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Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3702-E3711. doi: 10.1073/pnas.1715888115. Epub 2018 Mar 27.

Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding.

Author information

1
Department of Genetics, Stanford University, Stanford, CA 94305.
2
Department of Bioengineering, Stanford University, Stanford, CA 94305.
3
Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, CA 94305.
4
Department of Chemistry, Stanford University, Stanford, CA 94305.
5
Department of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel POB 653.
6
Department of Genetics, Stanford University, Stanford, CA 94305; pfordyce@stanford.edu.
7
Chan Zuckerberg Biohub, San Francisco, CA 94158.

Abstract

Transcription factors (TFs) are primary regulators of gene expression in cells, where they bind specific genomic target sites to control transcription. Quantitative measurements of TF-DNA binding energies can improve the accuracy of predictions of TF occupancy and downstream gene expression in vivo and shed light on how transcriptional networks are rewired throughout evolution. Here, we present a sequencing-based TF binding assay and analysis pipeline (BET-seq, for Binding Energy Topography by sequencing) capable of providing quantitative estimates of binding energies for more than one million DNA sequences in parallel at high energetic resolution. Using this platform, we measured the binding energies associated with all possible combinations of 10 nucleotides flanking the known consensus DNA target interacting with two model yeast TFs, Pho4 and Cbf1. A large fraction of these flanking mutations change overall binding energies by an amount equal to or greater than consensus site mutations, suggesting that current definitions of TF binding sites may be too restrictive. By systematically comparing estimates of binding energies output by deep neural networks (NNs) and biophysical models trained on these data, we establish that dinucleotide (DN) specificities are sufficient to explain essentially all variance in observed binding behavior, with Cbf1 binding exhibiting significantly more nonadditivity than Pho4. NN-derived binding energies agree with orthogonal biochemical measurements and reveal that dynamically occupied sites in vivo are both energetically and mutationally distant from the highest affinity sites.

KEYWORDS:

microfluidics; protein–DNA binding; transcription factor binding; transcription factor specificity; transcriptional regulation

PMID:
29588420
PMCID:
PMC5910820
DOI:
10.1073/pnas.1715888115
[Indexed for MEDLINE]
Free PMC Article

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