Proteomic identification of component proteins of orphan nuclear receptor COUP-TFI complexes in mammalian cells

Abstract

B168

Nuclear receptors, the transcription factors regulated by ligands, have become major targets for drug discovery, including new drug development for chemotherapy. Orphan nuclear receptor chicken ovalbumin upstream promoter transcription factor I (COUP-TFI) possesses the ability to either activate or repress the transcription of a diversity of target genes through undefined mechanisms. A proteomics-based, tandem affinity purification (TAP) procedure was used in this study to identify the component proteins of COUP-TFI complexes in mammalian cells. Several known proteins of transcriptional repressive complexes, including NCoR, HDAC1 and TIF1β/KAP-1, were found to co-purify with COUP-TFI, as were other transcriptional regulatory proteins, including the SWI/SNF family member Brahma, and its associated factors BAF155 and BAF170. Proteins not previously implicated in transcriptional regulation were also found to co-purify with COUP-TFI including the DNA repair protein DDB1, a pro-apoptotic protein that is deleted in breast cancer (DBC1), HSP70, HSP90 and the ubiquitin ligase HYD1. Finally, several components of the splicesome assembly were identified (SFR1, SF3A1 and SF3B1) in COUP-TFI complexes. Collectively, our TAP strategy revealed that COUP-TFI may associate with a number of transcriptional regulatory proteins in HeLa S3 cells as well as other classes of proteins that have not been previously implicated in the regulation of gene expression. Many of these proteins and COUP-TFI were demonstrated to co-occupy the promoter of retinoic acid-induced 1, a newly identified, COUP-TFI target gene in HeLa S3 cells. These results may underlie the complexity of COUP-TFI action in mammalian cells.