SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
- Liyang Zhang1,5,
- Gabriella D. Martini2,3,5,
- H. Tomas Rube2,3,
- Judith F. Kribelbauer2,3,
- Chaitanya Rastogi2,3,
- Vincent D. FitzPatrick2,3,
- Jon C. Houtman4,
- Harmen J. Bussemaker2,3 and
- Miles A. Pufall1
- 1Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA;
- 2Department of Biological Sciences, Columbia University, New York, New York 10027, USA;
- 3Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA;
- 4Department of Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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↵5 These authors contributed equally to this work.
Abstract
The DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding sites and regulate similarly distinct sets of target genes. To address this paradox, we determined the intrinsic specificities of the AR and GR DNA-binding domains using a refined version of SELEX-seq. We developed an algorithm, SelexGLM, that quantifies binding specificity over a large (31-bp) binding site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA-binding preferences of AR and GR homodimers differ significantly, both within and outside the 15-bp core binding site. The relative preference between the two factors can be tuned over a wide range by changing the DNA sequence, with AR more sensitive to sequence changes than GR. The specificity of AR extends to the regions flanking the core 15-bp site, where isothermal calorimetry measurements reveal that affinity is augmented by enthalpy-driven readout of poly(A) sequences associated with narrowed minor groove width. We conclude that the increased specificity of AR is correlated with more enthalpy-driven binding than GR. The binding models help explain differences in AR and GR genomic binding and provide a biophysical rationale for how promiscuous binding by GR allows functional substitution for AR in some castration-resistant prostate cancers.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.222844.117.
- Received March 14, 2017.
- Accepted November 22, 2017.
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