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Review A pervasive role of histone acetyltransferases and deacetylases in an NF-kB-signaling code Miriam Calao, Arsène Burny, Vincent Quivy, Ann Dekoninck and Carine Van Lint Laboratory of Molecular Virology, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 Rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium Most nuclear factor-kB (NF-kB) inducers converge to activate the IkB kinase (IKK) complex, leading to NF-kB nuclear accumulation. However, depending on the inducer and the cell line, the subset of NF-kB-induced genes is different, underlining a complex regulation network. Recent findings have begun to delineate that histone and non-histone protein acetylation is involved, directly and indirectly, in controlling the duration, strength and specificity of the NF-kB-activating signaling pathway at multiple levels. Acetylation and deacetylation events, in combination with other post-translational protein modifications, generate an ‘NF-kB-signaling code’ and regulate NF-kB-dependent gene transcription in an inducer- and promoter-dependent manner. Indeed, the intricate involvement of histone acetyltransferases and histone deacetylases modulates both the NF-kB-signaling pathway and the transcriptional transactivation of NF-kB-dependent genes. The interplay between protein acetylation and NF-kB activation The nuclear factor-kB (NF-kB) family of transcription factors comprises several evolutionarily conserved, structurally related interacting proteins that bind to DNA [1,2]. NF-kB plays a crucial part in the transcriptional regulation of genes involved in controlling cell proliferation, differentiation, apoptosis, inflammation and stress responses, in addition to other biological processes. Consistent with its role in regulating the immune response, abnormal NF-kB regulation has been linked to cancer, inflammatory and autoimmune diseases, septic shock, viral infections and improper immune development. To date, three NF-kB-activating signaling pathways have been reported (Box 1). Under most basal conditions, NFkB, typically a p50–p65 heterodimer, is sequestered in the cytoplasm in an inactive state through its interaction with an inhibitory protein of the inhibitor of NF-kB (IkB) family. After cell stimulation by a wide variety of inducers, the IkB kinase (IKK) complex is activated, leading to transcriptional transactivation of NF-kB-dependent genes (Box 1). Reversible acetylation is a post-translational protein modification that regulates many cellular processes, including chromatin assembly and gene transcription (Box 2). Specific acetylation marks, together with other covalent Corresponding author: Van Lint, C. ([email protected]). post-translational histone modifications (including phosphorylation and methylation), function sequentially or in combination to form the ‘histone code’, which is read by effector proteins to produce distinct biological outcomes [3]. Histone acetylation by histone acetyltransferases (HATs) is crucial for chromatin-compaction status and gene transcription (Box 2). Whereas increased histone acetylation promotes chromatin decompaction and increased DNA accessibility to transcription factors, usually leading to gene activation [4,5] (Box 2), histone deacetylase (HDAC)mediated deacetylation of lysine residues renders nucleosomal DNA less accessible to the transcriptional machinery, thereby usually favoring transcriptional silencing [5] (Box 2). Histone acetylation marks enable the recruitment of bromodomain-containing proteins (including chromatinremodeling enzymes, transcription factors and HATs), which in turn regulate gene expression. In addition to histones, HATs and HDACs have a wide range of nonhistone protein substrates (including transcription factors), functions of which are regulated by acetylation and deacetylation. It is now clearly established that reversible acetylation of histone and non-histone proteins plays a crucial part in regulating the entire NF-kB pathway. Several members of the NF-kB pathway regulate NF-kB-dependent and/or independent transcription through the recruitment of HATs and/or HDACs to gene promoters [6–12]. Moreover, direct acetylation of NF-kB family members and of proteins involved in the NF-kB-signaling pathway (in addition to other signaling pathways) regulates NF-kB activation and transcriptional activity [13–25]. The newly discovered post-translational modifications, serine and threonine protein