We wondered whether HMGD1 would be generally asso ciated with open chromatin

The onset of regula tion is evident as early as 10 minutes after treatment in many cases, similar to what we have observed previously following estrogen stimulation in MCF 7 cells. By 30 minutes, the majority of regulated transcripts have reached their maximal change, with most reflecting decreased expres sion. Interestingly, the majority of genes returned to near homeostatic levels 120 minutes INNO-406 ic50 post treatment. This temporal pattern follows a similar time scale as the oscillating patterns of activation and nuclear localization of NF κB previously observed. These changes are most likely explained as a direct readout of NF κBs presence on chromatin. When analyzing the response of individual classes of transcripts, we found that small non coding RNAs, lncRNAs, divergent RNAs, and antisense RNAs are up and down regulated with similar ratios and kinetics as protein coding transcripts.<br><br> Conversely, inter genic and enhancer transcripts are enriched for upregu lation at every time point of TNF treatment, which is consistent with their putative gene activation function. Overall, these analyses reveal a dynamic regulation of the AC16 transcriptome by TNF that fits with the logic of a pro inflammatory stress response broad repression of tran LBH589 scription, with rapid and robust activation of a selected set of target genes. This pattern of regulation is distinct from the mitogenic transcriptional response that we have characterized previously. GRO seq reveals different dynamics for the TNF dependent activation and repression of transcription GRO seq affords the opportunity to examine the dynamics of transcription on a short time scale.<br><br> To examine the dy namics of Pol II in response to TNF, we focused on the time dependent redistribution of Pol II at upregulated and downregulated RefSeq genes. Metagene analyses showing the average GRO seq signal オーダー LY2109761 mapped to 4 kb around the transcription start sites of all genes of interest re veal distinct Pol II dynamics for upregulated and downregulated genes. For genes upregulated upon TNF treatment, Pol II rapidly increased and re leased into the gene body, with a limited time spent at promoter proximal pause sites, which is consistent with previously characterized effects of the TNF NF κB signaling pathway on transcriptional elongation. The activation occurred as early as 10 min, was maximal at 30 min, and was partially attenuated by 120 min.<br><br> In contrast, for genes downregu lated upon TNF treatment, an accumulation of promoter proximally paused Pol II was evident prior to TNF treatment and was only reduced after 30 min. of TNF treatment. A reduction in gene body Pol II, how ever, was evident as early as 10 min. following TNF treatment. The levels of promoter proximally paused Pol II and gene body Pol II returned to basal levels after 120 min. Interestingly, Pol II shows different dynamics during an acute TNF dependent transcriptional response in AC16 cells than it does during a rapid estrogen dependent mitogenic re sponse in MCF 7 breast cancer cells. Specifically, estro gen upregulated genes show a greater induction of promoter proximally paused Pol II in response to the es trogen stimulus, suggesting a greater effect on Pol II loading or initiation than elongation.