PT  - JOURNAL ARTICLE
AU  - Can Sönmezer
AU  - Rozemarijn Kleinendorst
AU  - Dilek Imanci
AU  - Laura Villacorta
AU  - Dirk Schübeler
AU  - Vladimir Benes
AU  - Arnaud R Krebs
TI  - Single molecule occupancy patterns of transcription factors reveal determinants of cooperative binding <em>in vivo</em>
AID  - 10.1101/2020.06.29.167155
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.29.167155
4099  - http://biorxiv.org/content/early/2020/06/29/2020.06.29.167155.short
4100  - http://biorxiv.org/content/early/2020/06/29/2020.06.29.167155.full
AB  - Gene activation requires the cooperative activity of multiple transcription factors at cis-regulatory elements. Yet, most transcription factors have short residence time, questioning the requirement of their physical co-occupancy on DNA to achieve cooperativity. Here, we advance Single Molecule Footprinting to detect individual molecular interactions of transcription factors and nucleosomes with DNA at mouse cis-regulatory elements. We apply this strategy to quantify the simultaneous binding of multiple transcription factors on single DNA molecules. Analysis of the binary occupancy patterns at thousands of motif combinations reveals that for most types of transcription factors high DNA co-occupancy can occur in absence of direct physical interaction, at sites of competition with nucleosomes. Perturbation of pairwise interactions demonstrates the function of molecular co-occupancy for binding cooperativity. These findings elucidate the binding cooperativity mechanism used by transcription factors in absence of strict organisation of their binding motifs, a characteristic feature of most of enhancers.Competing Interest StatementThe authors have declared no competing interest.