acetylation, also can regulate the NF-kB-activating cascade [13,26]. Indeed, YopJ, a bacterial effector from Yersinia spp., acetylates IKKa at Thr179 and IKKb at Thr180, located in their respective activation loops, thus preventing their phosphorylation and subsequent activation [13]. Therefore, by inhibiting the NF-kB pathway, Yersinia cripples the host-cell defense system. No YopJ eukaryotic ortholog has been identified to date. In this review we propose that multi-level acetylation and deacetylation events in the NF-kB pathway, in concert with other post-translational protein modifications, generate an ‘NF-kB-signaling code’, which could, by analogy with the ‘histone code’, shape the distinct, and sometimes opposing, biological responses elicited by 0968-0004/$ – see front matter ß 2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.tibs.2008.04.015 339 Review Trends in Biochemical Sciences Vol.33 No.7 Box 1. Overview of the NF-kB-signaling pathway Box 2. HATs and HDACs The NF-kB family of transcription factors is present in most vertebrate cell types as homo- and heterodimers of five structurally related Rel and NF-kB proteins, namely p65 (also called RelA), RelB, c-Rel, NF-kB1 (p50 and its precursor p105) and NF-kB2 (p52 and its precursor p100) [1,2]. The transactivation domain (TAD) that is necessary for NF-kB-dependent transcriptional activity is present only in p65, c-Rel and RelB. However, RelB–p65 heterodimeric complexes are inhibitory because they cannot bind to DNA. Because they lack a TAD, DNA-bound p50 or p52 homodimers function as transcriptional repressors, but they can stimulate transcription when associated with the IkB-like nuclear protein Bcl-3 (B-cell lymphoma 3; which contains a TAD) or when heterodimerized with a transactivating Rel subunit. In unstimulated cells, NF-kB is sequestered in the cytoplasm in an inactive form via interaction with the inhibitors of NF-kB (IkBs). IkBa, IkBb and IkBe bind the Rel homology domain of NF-kB dimers, masking their nuclear-localization signals (NLSs). p105 and p100 also function as IkBs, tethering NF-kB subunits in the cytoplasm of unstimulated cells. The so-called classical NF-kB pathway is triggered by proinflammatory cytokines such as tumor necrosis factor a (TNFa) and promotes the recruitment and activation of the classical IkB-kinase (IKK) complex, which includes two catalytic subunits, IKKa and IKKb, and a scaffold protein, NF-kB essential modulator (IKKg; also known as NEMO). After activation, the IKK complex phosphorylates IkBa, which is subsequently ubiquitylated and degraded by the proteasome. IkBa masks only the p65 NLS, whereas the p50 NLS remains exposed and is responsible, together with the IkBa nuclearexport sequence, for shuttling IkBa–NF-kB complexes between the nucleus and the cytoplasm. IkBa degradation unmasks the p65 NLS, thereby promoting rapid NF-kB translocation into the nucleus. Nuclear NF-kB binds DNA and activates transcription of several genes, including those encoding proinflammatory chemokines and cytokines and several antiapoptotic genes. After NF-kB-dependent resynthesis, IkBa enters the nucleus, removes NF-kB from DNA and enhances NF-kB transit to the cytoplasm, thus restoring the pool of inducible NF-kB. A second pathway, the ‘alternative’ pathway, is engaged after lymphotoxin-b- or B-cell-activating-factor induction and activates an IKKa homodimer, which phosphorylates p100. After phosphorylation, p100 is ubiquitylated and cleaved to generate p52, which translocates as a heterodimer with RelB into the nucleus, where it stimulates transcription of genes that are important for secondary lymphoid organ development, B-cell homeostasis and adaptive immunity. A third NF-kB-activating pathway is classified as atypical because it involves IKK-independent IkBa phosphorylation and proteasome degradation [1,2]. Reversible acetylation is a post-translational protein modification involved in multiple biological processes, including nucleosomal assembly and gene transcription [5,27]. The packaging of eukaryotic DNA with histones into chromatin plays an active part in transcriptional regulation by modulating transcription-factor accessibility. Acetylation of lysine residues in histone N-terminal tails results in chromatin decompaction and increased transcription-factor access to DNA and, thus, usually correlates with gene activation, whereas histone deacetylation mediates transcriptional repression. Moreover, histone lysine acetylation, in concert