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Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription
Open accessAbstract
Recent studies suggest a hierarchical model in which lineage-determining factors act in a collaborative manner to select and prime cell-specific enhancers, thereby enabling signal-dependent transcription factors to bind and function in a cell-type-specific manner. Consistent with this model, TLR4 signaling primarily regulates macrophage gene expression through a pre-existing enhancer landscape. However, TLR4 signaling also induces priming of ∼3,000 enhancer-like regions de novo, enabling visualization of intermediates in enhancer selection and activation. Unexpectedly, we find that enhancer transcription precedes local mono- and dimethylation of histone H3 lysine 4 (H3K4me1/2). H3K4 methylation at de novo enhancers is primarily dependent on the histone methyltransferases Mll1, Mll2/4, and Mll3 and is significantly reduced by inhibition of RNA polymerase II elongation. Collectively, these findings suggest an essential role of enhancer transcription in H3K4me1/2 deposition at de novo enhancers that is independent of potential functions of the resulting eRNA transcripts.
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“Several studies have shown that the level of eRNA transcription correlates with enhancer activity [60,61].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [60]
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“Within cell-specific enhancers, DNA sequences provide information about the identities of key LDTFs and the activity states of signaling pathways that control the functions of SDTFs (31, 33–35).”
From An environment-dependent transcriptional network specifies human microglia identity (2017) · cites this paper as [33]
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“In untreated macrophages, H3K27ac was enriched both at the promoter region of Tet2 and a region lying 40kb upstream, thus constituting a putative distal enhancer element (Figure 2A).”
From TET2 Regulates the Neuroinflammatory Response in Microglia (2019) · cites this paper as Kaikkonen et al., 2013
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“Immune memory in microglia and macrophages are shaped by epigenetically mediated alterations in the enhancer repertoire of targeted genes [11, 32].”
From Transcriptional and Epigenetic Regulation of Microglia in Health and Disease (2019) · cites this paper as [32]
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Metadata
- Authors
- Kaikkonen, M. U., Spann, N. J., Heinz, S., Romanoski, C. E., Allison, K. A., Stender, J. D., Chun, H. B., Tough, D. F., Prinjha, R. K., Benner, C., & Glass, C. K.
- Affiliations
- University of Eastern Finland (FI)
- University of California San Diego (US)
- GlaxoSmithKline (United Kingdom) (GB)
- Salk Institute for Biological Studies (US)
- Corresponding author
- Glass, Christopher K.
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2013-08
- Volume
- 51
- Issue
- 3
- Pages
- 310-325
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC3779836
- OpenAlex
- W1998871958
- Cited by
- 672
- References
- 63
- Citations by year
- 2026: 26 · 2025: 36 · 2024: 43 · 2023: 35 · 2022: 52 · 2021: 56 · 2020: 50 · 2019: 46 · 2018: 69 · 2017: 73 · 2016: 61 · 2015: 66 · 2014: 48 · 2013: 11
- FWCI
- 27.79
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Fondation Leducq
- Academy of Finland
- Suomen Kulttuurirahasto
- Sydäntutkimussäätiö
- National Institutes of Health
- National Cancer Institute (R01CA173903, CA17390)
- National Institute of General Medical Sciences (T32GM008806)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK063491, DK091183, P01DK074868, P30DK063491, R01DK091183)
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- enhancer remodeling, macrophage activation, enhancer transcription, TLR4 signaling, H3K4 methylation, MLL1, MLL3, RNA polymerase II elongation, enhancer RNA, histone methyltransferase
- MeSH terms
- Proto-Oncogene Protein Spi-1, Animals, Base Sequence, Cells, Cultured, DNA-Binding Proteins, Enhancer Elements, Genetic, Gene Expression Regulation, Histones, Macrophage Activation, Macrophages, Male, Mice, Inbred C57BL, Histone-Lysine N-Methyltransferase, Proto-Oncogene Proteins, RNA Polymerase II, Transcription, Genetic, Signal Transduction, Trans-Activators, Gene Expression, NF-kappa B, Sequence Analysis, DNA, DNA Methylation, CCAAT-Enhancer-Binding Proteins, Toll-Like Receptor 4, Mice, Myeloid-Lymphoid Leukemia Protein, Transcription Factor RelA
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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