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• W2950641340 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 further shed light on how transcriptional networks are rewired throughout evolution. Here, we present a novel sequencing-based TF binding assay and analysis pipeline 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 for 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 (NN) and biophysical models trained on these data, we establish that dinucleotide specificities are sufficient to explain essentially all variance in observed binding behavior, with Cbf1 binding exhibiting significantly more epistasis 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." @default.
• W2950641340 created "2019-06-27" @default.
• W2950641340 creator A5007129727 @default.
• W2950641340 creator A5012212755 @default.
• W2950641340 creator A5023796755 @default.
• W2950641340 creator A5026276346 @default.
• W2950641340 creator A5037786810 @default.
• W2950641340 creator A5085863617 @default.
• W2950641340 date "2017-09-26" @default.
• W2950641340 modified "2023-09-27" @default.
• W2950641340 title "Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding" @default.
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• W2950641340 cites W1644724366 @default.
• W2950641340 cites W1963778673 @default.
• W2950641340 cites W1965991910 @default.
• W2950641340 cites W1975036436 @default.
• W2950641340 cites W1975924111 @default.
• W2950641340 cites W1976260744 @default.
• W2950641340 cites W1980253661 @default.
• W2950641340 cites W1980666661 @default.
• W2950641340 cites W1986723677 @default.
• W2950641340 cites W1986902849 @default.
• W2950641340 cites W1987591014 @default.
• W2950641340 cites W1990078835 @default.
• W2950641340 cites W1994122295 @default.
• W2950641340 cites W2012114217 @default.
• W2950641340 cites W2012627860 @default.
• W2950641340 cites W2013414181 @default.
• W2950641340 cites W2015622114 @default.
• W2950641340 cites W2019955264 @default.
• W2950641340 cites W2022891974 @default.
• W2950641340 cites W2023096418 @default.
• W2950641340 cites W2026690931 @default.
• W2950641340 cites W2029201460 @default.
• W2950641340 cites W2032548898 @default.
• W2950641340 cites W2034145535 @default.
• W2950641340 cites W2038282326 @default.
• W2950641340 cites W2041677964 @default.
• W2950641340 cites W2042392223 @default.
• W2950641340 cites W2057000344 @default.
• W2950641340 cites W2061851611 @default.
• W2950641340 cites W2062237921 @default.
• W2950641340 cites W2064604026 @default.
• W2950641340 cites W2069520341 @default.
• W2950641340 cites W2069985409 @default.
• W2950641340 cites W2076439598 @default.
• W2950641340 cites W2079321730 @default.
• W2950641340 cites W2087058596 @default.
• W2950641340 cites W2087177706 @default.
• W2950641340 cites W2095994064 @default.
• W2950641340 cites W2104525153 @default.
• W2950641340 cites W2107528836 @default.
• W2950641340 cites W2111234263 @default.
• W2950641340 cites W2111826500 @default.
• W2950641340 cites W2116109811 @default.
• W2950641340 cites W2119278037 @default.
• W2950641340 cites W2121763778 @default.
• W2950641340 cites W2122429294 @default.
• W2950641340 cites W2122452605 @default.
• W2950641340 cites W2125235344 @default.
• W2950641340 cites W2127593441 @default.
• W2950641340 cites W2132955708 @default.
• W2950641340 cites W2133747691 @default.
• W2950641340 cites W2135046866 @default.
• W2950641340 cites W2143855992 @default.
• W2950641340 cites W2146393977 @default.
• W2950641340 cites W2147946837 @default.
• W2950641340 cites W2151670888 @default.
• W2950641340 cites W2152121035 @default.
• W2950641340 cites W2158531097 @default.
• W2950641340 cites W2159324718 @default.
• W2950641340 cites W2159942968 @default.
• W2950641340 cites W2160378721 @default.
• W2950641340 cites W2167296922 @default.
• W2950641340 cites W2170942986 @default.
• W2950641340 cites W2268267797 @default.
• W2950641340 cites W2336509392 @default.
• W2950641340 cites W2345943684 @default.
• W2950641340 cites W2462656404 @default.
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• W2950641340 cites W2527322609 @default.
• W2950641340 cites W2572573235 @default.
• W2950641340 cites W2574732129 @default.
• W2950641340 cites W2587481461 @default.
• W2950641340 cites W2737196618 @default.
• W2950641340 cites W2807907133 @default.
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• W2950641340 doi "https://doi.org/10.1101/193904" @default.
• W2950641340 hasPublicationYear "2017" @default.
• W2950641340 type Work @default.
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• W2950641340 hasAuthorship W2950641340A5007129727 @default.
• W2950641340 hasAuthorship W2950641340A5012212755 @default.

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