with other post-translational epigenetic histone modifications, forms the basis for the ‘histone code’. The combination of different modifications provides unique interaction surfaces for effector proteins, including chromatin-remodeling enzymes and transcription factors, thus further regulating gene expression [3]. The histone-acetylation state is a product of competition between two families of enzymes: histone acetyltransferases (HATs) and histone deacetylases (HDACs). On the one hand, enzymes with HAT activity catalyze the transfer of an acetyl group from acetyl coenzyme A to the e-amino group of a specific internal lysine residue, thereby resulting in neutralization of one positive charge on the histone protein. As a result, the electrostatic properties of the protein are strongly modified. On the other hand, enzymes possessing HDAC activity remove acetyl groups from acetylated proteins. Approximately 30 proteins (including hGCN5, CBP, p300, PCAF and steroid-receptor coactivator 1, SRC-1) are known to possess acetyltransferase activity. Each HAT has particular histone substrate specificity. Moreover, HATs present high specificity related to which histone lysine they can acetylate. Mammals express at least 18 HDACs (HDAC-1 to HDAC-11 and the sirtuins, SIRT1 to SIRT7), which are grouped into three classes based on their similarity with yeast genes. Like HATs, HDACs also possess substrate specificity. In addition to histones, HATs and HDACs have a wide range of non-histone protein substrates, of which regulated acetylation and deacetylation determines cellular fate and survival. These substrates include general and specific transcription factors, non-histone structural chromosomal proteins, HATs themselves, viral proteins, non-nuclear proteins (e.g. a-tubulin) and nuclear import factors (such as human importin-a). Depending on the functional domain that is modified, acetylation regulates different functions of these non-histone proteins: for example, DNA recognition, protein stability, protein–protein interactions and subcellular localization. different classes of NF-kB-inducing stimuli in a cell-line- and promoter-dependent manner. We describe and discuss the complex involvement of protein acetylation and deacetylation events regulating the entire NF-kBsignaling pathway. NF-kB recruits antagonistic coregulatory proteins: acetyltransferases and deacetylases NF-kB-dependent gene expression requires the involvement of transcriptional coactivators, which bridge specific transcription factors to the basal transcriptional machinery and also alter chromatin structure (Table 1). Consistent with their role in modifying chromatin structure, many NF-kB coactivators, including p300, CREB-binding protein (CBP), p300/CBP-associated factor (PCAF), members of the p160 family of steroid-receptor coactivators and tat-interactive protein of 60 kDa (Tip60) [27,28], possess a HAT domain, which catalyzes the acetylation of specific internal lysine residues in the core-histone N-terminal tails (Table 1). Moreover, a growing list of proteins can 340 interact with NF-kB dimers and affect NF-kB–DNA binding and NF-kB-dependent transcription, in some cases in concert with HATs. The arginine methyltransferase CARM1 (coactivator-associated arginine methyltransferase 1) interacts directly with p65 at specific promoters, where it functions as a p300/CBP-dependent coactivator for NF-kB-mediated transcriptional activation [29]. Similarly, PRMT1 (protein arginine methyltransferase 1) coactivates NF-kB-dependent gene expression at the macrophage inflammatory protein 2 (MIP2) and HIV-1 promoters synergistically with p300, CARM1 and poly (ADP-ribose) polymerase 1 (PARP1; another NF-kB coactivator [30]) [31]. Similarly to CARM1, which methylates p300 and CBP thereby altering their function [32], PRMT1 also might methylate – and influence the function of – NFkB transcriptional coactivators [31]. It will be interesting to determine whether these two methyltranferases directly modify NF-kB, thereby altering its transcriptional activity. The promoter-specific involvement of different NF-kB coactivators indicates that these coactivators combinatorially assemble at different NF-kB-regulated promoters to achieve distinct functional specificity. However, whereas the kB-site nucleotide sequence governs cofactor binding Review Trends in Biochemical Sciences Vol.33 No.7 Table 1. p50–p65-interacting HATs and HDACsa NF-kB subunit Interacting HAT p65 p300 NF-kB subunit