Cell Systems
Volume 11, Issue 3, 23 September 2020, Pages 315-327.e5
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A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding

https://doi.org/10.1016/j.cels.2020.08.004Get rights and content
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Highlights

  • Interactions between transcription factors regulate their genomic binding

  • A genomically integrated high-throughput screen for transcription factor binding

  • Measures sequence determinants of Tcf7l2 binding

  • Tcf7l2 binding depends on nearby and in-phase Oct4 and Klf4 motifs

Summary

Predicting where transcription factors bind in the genome from their in vitro DNA-binding affinity is confounded by the large number of possible interactions with nearby transcription factors. To characterize the in vivo binding logic for the Wnt effector Tcf7l2, we developed a high-throughput screening platform in which thousands of synthesized DNA phrases are inserted into a specific genomic locus, followed by measurement of Tcf7l2 binding by DamID. Using this platform at two genomic loci in mouse embryonic stem cells, we show that while the binding of Tcf7l2 closely follows the in vitro motif-binding strength and is influenced by local chromatin accessibility, it is also strongly affected by the surrounding 99 bp of sequence. Through controlled sequence perturbation, we show that Oct4 and Klf4 motifs promote Tcf7l2 binding, particularly in the adjacent 50 bp and oscillating with a 10.8-bp phasing relative to these cofactor motifs, which matches the turn of a DNA helix.

Keywords

Tcf7l2
DamID
transcription factor
CRISPR-Cas9
Gaussian process

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