed comparison with DNA methylation and H3K9me3 found no passage establishing how MAPT is repressed; the copy also does not establish its expression change during neuronal differentiation. Page numbers were not available in the indexed passages. (LLM, conf=0.76)
Experimental — accuracy not yet measured
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- Authors
- Guenther, M. G., Frampton, G. M., Soldner, F., Hockemeyer, D., Mitalipova, M., Jaenisch, R., & Young, R. A.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- Corresponding author
- Young, Richard A.
- ORCID
- Venue
- Cell Stem Cell
- Publisher
- Elsevier BV
- Published
- 2010-08
- Volume
- 7
- Issue
- 2
- Pages
- 249-257
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- PMC
- PMC3010384
- OpenAlex
- W2119885620
- Cited by
- 456
- References
- 4
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 15 · 2023: 12 · 2022: 14 · 2021: 20 · 2020: 12 · 2019: 19 · 2018: 11 · 2017: 25 · 2016: 45 · 2015: 39 · 2014: 40 · 2013: 60 · 2012: 55
- FWCI
- 24.77
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 1117 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell stem cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- National Institutes of Health (2r01ca084198-10)
- Bhabha Atomic Research Centre
- National Human Genome Research Institute (R01HG002668)
- National Cancer Institute (R01-CA084198, R01CA146445)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R37HD045022)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- human embryonic stem cells, induced pluripotent stem cells, chromatin structure, transcriptional programs, pluripotency, nucleosome mapping, histone H3K4me3, histone H3K27me3, epigenetic modifications
- MeSH terms
- Cell Line, Chromatin, Gene Expression Regulation, Histones, Humans, Genome, Human, Cluster Analysis, Chromatin Assembly and Disassembly, Embryonic Stem Cells, Induced Pluripotent Stem Cells
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