acetylated lysine b Lys314, Lys315 p300 Lys310 Lys218, Lys221 Lys221 – CBP – CBP and PCAF – p300 and PCAF Lys122, Lys123 PCAF and SRC-1 – p300 Lys431, Lys440, Lys441 SRC-1 – p50 via Bcl-3 Tip60 – NF-kB subunit Interacting HDAC p65 SIRT1 NF-kB subunit deacetylated lysine b Lys310 p50 p65 and p50 p50 HDAC-1 and HDAC-2 – HDAC-3 Lys122, Lys123 (Lys218, Lys221, Lys310) c HDAC-4 and HDAC-5 – HDAC-6 HDAC-1 – – HDAC-3 d – Functional consequences Refs Both gene-specific transcriptional activation and repression, although NF-kB–DNA binding and shuttling are not affected Enhanced NF-kB transcriptional activity Inhibition of IkBa binding Enhanced DNA binding Histone H3 and H4 acetylation at the E-selectin and VCAM promoters after TNFa induction Histone H3 and H4 acetylation at the HIV-1 promoter after cell cycle arrest in G2 or PMA induction Histone H3 and H4 acetylation at the TNFa and COX-2 promoter after TNFa or high glucose inductions Reduced NF-kB–DNA binding and postinduction repression of NF-kB-mediated transcription Enhanced p65-dependent transcriptional activation at the E-selectin promoter Enhanced p50–DNA binding in vitro Enhanced p50 recruitment to the COX-2 and iNOS promoters Stimulation of NF-kB-mediated transactivation of an IL-2- (kB)4luciferase reporter gene After IL-1b induction, H3 and H4 KAI1/CD82 promoter acetylation and transcriptional activation [53] [23] [23] [23] [80,81] [82,83] [84] [20] [12] [16] [17,18] [85] [41] Functional consequences Refs Apoptosis induction in response to TNFa via SIRT1-mediated inhibition of p65 transactivation potential Inhibition of proinflammatory mediator release in response to cigarette smoke via SIRT1-mediated inhibition of p65 transactivation potential Inhibition of NF-kB-regulated gene expression, including IL-8, by deacetylating histones within the surrounding chromatin Enhanced NF-kB–DNA binding Enhanced NF-kB–IkBa binding and postinduction repression of the NF-kB transcriptional response Repression of the MIS promoter, which does not contain kB sites. The NF-kB–HDAC complex is recruited by the orphan nuclear receptor SF-1, which binds to its responsive element located within MIS promoter Repression of the HKa2 promoter Local histone deacetylation at the HIV-1 and IL-6 promoters and repression of NF-kB-mediated transcription HDAC-3 is part of corepressor complexes recruited by p50 to the KAI1, cIAP-2 and IL-8 promoters in unstimulated cells to repress basal transcription [21] [22] [35,36] [20] [19] [38] [37] [36,43] [39,41] a Abbreviations: HKa 2, H+-K+-ATPasea2; MIS, mullerian inhibiting substance; SRC-1, steroid-receptor coactivator 1; SF-1, steroidogenic factor 1; VCAM, vascular cell adhesion molecule. b –, functional effects mentioned have not been demonstrated to directly depend on lysine acetylation of the NF-kB subunit considered. c Not directly established. d HDAC3–p50 interaction has not been demonstrated by coimmunoprecipitation assays. and NF-kB–DNA binding affinity in some cases, the specificity of the NF-kB response cannot be reduced to kB sites alone. Recent studies have identified proteins that serve as ‘specifiers’ that select particular genomic kB sites to be activated under certain conditions. In this regard, ribosomal protein S3 (RPS3) is a functional subunit of specific NF-kB–DNA-binding complexes that can confer gene target specificity by binding to DNA with some sequence specificity [33]. Another nuclear protein, Akirin2, fine-tunes NF-kB transcriptional activity by modulating the expression of a subset of lipopolysaccharide (LPS)- and interleukin (IL)-1b-inducible NF-kB-dependent genes through its interaction with components of the chromatin machinery [34]. However, how Akirin2 controls and specifies gene expression requires further investigation. In addition to coactivators, NF-kB also directly or indirectly recruits corepressor complexes, which possess HDAC activity and repress both basal and induced NF-kB-dependent or -independent transcription (i.e. transcription from gene promoters containing or lacking kB sites, respectively) [19,20,35–38] by deacetylating histone N-terminal tails in addition to the p50 and p65 NF-kB subunits (Table 1). Specific HDAC isoforms are recruited via distinct NF-kB complexes, depending on the promoter context and on other coregulatory molecules. In unstimulated cells, promoters containing NF-kBbinding sites are repressed by transcriptionally inactive p50 or p52 homodimers that directly or indirectly bind DNA and recruit