An evolutionarily conserved DNA architecture determines target specificity of the TWIST family bHLH transcription factors
- Andrew T. Chang1,2,9,
- Yuanjie Liu3,9,
- Kasirajan Ayyanathan3,
- Chris Benner4,
- Yike Jiang1,5,
- Jeremy W. Prokop6,
- Helicia Paz1,
- Dong Wang7,
- Hai-Ri Li7,
- Xiang-Dong Fu7,
- Frank J. Rauscher III3 and
- Jing Yang1,8
- 1Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093, USA;
- 2The Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, 92093, USA;
- 3The Wistar Institute, Philadelphia, Pennsylvania 19104, USA;
- 4Salk Institute for Biological Studies, La Jolla, California 92037, USA;
- 5The Biological Science Graduate Program, University of California at San Diego, La Jolla, California, 92093, USA;
- 6Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA;
- 7Department of Cell and Molecular Medicine, University of California at San Diego, La Jolla, California, 92093, USA;
- 8Department of Pediatrics, University of California at San Diego, La Jolla, California, 92093, USA
- Corresponding authors: jingyang{at}ucsd.edu, rauscher{at}wistar.org
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↵9 These authors contributed equally to this work.
Abstract
Basic helix–loop–helix (bHLH) transcription factors recognize the canonical E-box (CANNTG) to regulate gene transcription; however, given the prevalence of E-boxes in a genome, it has been puzzling how individual bHLH proteins selectively recognize E-box sequences on their targets. TWIST is a bHLH transcription factor that promotes epithelial–mesenchymal transition (EMT) during development and tumor metastasis. High-resolution mapping of TWIST occupancy in human and Drosophila genomes reveals that TWIST, but not other bHLH proteins, recognizes a unique double E-box motif with two E-boxes spaced preferentially by 5 nucleotides. Using molecular modeling and binding kinetic analyses, we found that the strict spatial configuration in the double E-box motif aligns two TWIST–E47 dimers on the same face of DNA, thus providing a high-affinity site for a highly stable intramolecular tetramer. Biochemical analyses showed that the WR domain of TWIST dimerizes to mediate tetramer formation, which is functionally required for TWIST-induced EMT. These results uncover a novel mechanism for a bHLH transcription factor to recognize a unique spatial configuration of E-boxes to achieve target specificity. The WR–WR domain interaction uncovered here sets an example of target gene specificity of a bHLH protein being controlled allosterically by a domain outside of the bHLH region.
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Footnotes
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Supplemental material is available for this article.
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Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.242842.114.
- Received April 1, 2014.
- Accepted February 9, 2015.
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