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We observed increased expression of ADAMDEC1 RNA in monocytes from patients with systemic lupus erythematosus. The precise role of ADAMDEC1 is uncertain and uniquely among metalloproteinases it utilizes a zinc-coordinating aspartic acid residue which allows it to escape inhibition by tissue inhibitor of metalloprotease-3 (TIMP-3). A closely related gene encodes the protein ADAM28, which is not up-regulated in lupus. We leveraged the ability to look at both gene’s promoters and enhancers simultaneously. ADAMDEC1 was up-regulated by LPS while ADAM28 was not upregulated in the short term. We identified MAP kinases and NFκB as critical cell pathways regulating the expression of ADAMDEC1. These same pathways were implicated in driving the expression of the ADAMDEC1 upstream enhancer RNAs. We demonstrated that binding of the enhancer RNAs produced from the upstream enhancer were critically important and that p300 bound to both the RNA from the enhancer and the DNA at the enhancer. P300 binding to the enhancer was dependent on NFκB. These data define the critical pathways regulating the expression of ADAMDEC1 and extend our knowledge of the roles of enhancer RNAs and mechanistically links p300 and enhancer RNAs.

The SERPINB2 gene is strongly upregulated in inflammatory states. In monocytes, it can constitute up to 1% of total cellular protein. It functions in protection from proteotoxic stress and plays a role in angioedema. The purpose of this study was to define the roles of enhancer RNAs embedded in the SERPIN gene complex. We found that the upstream enhancer RNAs upregulated SERPINB2 and the enhancer RNAs were expressed prior to those of SERPINB2 mRNA. Studies of the SERPINB2 promoter demonstrated the presence of an RNA polymerase II pause-inducing protein, NELF. Stimulation with LPS led to recruitment of the pause-releasing kinase P-TEFb and departure of the pause-inducing protein NELF. RNA immunoprecipitation revealed that NELF and the CDK9 component of P-TEFb bound to the enhancer RNAs after stimulation with distinct kinetics. Knock-down of the enhancer RNAs compromised stimulus induction of promoter and enhancer chromatin changes. Conversely, over-expression was associated with enhanced recruitment of c-JUN and increased expression of SERPINB2 mRNA expression. This study is the first to associate enhancer RNAs with SERPINB2 and is the first demonstration of acquisition of NELF binding by enhancer RNAs on chromatin.

We have shown that CD40 engagement induces TRAF1 gene expression in B lymphocytes. Here we report that CD40-dependent TRAF1 gene transcription in murine B cells is controlled by two enhancer regions. One region is located approximately 2 kb upstream of the transcription start site and the other lies in the intron between exons 5 and 6. The upstream enhancer contains a single NF-kappaB site in addition to sites that bind constitutive transcription factors. Mutation of this NF-kappaB site completely abrogates CD40-driven TRAFl transcription. The intronic enhancer contains two sites that strongly bind the CD40-inducible factors NF-kappaB and AP-1. Simultaneous mutation of the AP-1 site and of the NF-kappaB site abolishes transcription driven by this enhancer. When cloned together into reporter constructs, the two TRAF1 enhancers do not synergize, suggesting that each enhancer may separately participate in the induction of TRAF1 transcription in B cells following CD40 activation.

CD200 plays an important role in prevention of graft rejection, autoimmune diseases and spontaneous abortion by delivering an immunoregulatory signal through interaction with its receptor. It also plays a role in regulating tumor immunity. We previously documented evidence for C/EBP beta as being important in the regulation of constitutive expression of CD200. However, the molecular mechanism(s) controlling inducible expression of CD200 are yet to be explored. Here we address the regulated expression of human CD200 by T cells in response to Con A, IFN-gamma or/and TNF-alpha. A prominent DNase I hypersensitivity site (DHS) was localized approximately 5.4 kb upstream of the major transcriptional start site. Four cis-elements were identified within this genomic region: one nuclear factor-kappaB (NF-kappaB) site, one IFN-gamma activation site (GAS) element and two IFN-stimulated response element (ISRE) for binding of interferon-regulatory factors (IRFs), respectively. Mutation of the NF-kappaB site, GAS or one but not the other of ISREs dramatically reduced the luciferase activity. These findings were further confirmed by chromatin immunoprecipitation (ChIP) assays using antibodies against NF-kappaB p65, STAT1alpha, and IRF-1. All the above findings suggest that IFN-gamma and TNF-alpha induce CD200 expression through a 5' upstream enhancer and that NF-kappaB, STAT1 and IRF-1 play pivotal roles in this process.