Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors

• Published in: Cell reports (Cambridge) 2019-09, Vol.28 (10), p.2689-2703.e4
• Main Authors: Li, Sai, Zheng, Eric Bo, Zhao, Li, Liu, Shixin
• Format: Article
• Language: English
• Subjects: Binding Sites; cooperative binding; DNA - metabolism; gene regulatory network; Genetic Loci; HeLa Cells; Humans; Kinetics; nucleosome; Nucleosomes - metabolism; Nucleotide Motifs; Oct4; Octamer Transcription Factor-3 - metabolism; pioneer activity; Pluripotent Stem Cells - metabolism; Protein Binding; RNA - metabolism; Single Molecule Imaging; single-molecule fluorescence; Sox2; SOXB1 Transcription Factors - metabolism; transcription factor
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2019.07.103

Cooperative binding of transcription factors (TFs) to chromatin orchestrates gene expression programming and cell fate specification. However, the biophysical principles of TF cooperativity remain incompletely understood. Here we use single-molecule fluorescence microscopy to study the partnership between Sox2 and Oct4, two core members of the pluripotency gene regulatory network. We find that the ability of Sox2 to target DNA inside nucleosomes is strongly affected by the translational and rotational positioning of its binding motif. In contrast, Oct4 can access nucleosomal sites with equal capacities. Furthermore, the Sox2-Oct4 pair displays nonreciprocal cooperativity, with Oct4 modulating interaction of Sox2 with the nucleosome but not vice versa. Such cooperativity is conditional upon the composite motif’s residing at specific nucleosomal locations. These results reveal that pioneer factors possess distinct chromatin-binding properties and suggest that the same set of TFs can differentially regulate gene activities on the basis of their motif positions in the nucleosomal context. [Display omitted] •Nucleosome engagement by Sox2 is sensitive to the position of its binding motif•Oct4 stabilizes Sox2 binding to nucleosome ends but mildly inhibits dyad binding•Sox2 has little effect on Oct4 binding, thus their cooperativity is not reciprocal•Pioneer activities of transcription factors are multimodal and context dependent Using single-molecule fluorescence imaging, Li et al. investigate the pioneer activities of pluripotency factors Sox2 and Oct4 and find that they exhibit distinct nucleosome binding preferences as well as context-dependent cooperativity, which potentially allows gene-specific transcriptional regulation.