HDACs and/or other corepressor proteins [39–43]. HDACs usually are components of large corepressor complexes containing proteins such as mouse SWIindependent 3A (mSin3A), nuclear receptor corepressor (N-CoR) and/or silencing mediator of retinoic acid and thyroid hormone receptor (SMRT). For transcription 341 Review Trends in Biochemical Sciences Vol.33 No.7 Figure 1. Derepression of NF-kB-regulated genes repressed by p50 homodimers. p50 (red) homodimers recruit repressor complexes composed of SMRT (dark gray) and HDAC-3 (orange) (a) or Bcl-3 (purple), N-CoR (light blue) and HDAC-3 (b). (a) (i) In the unstimulated state, the SMRT–HDAC-3 complex, tethered by p50 homodimers, regulates the basal repression of classical NF-kB-regulated genes, including cIAP-2, also known as BIRC3. (ii) Upon cellular stimulation, IKKa (light green) promotes the removal of the SMRT–HDAC-3 complex. Indeed, IKKa-mediated SMRT phosphorylation induces its nuclear export and proteasomal degradation, thereby releasing HDAC-3 from the promoter (iii). This initial derepression enables transcriptionally active p50–p65 heterodimers to bind the promoter; concomitantly, the SMRT corepressor returns to the chromatin-bound NF-kB complex (iv). In the context of the appropriate stimuli, IKKa remains chromatin associated and phosphorylates both p65 (dark green) and SMRT, thereby preventing HDAC-3 recruitment. p300 (light pink) then binds p65–p50 heterodimers, thereby facilitating subsequent p65 acetylation, which is required for full NF-kB-mediated transcription [24]. (b) In the small subset of NF-kB-regulated promoters that tether Bcl-3 (i), such as the Kangai 1 (KAI1; also known as CD82) promoter, 342 Review to proceed, these corepressors must be replaced by coactivator proteins, a mechanism termed derepression. Derepression requires phosphorylation of the repressor protein for two genes that are basally repressed by p50 homodimers: the classical NF-kB-regulated gene cellular inhibitor of apoptosis 2 (cIAP2), also called baculoviral IAP repeat-containing 3 (BIRC3) [24,39] (Figure 1a), and Kangai 1 (KAI1), also termed CD82 (Figure 1b), which belongs to the small subset of NF-kB-regulated genes that tether Bcell CLL/lymphoma 3 (Bcl-3) [24,39,41]. The Perkins group [44] reported that the NF-kB p52 subunit switches from recruiting activator (Bcl-3) to repressor (HDAC-1) proteins to target promoters in response to UV light and subsequent p53 induction. Moreover, although p52 is required for HDAC-1 recruitment at some promoters, resulting in transcriptional repression, it contributes to p300 coactivator recruitment and transcriptional stimulation at other promoters [42]. Although the NF-kB p65 subunit possesses a transactivation domain, it can function either as a transcriptional activator or as a repressor by interacting with HATs or HDACs, respectively [45]. This dual functionality of p65, indicating that several distinct stimuli can produce repressive forms of NF-kB, is regulated on at least two levels: inducible p65 post-translational modifications and the action of coregulatory proteins. Indeed, PKAc (the catalytic subunit of the cAMP-dependent protein kinase)-mediated phosphorylation of p65 at Ser276 (within its Rel homology domain) enhances p300 and CBP recruitment and simultaneously decreases HDAC-1 affinity for p65 [10,36]. Moreover, Mayo and colleagues [24] demonstrated that IKKa-mediated phosphorylation of p65 at Ser536 (within its transactivation domain) displaces the SMRT–HDAC-3 corepressor complex, enabling p300 to interact with p65. Among the NFkB coregulatory proteins, ARF (alternative reading frame), a tumor suppressor, expression of which is induced upon oncogene activation, and LZAP (LxxLL/leucine-zipper-containing ARF-binding protein) inhibit NF-kBinduced antiapoptotic gene expression by increasing the interaction between HDACs and p65, without altering NF-kB–DNA binding [46,47]. ARF- and LZAP-dependent inhibition of p65-mediated antiapoptotic gene expression reflects differential p65 phosphorylation status: ARF activation induces p65 phosphorylation at Thr505, whereas LZAP expression decreases phosphorylation of p65 at Ser536 [47,48]. Importantly, increased NF-kB association with HDAC-containing corepressor complexes is a common mechanism through which many tumor-suppressor proteins inhibit the antiapoptotic function of NF-kB, which contributes to tumorigenesis. Therefore, stimulus-dependent phosphorylation events modulate switches between