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. 2021 Mar 22;11:6518. doi: 10.1038/s41598-021-86032-5

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Identification of direct VDR target genes. Three different approaches have been used to predict primary vitamin D target genes from early or late 1,25(OH)₂D₃-responding genes measured with RNA-seq¹¹ (a). The first two identified direct target genes using VDR ChIP-seq peaks that were (i) located in a window of ± 25 kb around the TSS of genes or ii) overlapping a regulatory element (REM) in the EpiRegio database that was linked to a DEG. The third (iii) used FAIRE-seq peaks with a predicted VDR binding motif that are located in a window of ± 25 kb around the TSS of DEGs (b). The proportions of primary vitamin D target genes predicted by at least one of the three methods are shown for both early and late DEGs. The numbers of primary VDR target genes predicted by one, two, or all three of the approaches are depicted in upset plots for early (2.5 or 4 h; c) and late (24 h; d) DEGs after 100 nM 1,25(OH)₂D₃ treatment of THP-1 cells^11,15.