Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding
Year: 2025
Type: article
Abstract: Transcription factors (TFs) such as RBPJ in Notch signaling bind to specific DNA sequences to regulate transcription. How TF-DNA binding kinetics and cofactor interactions modulate gene regulation is mostly unknown. We determine the binding kinetics, transcriptional activity, and genome-wide chromatin occupation of RBPJ and mutant variants by live-cell single-molecule tracking, reporter assays, and ChIP-Seq. Importantly, the search time of RBPJ exceeds its residence time, indicating kinetic rather than thermodynamic binding stability. Impaired RBPJ-DNA binding as in Adams-Oliver-Syndrome affect both target site association and dissociation, while impaired cofactor binding mainly alters association and unspecific binding. Moreover, our data point to the possibility that cofactor binding contributes to target site specificity. Findings for other TFs comparable to RBPJ indicate that kinetic rather than thermodynamic DNA binding stability might prevail in vivo. We propose an effective in vivo binding energy landscape of TF-DNA interactions as instructive visualization of binding kinetics and mutation-induced changes.
Source: Nature Communications
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $6,990
Awards: Entschlüsselung molekularer und kinetischer Grundlagen der Transkription mit Einzelmolekülmethoden, G1929892627, NSF/MCB-BSF: Quantitative analysis and modeling of Notch signaling using in vivo synthetic biology, TRR 81: ChromatinVeränderungen in Differenzierung und Malignität, SFB 1279: Nutzung des menschlichen Peptidoms zur Entwicklung neuer antimikrobieller und antiKrebs Therapeutika, Zentrum für Translationale Bildgebung (MoMAN) Phase II, SFB 1074: Experimentelle Modelle und klinische Translation bei Leukämien, Untersuchungen zur Bildung und Dynamik von RBPJ TranskriptionsfaktorKomplexen mittels Einzelmolekülmikroskopie in lebenden Zellen, G434337789, G4402300847, SFB 1506: Alterung an Schnittstellen, G6496846170, G689005322, Einzelmolekülmikroskopie von Architekturproteinen während der Entwicklung von Zebrafischembryonen, G7834482769, G8400849260
OpenAlex ID: W4407052407