HDAC-containing NF-kB repressor complexes and HAT-containing NFkB-activator complexes. The mechanisms through which HATs and other coactivators enhance NF-kB transcriptional activity (whereas it is inhibited by HDACs and Trends in Biochemical Sciences Vol.33 No.7 other corepressors) are multifactorial and involve direct effects on NF-kB, other transcription factors and chromatin structure. Regulation of NF-kB biological functions by direct acetylation In addition to acetylating the N-terminal tails of core histones that surround NF-kB-regulated genes, HATs also directly acetylate several NF-kB subunits: p52 and its precursor p100, p50 and p65. Hu and Colburn [14] have reported that p100 acetylation enhances processing of p100 to p52, whereas Wu and colleagues [15] demonstrated that p300-dependent p52 acetylation enhances its DNAbinding activity. These differences could reflect acetylation at different lysine residues; however, the acetylation sites in p52 and its precursor p100 have not been mapped. The p50 subunit of the classical NF-kB p50–p65 heterodimer is acetylated in vitro and in vivo (Figure 2; Table 1). In vitro, p300-mediated acetylation of p50 occurs only in the presence of the HIV-1 viral protein Tat [16]; however, in vivo, in the absence of Tat, p300 overexpression enhances p50 acetylation [17,18]. One possible explanation for this discrepancy is that, under physiological conditions, p300-mediated p50 acetylation relies on a Tat-like cofactor. The acetylated form of p50 binds to target sites with higher affinity than the unacetylated form in vitro does [16]. In agreement with these data, enhanced in vivo p50 acetylation correlates with increased binding of p50 to two NFkB-regulated promoters: cyclooxygenase-2 (COX-2) and inducible NO synthase (iNOS) [17,18]. Three p50 lysines, Lys431, Lys440 and Lys441, are acetylated in vitro [16], but the specific role for each acetylated residue has not been demonstrated (Figure 2). p65 is acetylated by p300 and is deacetylated through specific interactions with HDAC-3 [19,20] or SIRT1 [21,22] (Figure 2; Table 1). p65 acetylation is functionally important; indeed, endogenous p65 is acetylated in response to many different stimuli, including exposure to tumor necrosis factor a (TNFa), phorbol 12-myristate 13-acetate (PMA) or transforming growth factor 1 (TGFb1) [19,20,24,49]. Accordingly, inhibition of TNFa-induced IKK- and Aktkinase activity correlates with suppression of p65 acetylation [50,51]. Furthermore, doxorubicin-dependent NF-kB induction, which does not affect p65 phosphorylation or acetylation, is not associated with NF-kB-dependent transcriptional activation [52]. The Greene group [23] demonstrated that p65 acetylation occurs on three lysine residues: Lys218, Lys221 and Lys310. p300-mediated acetylation at Lys221 enhances p65–DNA-binding activity and, together with Lys218 acetylation, impairs the p65– IkBa interaction, thus impeding IkBa-dependent nuclear export of NF-kB complexes and prolonging the NF-kB response [19,23]. Thus, HDAC-3-mediated p65 deacetylation at Lys221 and Lys218 is involved in terminating the NF-kB response by promoting IkBa–p65 interaction and NF-kB nuclear export. Lys310 acetylation is required for full p65 transcriptional activity on the E-selectin promoter IL-1b-induced derepression involves MEKK1 (MAP/ERK kinase kinase 1)-mediated TAK1-binding protein 2 (TAB2; pink) phosphorylation, which causes the nuclear export of the N-CoR–TAB2–HDAC-3 complex (ii) and the recruitment of the HAT Tip60 (brown) to the promoter (iii). This recruitment is accompanied by histones H3 (light purple) and H4 (blue) acetylation and subsequent transcription initiation [41]. Adapted, with permission, from Refs [24,41]. 343 Review Trends in Biochemical Sciences Vol.33 No.7 Figure 2. Acetylation and deacetylation of the NF-kB p50 and p65 subunits. The NF-kB p65 (green) subunit is acetylated by p300 or PCAF and deacetylated through specific interactions with HDAC-3 [19,20] or SIRT1 [5,21]. Lys221 acetylation enhances p65 DNA-binding activity and, together with acetylation at Lys218, impairs its assembly with IkBa (brown), thus impeding IkBa-dependent nuclear export of the NF-kB complex and enabling prolongation of the NF-kB response [23]. p65 acetylation at Lys310 is required for its full transcriptional activation [23]. Although a specific role for p65 Lys314 and Lys315 acetylation has not been demonstrated, these modifications are not involved in NF-kB–DNA binding or