A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding.

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  • Additional Information
    • Source:
      Publisher: Cell Press Country of Publication: United States NLM ID: 101656080 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2405-4720 (Electronic) Linking ISSN: 24054712 NLM ISO Abbreviation: Cell Syst Subsets: MEDLINE
    • Publication Information:
      Original Publication: [Cambridge, MA] : Cell Press, [2015]-
    • Subject Terms:
      High-Throughput Screening Assays/*methods ; Transcription Factor 7-Like 2 Protein/*metabolism ; Transcription Factors/*genetics; Binding Sites ; Humans ; Kruppel-Like Factor 4
    • Abstract:
      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.
      Competing Interests: Declaration of Interests The authors declare no competing interests.
      (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)
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    • Grant Information:
      K01 DK101684 United States DK NIDDK NIH HHS; R01 HG008363 United States HG NHGRI NIH HHS; R01 HG008754 United States HG NHGRI NIH HHS; R21 OD025309 United States OD NIH HHS
    • Contributed Indexing:
      Keywords: CRISPR-Cas9; DamID; Gaussian process; Tcf7l2; transcription factor
    • Accession Number:
      0 (KLF4 protein, human)
      0 (Klf4 protein, mouse)
      0 (Kruppel-Like Factor 4)
      0 (TCF7L2 protein, human)
      0 (Transcription Factor 7-Like 2 Protein)
      0 (Transcription Factors)
    • Publication Date:
      Date Created: 20200910 Date Completed: 20211001 Latest Revision: 20240329
    • Publication Date:
      20240329
    • Accession Number:
      PMC7530048
    • Accession Number:
      10.1016/j.cels.2020.08.004
    • Accession Number:
      32910904