Chromatin scanning by dynamic binding of pioneer factors
Open accessAbstract
Pioneer factors such as FoxA target nucleosomal DNA and initiate cooperative interactions at silent genes during development, cellular reprogramming, and steroid hormone induction. Biophysical studies previously showed that the nuclear mobility of FoxA1 is slower than for many other transcription factors, whereas a new single molecule study (Swinstead et al., 2016, Cell) shows comparable chromatin residence times for FoxA1 and steroid receptors. Despite that steroid receptors engage nucleosome-remodeling complexes, the vast majority of co-bound sites with FoxA are dependent upon FoxA, not vice versa. Taken together, the distinguishing feature of pioneer factors remains nucleosomal access rather than an exceptional residence time in chromatin.
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No significant biological processes were associated with C4 regions, suggesting C4 represents non-specific binding or scanning by SOX9.
“we did not identify significant biological processes associated with the regions in C4, although this was the largest of the four clusters, suggesting that this cluster represents non-specific binding or scanning by SOX9 (63).”
From SOX9 reprograms endothelial cells by altering the chromatin landscape (2022) · cites this paper as [63]
In the passage labeled Abstract (page unavailable), the paper links nonspecific FoxA1 binding to its potential to scan closed chromatin. It does not examine SOX9 or C4 regions, so it supports the proposed scanning mechanism only by analogy, not its application to C4. The absence of significant biological processes is presented as the citing authors’ own finding. (LLM, conf=0.85)
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- Authors
- Zaret, K. S., Lerner, J., & Iwafuchi-Doi, M.
- Affiliations
- University of Pennsylvania (US)
- Corresponding author
- Zaret, Kenneth S.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2016-06
- Volume
- 62
- Issue
- 5
- Pages
- 665-667
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC4893772
- OpenAlex
- W2409952065
- Cited by
- 68
- References
- 32
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 4 · 2023: 9 · 2022: 9 · 2021: 3 · 2020: 3 · 2019: 9 · 2018: 11 · 2017: 9 · 2016: 3
- FWCI
- 4.56
- 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)
- Funders
- National Institute of General Medical Sciences (R01GM036477, P01GM099134)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- pioneer transcription factors, FOXA1, FoxA, nucleosome binding, nuclear mobility, silent genes, steroid hormone receptors, single-molecule biophysics
- MeSH terms
- Animals, Binding Sites, Cell Nucleus, DNA, Humans, Nucleosomes, Protein Binding, Receptors, Steroid, Gonadal Steroid Hormones, Gene Expression Regulation, Developmental, Chromatin Assembly and Disassembly, Hepatocyte Nuclear Factor 3-alpha, Cellular Reprogramming
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