ArticleNucleic acids research2013
Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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68 citing papers in PubMed.
- Review
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- Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs.bioRxiv : the preprint server for biology · 2025Article
- Transcription factors that define the epigenome structures and transcriptomes in microglia.Experimental hematology · 2025Review
- Single-cell analysis of gene regulatory networks in the mammary glands of P4HA1-knockout mice.PLoS genetics · 2025Article
- Cellular imbalance in proximal and distal lung of CFTRMolecular medicine (Cambridge, Mass.) · 2025Article
- The ETS domain-containing hematopoietic transcription factor PU.1 mediates the induction of arachidonate 5-lipoxygenase by multi-walled carbon nanotubes in macrophages in vitro.Archives of toxicology · 2025Article
- Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers.Nature communications · 2024Article
- Transcriptional network dynamics in early T cell development.The Journal of experimental medicine · 2024Review
- Pharmacological restriction of genomic binding sites redirects PU.1 pioneer transcription factor activity.Nature genetics · 2024Article
- Chemical restriction of PU.1 genomic binding sites activates alternate gene networks.Nature genetics · 2024Article
- HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages.Nature communications · 2024Article
- Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα.Nature structural & molecular biology · 2024Article
- Case report: Rapidly progressive neurocognitive disorder with a fatal outcome in a patient with PU.1 mutated agammaglobulinemia.Frontiers in immunology · 2024Article
- Exploring shared biomarkers and shared pathways in insomnia and atherosclerosis using integrated bioinformatics analysis.Frontiers in molecular neuroscience · 2024Article
- Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms.Nature immunology · 2023Article
- Article
- DNA selection by the master transcription factor PU.1.Cell reports · 2023Article
8 more citing papers are in PubMed but not listed here.
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9 authors.
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Abstract
The transcription factor PU.1 is crucial for the development of many hematopoietic lineages and its binding patterns significantly change during differentiation processes. However, the 'rules' for binding or not-binding of potential binding sites are only partially understood. To unveil basic characteristics of PU.1 binding site selection in different cell types, we studied the binding properties of PU.1 during human macrophage differentiation. Using in vivo and in vitro binding assays, as well as computational prediction, we show that PU.1 selects its binding sites primarily based on sequence affinity, which results in the frequent autonomous binding of high affinity sites in DNase I inaccessible regions (25-45% of all occupied sites). Increasing PU.1 concentrations and the availability of cooperative transcription factor interactions during lineage differentiation both decrease affinity thresholds for in vivo binding and fine-tune cell type-specific PU.1 binding, which seems to be largely independent of DNA methylation. Occupied sites were predominantly detected in active chromatin domains, which are characterized by higher densities of PU.1 recognition sites and neighboring motifs for cooperative transcription factors. Our study supports a model of PU.1 binding control that involves motif-binding affinity, PU.1 concentration, cooperativeness with neighboring transcription factor sites and chromatin domain accessibility, which likely applies to all PU.1 expressing cells.
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