Epigenomic PU.1-VDR crosstalk modulates vitamin D signaling

The ETS-domain transcription factor PU.1 acts as a pioneer factor for other transcription factors including nuclear receptors. In this study, we report that in THP-1 human monocytes the PU.1 cistrome comprises 122,319 genomic sites. Interestingly, at 6498 (5.3%) of these loci PU.1 binding was significantly modulated by the vitamin D receptor (VDR) ligand 1α,25-dihydroxyvitamin D₃ (1,25(OH)₂D₃). In most cases 1,25(OH)₂D₃ increased PU.1 association, which correlated strongly with VDR co-location and overlap ratios for canonical DR3-type VDR binding sites. Genome-wide 6488 sites associating both with PU.1 and VDR as well as 5649 non-VDR overlapping, 1,25(OH)₂D₃-sensitive PU.1 loci represent the PU.1-VDR crosstalk and can be described by four gene regulatory scenarios, each. Chromatin accessibility was the major discriminator between these models. The location of the PU.1 binding loci in open chromatin coincided with a significantly smaller mean distance to the closest 1,25(OH)₂D₃ target gene. PU.1 knockdown indicated that the pioneer factor is relevant for the transcriptional activation of 1,25(OH)₂D₃ target genes but its impact differed in magnitude and orientation. In conclusion, PU.1 is an important modulator of VDR signaling in monocytes, including but also exceeding its role as a pioneer factor, but we found no evidence for a direct interaction of both proteins.