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.

雄激素（AR）和糖皮质激素（GR）受体的DNA结合界面实际上是相同的，但是这些转录因子仅共享其基因组结合位点的大约三分之一，并调节相似的不同靶基因组。为了解决这一矛盾，我们使用SELEX-seq的改进版本确定了AR和GR DNA结合域的内在特异性。我们开发了一种算法SelexGLM，它通过迭代地将基于特征的广义线性模型拟合到SELEX探针数量来量化在大（31 bp）结合位点上的结合特异性。这项分析表明，AR和GR同型二聚体的DNA结合偏好在15 bp核心结合位点之内和之外都存在显着差异。可以通过改变DNA序列在较大范围内调整两个因素之间的相对偏好，而AR对序列变化的敏感性比GR更敏感。AR的特异性延伸到核心15 bp位点的侧翼区域，在那里等温量热法测量显示，通过焓驱动的与狭窄的小凹槽宽度相关的poly（A）序列的焓驱动读数增加了亲和力。我们得出结论，与GR相比，AR的特异性增加与更多的焓驱动结合有关。