TNF induced inflammatory transcription dynamics and epigenetic changes
TNF can induce inflammatory responses in cells, including transcriptional and epigenetic changes. To investigate the long-term influence of TNF stimulation on epigenetic modifications, we did transcriptomic and epigenomic profiling of TNF-treated cells with various time length or stages. Overall design: HEK 293 cells were treated with short-term (12 h) and long-term (12 d) TNF, withdrawn TNF to recover 10 d (12 d + 10 d), and treated with 12 h TNF again (12 d + 10 d + 12 h). p65 ChIP-seq and RNA-seq were done for those samples, in WT and TET gene KO cells respectively. WGBS experiments were also performed to obtain DNA methylation data for these samples. H3K27ac ChIP-seq were used to profile histone modifications at p65 binding sites. ATAC-seq experiments were performed to measure chromatin accessibility under various types of treatments.