intracellular shuttling [53]. Lys431, Lys440 and Lys441 of p50 (red) are acetylated in vitro, but the specific functional role of these modifications has not been demonstrated; however, in vitro, the acetylated form of p50 binds target sequences with higher affinity than the unacetylated form does [16]. In agreement with these data, enhanced p50 acetylation correlates with increased p50 binding to some NF-kB-regulated promoters in vivo [17,18]. Green arrows represent increased DNA-binding affinity, red lines pointing toward DNA represent decreased DNA-binding affinity, red lines pointing toward acetylated residues represent deacetylation events, and red lines pointing toward IkBa represent decreased p65–IkBa interaction. [23]. TNFa-dependent phosphorylation of p65 at either Ser276 or Ser536 increases its interaction with p300 and its subsequent acetylation at Lys310, indicating that p65 phosphorylation regulates subsequent acetylation [24,25] (Figure 3). By contrast, Benkirane and colleagues [20] have shown that Lys122 and Lys123 are the only acetylated residues in p65 and that p300- or PCAF-mediated p65 acetylation lowers its binding affinity for target sequences. Recently, two additional acetyl acceptor sites (Lys314 and Lys315) were identified by the Hottiger group [53], who Figure 3. NF-kB-dependent transcription requires histone acetylation. When NF-kB enters the nucleus after cell stimulation, it activates two subsets of target promoters: those that were heavily acetylated before stimulation (i.e. constitutively and immediately accessible) (a) and those requiring stimulus-dependent modifications in chromatin structure to make NF-kB sites accessible (b) [60]. (a) The subset of NF-kB target genes, of which the promoter chromatin is immediately accessible to NF-kB (green), is transcribed immediately after NF-kB activation. (b) By contrast, for NF-kB target genes that are not immediately accessible (i), stimulus-dependent chromatin remodeling and histone hyperacetylation are prerequisites for NF-kB recruitment. As an example, mcp-1 (also known as ccl2) transcription requires binding of AP-1 (light blue)inducible transcription factors to the promoter and subsequent ATP-dependent chromatin remodeling by the SWI/SNF (switch/sucrose nonfermentable) complex (orange) (ii). This remodeling enables NF-kB-binding-site accessibility, HAT (purple) recruitment and activity and, thus, mcp-1 gene activation (iii). Green arrows represent gene transcription and red arrows represent transcriptional repression. Adapted, with permission, from Ref. [79]. 344 Review also confirmed the presence of Lys310 acetylation. They found that Lys314 and Lys315 acetylation is not involved in DNA-binding activity or shuttling of NF-kB. The discrepancies between the conclusions reached by the Greene, Benkirane and Hottiger groups regarding p65 acetylation might result from differences in the experimental approaches, stimuli (e.g. none, PMA and/or HDAC inhibitor, and TNFa and/or HDAC inhibitor, respectively) and cell lines (i.e. Jurkat, Cos-7 or HEK 293T) used. Importantly, the study by the Hottiger group [53] also provides evidence that, after TNFa stimulation, specific subsets of genes are either stimulated or represssed by p300mediated p65 Lys310, Lys314 and Lys315 acetylation. Thus, distinct p65 acetylation events regulate the specificity of NF-kB-dependent gene expression [53]. Taken together, the results from several laboratories demonstrate that NF-kB acetylation regulates NF-kB transcriptional potential, DNA-binding activity and protein–protein interactions with several transcription cofactors. Indeed, the unique combinations of NF-kB post-translational modifications form a recognition code that regulates the interactions between NF-kB and these cofactors. IkBa- and IKK-dependent gene regulation through HAT and/or HDAC recruitment In addition to their cytoplasmic role in the NF-kB-activating cascade, IkBa and some members of the IKK complex have a nuclear function involving HAT and HDAC recruitment. IkBa interacts with HDAC-1, -3 and -5 [6,7]. Although IkBa was first identified as the specific cytoplasmic inhibitor of NF-kB, it now is clear that it shuttles between the nucleus and the cytoplasm [54]. In the nucleus, IkBa represses NF-kB-dependent and -independent transcription. Indeed, on the one hand, IkBa induces NF-kB nuclear export, leading to the termination of NF-kB transcriptional activation [55]. On the other hand, transcription from the promoter