Fig. 5: MAFF target gene identification by genome-wide analysis.
From: The HIF target MAFF promotes tumor invasion and metastasis through IL11 and STAT3 signaling
MDA-MB-231 cells were treated under normoxia or hypoxia with or without siMAFF for 24 h. MAFF target genes were determined by analyzing RNA-sequencing and ChIP-sequencing data. a When MAFF was knocked down, 415 or 240 genes were significantly altered under normoxia or hypoxia, respectively and among them 106 genes were affected both under normoxia and hypoxia. b Volcano plot showed that 192 genes were downregulated and 223 genes were upregulated under normoxia. Under hypoxia, 68 genes were downregulated and 172 genes were upregulated. c DAVID20,21 analysis determined that genes involved in pathways of “Blood vessel development”, “TGFβ signaling”, and “Regulation of cell adhesion/morphogenesis” were significantly altered in the absence of MAFF expression. d GSEA analysis revealed that genes involved in metastasis (normoxia) or migration (hypoxia) were regulated by MAFF expression. e The genomic location of MAFF binding sites was identified by cis-regulatory element annotation system (CEAS). f A MAFF binding motif based on MARE was identified using the motif discovery algorithm, Multiple Expectation Maximizations for Motif Elicitation (MEME). g When we combined RNA-sequencing and ChIP-sequencing, 292 genes were regulated under normoxia and 70 genes under hypoxia. 66 genes were regulated both under normoxia and hypoxia. h ChIP-sequencing data showed enriched DNA sequence tags, which were highlighted in red using the UCSC genome browser. While HMOX1 showed two peaks from previously known MAFF binding sites, MAFF binding peak was found in IL11 promoter, which included the MARE/ARE sequence (GCGAGCTCA).
