SOX4 and RELA function as transcriptional partners to regulate the expression of TNF-responsive genes in fibroblast-like synoviocytes [RNA-Seq]

Purpose: Our goal was to evaluate the transcriptional profiles of FLS. We used genome wide approaches to uncover the interactions between SOXC transcription factors and RELA/p65 transcription factor, downstream of TNF signaling. Methods: We analyzed RNA-seq of TNF-treated FLS in control and SOXC gene knockout backgrounds. FLS isolated from Sox4fl/fl 11fl/fl 12fl/fl mice were transduced with Ade5CMV-eGFP virus for controls or transduced with Ade5CMV-Cre adenovirus for knockout of the three SOXC family genes, Sox4, Sox11 and Sox12 Results: paired-end reads were mapped to the mm10 genome assembly. RNA levels were normalized using DESeq. Conclusion: SOXC family genes regulate TNF mediated gene expression. Identification of SOXC-dependent and independent aspects of the TNF-regulated transcriptome.