Two Modes of Transcriptional Activation at Native Promoters by NF-κB p65

Max Planck Institute for Immunobiology, Freiburg, Germany.
PLoS Biology (Impact Factor: 9.34). 04/2009; 7(3):e73. DOI: 10.1371/journal.pbio.1000073
Source: PubMed


The NF-kappaB family of transcription factors is crucial for the expression of multiple genes involved in cell survival, proliferation, differentiation, and inflammation. The molecular basis by which NF-kappaB activates endogenous promoters is largely unknown, but it seems likely that it should include the means to tailor transcriptional output to match the wide functional range of its target genes. To dissect NF-kappaB-driven transcription at native promoters, we disrupted the interaction between NF-kappaB p65 and the Mediator complex. We found that expression of many endogenous NF-kappaB target genes depends on direct contact between p65 and Mediator, and that this occurs through the Trap-80 subunit and the TA1 and TA2 regions of p65. Unexpectedly, however, a subset of p65-dependent genes are transcribed normally even when the interaction of p65 with Mediator is abolished. Moreover, a mutant form of p65 lacking all transcription activation domains previously identified in vitro can still activate such promoters in vivo. We found that without p65, native NF-kappaB target promoters cannot be bound by secondary transcription factors. Artificial recruitment of a secondary transcription factor was able to restore transcription of an otherwise NF-kappaB-dependent target gene in the absence of p65, showing that the control of promoter occupancy constitutes a second, independent mode of transcriptional activation by p65. This mode enables a subset of promoters to utilize a wide choice of transcription factors, with the potential to regulate their expression accordingly, whilst remaining dependent for their activation on NF-kappaB.

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Available from: Simona Saccani, Jan 28, 2014
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    • "Table 3. DNA-binding TFs and their identified Mediator subunit target(s)*. Gene TF Reference Organism Gene TF Reference Organism MED1 TRa Fondell et al., 1996 MED15 Smad2/4 Kato et al., 2002 Yuan et al., 1998 Smad3/4 Kato et al., 2002 Malik et al., 2004 NHR-49 Taubert et al., 2006 C. elegans TRb Yuan et al., 1998 Oaf1 Thakur et al., 2009 Yeast Zhu et al., 1997 Pdr1 Thakur et al., 2008 Yeast VDR Yuan et al., 1998 Pdr3 Thakur et al., 2008 Yeast Rachez et al., 1999 VP16 Park et al., 2000 Yeast RARa Yuan et al., 1998 Gal4 Park et al., 2000 Yeast Zhu et al., 1997 Gcn4 Park et al., 2000 Yeast Shao et al., 2000 Swanson et al., 2003 Yeast Lee et al., 2007 Zhang et al., 2004 RXRa Yuan et al., 1998 SREBP-1a Yang et al., 2006 Zhu et al., 1997 MED16 Dif Kim et al., 2004 PPARa Yuan et al., 1998 Gcn4 Swanson et al., 2003 Yeast Zhu et al., 1997 MED17 VP16 Ito et al., 1999 PPARg Yuan et al., 1998 Park et al., 2003 Drosophila Ge et al., 2002 p53 Ito et al., 1999 Ge et al., 2008 Meyer et al., 2010 ER Kang et al., 2002 ER Burakov et al., 2000 Zhang et al., 2005 Hsf Park et al., 2001b Drosophila Burakov et al., 2000 Park et al., 2003 Drosophila Kim et al., 2008 Kim et al., 2004 Warnmark et al., 2001 Dif Park et al., 2003 Drosophila AR Wang et al., 2002 Kim et al., 2004 GR Hittelman et al., 1999 STAT2 Lau et al., 2003 Chen et al., 2006 Gal4 Koh et al., 1998 Yeast Chen & Roeder, 2007 RXR Park et al., 2003 Drosophila Kim et al., 2008 p65 van Essen et al., 2009 HNF4 Malik et al., 2002 MED19 REST Ding et al., 2009 p53 Ito et al., 1999 MED21 TRa Nevado et al., 2004 Yeast Frade et al., 2000 Tup1 Hallberg et al., 2006 Yeast Drane et al., 1997 MED22 GCN4 Swanson et al., 2003 Yeast Meyer et al., 2010 MED23 "
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    ABSTRACT: Abstract The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
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    • "While these results do not rule out a direct role for MED25 in PEA3 target gene activation, they suggest the existence of a MED25-independent PEA3 regulation. This selectivity of MED25 action is reminiscent of the reported Mediator-dependent and -independent regulation by NF-κB p65 (MED17) and nuclear receptors (MED1) in mammals (55,56). Alternatively, the Mediator may also be recruited to PEA3 target genes through direct interactions with other DNA-binding transcription factors and/or coactivators that act synergistically with the PEA3 group members on specific genes. "
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    • "Our evidence that exogenous FOXP3 failed to trans activate Cd25 promoter in the absence of κB site occupancy by RelA, supports a model whereby RelA binding to κB sites is required to modulate FOXP3 transcriptional function. The evidence that in a subset of RelA-dependent genes, without the binding of RelA, NF- κB target promoters cannot be bound by many other transcription factors, supports this possibility [37]. "
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