Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo
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Abstract
Gene activation requires the cooperative activity of multiple transcription factors at cis-regulatory elements (CREs). Yet, most transcription factors have short residence time, questioning the requirement of their physical co-occupancy on DNA to achieve cooperativity. Here, we present a DNA footprinting method that detects individual molecular interactions of transcription factors and nucleosomes with DNA in vivo. We apply this strategy to quantify the simultaneous binding of multiple transcription factors on single DNA molecules at mouse CREs. Analysis of the binary occupancy patterns at thousands of motif combinations reveals that high DNA co-occupancy occurs for most types of transcription factors, in the absence of direct physical interaction, at sites of competition with nucleosomes. Perturbation of pairwise interactions demonstrates the function of molecular co-occupancy in binding cooperativity. Our results reveal the interactions regulating CREs at molecular resolution and identify DNA co-occupancy as a widespread cooperativity mechanism used by transcription factors to remodel chromatin.
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Single molecule footprinting adapted to mammalian cells detected widespread co-occupancy of cooperative transcription factors at enhancers.
“SMF has also recently been adapted to mammalian cells, detecting widespread co-occupancy of cooperative TFs at enhancers [119].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [119]
The Introduction says the authors adapted SMF for mammalian genomes and found DNA co-occupancy widespread at sites of TF cooperativity. The Results describe measurements at mouse cis-regulatory elements, but the passages do not establish that the widespread finding applies specifically to enhancers rather than cis-regulatory elements more broadly. (LLM, conf=0.82)
Experimental — accuracy not yet measuredAt non-dimeric sites, physical interactions between co-bound transcription factors were not necessary.
“Interestingly, at non-dimeric sites, physical interactions between co-bound TFs were not necessary [119], consistent with evidence from Drosophila where co-occupied DNA-bound TFs were often spaced quite widely apart (> 50 bp) [118].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [119]
At dimeric motif sites, transcription factors tended to bind initially as monomers with subsequent dimerisation presumably stabilising the DNA-protein complex.
“Notably, at dimeric motif sites, TFs tended to bind initially as monomers with subsequent dimerisation presumably stabilising the DNA–protein complex [119].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [119]
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- Authors
- Sönmezer, C., Kleinendorst, R., Imanci, D., Barzaghi, G., Villacorta, L., Schübeler, D., Benes, V., Molina, N., & Krebs, A. R.
- Affiliations
- Heidelberg University (DE)
- European Molecular Biology Laboratory (DE)
- Friedrich Miescher Institute (CH)
- University of Basel (CH)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Krebs, Arnaud Regis
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2021-01
- Volume
- 81
- Issue
- 2
- Pages
- 255-267.e6
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC7612519
- OpenAlex
- W3111715132
- Cited by
- 162
- References
- 15
- Citations by year
- 2026: 21 · 2025: 30 · 2024: 35 · 2023: 29 · 2022: 23 · 2021: 21 · 2020: 2 · 2013: 1
- FWCI
- 6.08
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, other-oa)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion, cc-by-nc)
- Funders
- Deutsche Forschungsgemeinschaft (KR 5247/1-1)
- European Molecular Biology Laboratory
- Novartis Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (ANR-10-LABX-0030-INRT, PZOOP3_161493)
- European Research Council
- 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
- cooperative binding, cis-regulatory elements, DNA footprinting, transcription factor-DNA interaction, chromatin remodeling, motif combinations
- MeSH terms
- Mouse Embryonic Stem Cells, Animals, Binding Sites, DNA, Male, Nucleosomes, Protein Binding, Transcription Factors, Transcription, Genetic, DNA Footprinting, Regulatory Elements, Transcriptional, Mice
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