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. 2020 Jul 29;48(16):9019–9036. doi: 10.1093/nar/gkaa625

Figure 3.

Figure 3.

Identification of TFBS motifs in the promoters of genes that are downregulated in Rfx2 and/or Rfx3 KO cells. The promoters (−1000 to +500 pb relative to the TSS) of different sets of downregulated genes were examined by two unbiased approaches for the presence of specific TFBS motifs. (A) Selected region of a heatmap focusing on the most enriched motifs, determined using Pscan for the complete set of TFBS motifs from the JASPAR database, in the promoters of the indicated sets of downregulated genes. The full heatmap is presented in Supplementary Figure S5. Colour key: blue, under-represented motifs; yellow, over-represented motifs. In most gene sets examined, the most strongly enriched TFBS motifs were the X-box motifs previously defined for RFX factors (the corresponding sequence logos are provided in (B)). Only promoters of genes that are downregulated exclusively in Rfx2−/− cells did not exhibit an enrichment in these X-box motifs. (B) Sequence logos of RFX motifs from JASPAR database enriched in RFX-regulated genes. (C) A de novo motif discovery approach (cosmo package) was applied to the promoters (−250 to +50 pb relative to the TSS) of the same sets of downregulated genes. Typical X-box motifs were again revealed in the promoters of most sets of downregulated genes. As in (A) no motif resembling the X-box was revealed in the promoters of genes downregulated only in Rfx2−/− cells. In the latter gene set, a G-rich motif was instead identified, which could be related to the Egr1 motif (UP00007_1).