SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

• Published in: Genome research Vol. 28; no. 1; pp. 111 - 121
• Main Authors: Zhang, Liyang, Martini, Gabriella D, Rube, H Tomas, Kribelbauer, Judith F, Rastogi, Chaitanya, FitzPatrick, Vincent D, Houtman, Jon C, Bussemaker, Harmen J, Pufall, Miles A
• Format: Journal Article
• Language: English
• Published: United States Cold Spring Harbor Laboratory Press 01-01-2018
• Subjects: Androgens; Binding sites; Calorimetry; Castration; Deoxyribonucleic acid; DNA; Enthalpy; Generalized linear models; Glucocorticoids; Interfaces; Method; Nucleotide sequence; Polyadenine; Preferences; Prostate cancer; Transcription factors
• ISSN: 1088-9051; 1549-5469
• DOI: 10.1101/gr.222844.117

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,
, 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.