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ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

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  • Gabriel E. Zentner

    (Fred Hutchinson Cancer Research Center
    Present address: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA)

  • Sivakanthan Kasinathan

    (Fred Hutchinson Cancer Research Center
    Medical Scientist Training Program, University of Washington School of Medicine
    Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine)

  • Beibei Xin

    (Molecular and Computational Biology Program, Chemistry, Physics, and Computer Science, University of Southern California)

  • Remo Rohs

    (Molecular and Computational Biology Program, Chemistry, Physics, and Computer Science, University of Southern California)

  • Steven Henikoff

    (Fred Hutchinson Cancer Research Center
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center)

Abstract

Chromatin endogenous cleavage (ChEC) uses fusion of a protein of interest to micrococcal nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo. Here we report the combination of ChEC with high-throughput sequencing (ChEC-seq) to map budding yeast transcription factor (TF) binding. Temporal analysis of ChEC-seq data reveals two classes of sites for TFs, one displaying rapid cleavage at sites with robust consensus motifs and the second showing slow cleavage at largely unique sites with low-scoring motifs. Sites with high-scoring motifs also display asymmetric cleavage, indicating that ChEC-seq provides information on the directionality of TF-DNA interactions. Strikingly, similar DNA shape patterns are observed regardless of motif strength, indicating that the kinetics of ChEC-seq discriminates DNA recognition through sequence and/or shape. We propose that time-resolved ChEC-seq detects both high-affinity interactions of TFs with consensus motifs and sites preferentially sampled by TFs during diffusion and sliding.

Suggested Citation

  • Gabriel E. Zentner & Sivakanthan Kasinathan & Beibei Xin & Remo Rohs & Steven Henikoff, 2015. "ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo," Nature Communications, Nature, vol. 6(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9733
    DOI: 10.1038/ncomms9733
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    Cited by:

    1. Vishaka Datta & Sridhar Hannenhalli & Rahul Siddharthan, 2019. "ChIPulate: A comprehensive ChIP-seq simulation pipeline," PLOS Computational Biology, Public Library of Science, vol. 15(3), pages 1-32, March.

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