Determinants of the DNA binding and gene regulatory specificity for type II nuclear receptor signaling
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Abstract
The type II nuclear receptors (NRs) function as heterodimeric transcription factors with the retinoid X receptor (RXR) to regulate diverse biological processes in response to endogenous ligands and therapeutic drugs. Due to their importance as therapeutic targets, the NRs have been extensively studied; however, the rules dictating NR transcriptional specificity remain unclear.
Type II NRs regulate both distinct and overlapping gene programs. DNA-binding specificity has been proposed as a primary mechanism dictating how individual NRs distinguish their genomic targets. However, many in vivo targets of NRs identified in ChIP-seq data lack an identifiable binding site, suggesting that current models of DNA binding specificity of the type II NRs are incomplete. A more thorough characterization of the DNA binding and gene regulatory specificity of the type II NRs will be informative for understanding the role of DNA binding in achieving NR transcriptional specificity. NRs function can be altered by ligand binding, post-translational modifications (PTMs), and interactions with other proteins. Therefore, to understand how cellular context may alter NR regulatory specificity, analysis of NR DNA binding in the presence of different ligands or cell-specific coregulator proteins will be informative.
I used protein binding microarrays (PBMs) to characterize the DNA binding preferences of twelve NR:RXRα heterodimers. I find more promiscuous NR DNA binding than has been reported, challenging the view that NR binding is defined by half-site spacing. I show that NRs bind DNA using two distinct modes, explaining widespread half-site binding in vivo. Finally, we show that current models of NR DNA binding preferences better reflect binding-site activity rather than binding-site affinity. Examining how DNA binding is altered in a cellular context, I find that NR-DNA binding is significantly altered in the presence of soluble nuclear components, such as other transcription factors and transcriptional coregulators. In the presence of other nuclear proteins NR DNA binding is less promiscuous, suggesting interactions with nuclear proteins can modulate NR DNA binding specificity. Our rich PBM dataset and revised NR binding models provide a framework for understanding NR specificity and will facilitate more accurate analyses of genomic datasets.
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