Raw concentration profiles for the greatest changing metabolites are provided

secondary pathways. In the context of inflammation, both immediate and delayed regulatory events are clinically relevant as they Chinenov et al. BMC Genomics 2014, 15:656 http://www.biomedcentral.com/1471-2164/15/656 Page 15 of 19 reflect typical glucocorticoid treatment modalities. We reasoned that by analyzing early transcriptomes elicited by the inflammatory and glucocorticoid exposure in M, a clinically relevant cell type, we will be able to isolate a key set of immediate GR targets responsible for the delayed gene expression patterns. Our results indicate that early glucocorticoid- and LPS-dependent changes establish a highly organized program of gene expression with distinct groups of genes following cooperative and antagonistic regulation. As expected from previous work a large group of LPS-induced genes that included among others inflammatory cytokines, was rapidly downregulated by glucocorticoids. Another group encompassing glucocorticoid-induced genes, some PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19801398 of which encode TFs or signaling proteins, are involved in curbing inflammatory signaling. We identified several previously unreported glucocorticoid-induced genes whose products are involved in signaling, regulation of transcription and mRNA stability. Several of these genes add to the arsenal of anti-inflammatory mediators regulated by GR. For example, KLF2 interferes with AP1- and NFB-mediated transcription of Tnf and several chemokines including Ccl2, 3 and 4. Furthermore, Klf2 haploinsufficiency in mice results in an exaggerated inflammatory response and more severe disease in arthritis models. CCL17, another previously unreported glucocorticoid-induced chemokine, is a marker and promoter of the polarization of `alternatively activated’ M2 M, which are considered antiinflammatory and mediate tissue repair and wound healing. In addition to repressing cytokine gene transcription, glucocorticoids downregulate expression of several TFs including Atf3, Junb, Irf1, Bcl3, Tgif1, some in the context of LPS induction, and, unexpectedly, Pparg An enrichment in positive regulators of inflammation and cell proliferation among Dex-downregulated TFs is consistent with the anti-inflammatory and anti-proliferative effects of glucocorticoids. The role of GR in repression of the Pparg gene in M has not been previously reported, the effect might be indirect and mediated by a well-established GR target GILZ, which may also account for the delay. Finally, we described a previously overlooked group of LPS-downregulated genes encoding proteins with the C2H2 Zinc-fingers adjacent to the KRAB domain. Despite being one of the largest TF family, KRAB proteins remain poorly characterized. Among those whose functions were described, several are involved in transcriptional regulation, RNA and DNA binding and splicing. KRAB domains interact with a scaffolding co-repressor TRIM28 which in turn binds the heterochromatin protein 1, chromatin remodeler MI2A and H3K9-specific methyltransferase. Indeed, some KRAB proteins reportedly repress transcription by heterochromatin spreading. Interestingly, several KRAB proteins have been linked to NR actions. The role of KRAB proteins in inflammation is essentially unknown; Rutin however, genomic studies indicate that inflammatory signaling increases accessibility of large sections of the genome. It is tempting to speculate that a broad downregulation of proteins involved in heterochromatin maintenance and spreading serves to increase DNA accessibility and inflammatory