of the Notch-target gene Hes1 (which is not a classical NF-kB target gene) is repressed by IkBa, which is recruited to this promoter together with NCoR, HDAC-1 and HDAC-5 [7]. TNFa treatment causes a temporary release of IkBa from the Hes1 promoter, which is correlated with increased histone acetylation and transcriptional activation. Because IkBa is not detected on the IL-6 or RANTES (regulated upon activation, normally T cell expressed and presumably secreted) NF-kB-dependent promoters, this regulatory mechanism probably does not operate on classical NF-kB target genes [7]. Thus, IkBa probably represses transcription by tethering HDACs to promoter regions, a mechanism that could be involved in the termination of NF-kB-independent transcriptional activation. In addition to its cytoplasmic role in the IKK complex, IKKa is recruited to NF-kB-dependent promoters after TNFa treatment, where it phosphorylates histone H3 Ser10. Because IKKa interacts with CBP [8] and histone phosphorylation is often associated with histone acetylation [56,57], the association of a kinase such as IKKa with an acetyltransferase (e.g. CBP) could enable the removal of a repressive chromatin structure associated with NF-kB-dependent genes. It recently was proposed Trends in Biochemical Sciences Vol.33 No.7 that IKKa could promote p65 acetylation at some promoters via both CBP recruitment and p65 phosphorylation [24,58]. Furthermore, IKKa modifies HDAC-3 recruitment on NF-kB-dependent genes in a promoterspecific manner [58]. Indeed, although this kinase is necessary for the removal of SMRT and HDAC-3 from some promoters where HDAC-3 inhibits p65 binding [39], IKKa also might function as a repressor that tethers small quantities of HDAC-3 to the IkBa promoter, thereby preventing excessive p65–DNA binding [39,58]. Moreover, trichostatin A (TSA), an HDAC inhibitor, treatment impairs IKKa recruitment to the IkBa promoter, indicating a role for HDACs in this recruitment [59]. IKKg (also called NEMO), the IKK complex regulatory subunit, shuttles between the cytoplasm and the nucleus and interacts directly with CBP [9]. In addition to the key role of IKKg in regulating cytokine-induced IKK activity, this regulatory subunit competes with p65 and IKKa for binding to the CBP N terminus, thereby inhibiting p65- and IKKa-induced CBP-dependent transcriptional activation [9]. These findings could explain the downregulation of NF-kB activity that occurs under basal conditions and the post-induction repression of the NF-kB pathway [9]. Thus, the recruitment of HATs and HDACs by IkBa, IKKa and IKKg adds a level of complexity to the interplay between acetylation-dependent transcriptional regulation and NF-kB-dependent transcriptional regulation. Acetylation-dependent crosstalk between the NF-kB pathway and other signaling pathways The cell must integrate the functions of different pathways to generate a coherent biological response to environmental changes. In agreement with this, the NF-kB response results from the integration of the NF-kB and other signaling pathways, which can modulate either kB-site accessibility or NF-kB activity through histone and non-histone protein post-translational modifications. In this section we discuss the prominent role of acetylation and deacetylation events and HAT and/or HDAC recruitment in the crosstalk between the NF-kB and other signaling pathways. In unstimulated cells, NF-kB binding sites in the promoter regions of genes such as RANTES, chemokine (C-C motif) ligand 2 (ccl2) also known as monocyte chemoattractant protein-1 (mcp-1), and IL-6 are in a repressedchromatin environment that prevents NF-kB–DNA binding. These sites become accessible after histone acetylation mediated by the activation of other signaling pathways [60] (Figure 3). IKKa, after cytokine stimulation or contextual conditioned fear memory retrieval, and p38 MAPK (mitogen-activated protein kinase), after LPS stimulation, are recruited to specific NF-kB-responsive promoters where they phosphorylate histone H3 at Ser10, thus promoting subsequent H3 Lys14 acetylation and transcriptional activation [8,56,57,61,62]. Importantly, after cytokine stimulation IKKa also phosphorylates CBP at Ser1382 and Ser1386, thus enhancing CBP-binding affinity for p65 and CBP HAT activity and, consequently, histone H3 acetylation [63]. Similarly, MAPK p38- or Akt-mediated p300 phosphorylation enhances its acetyltransferase activity and might facilitate p65–p300 complex formation, 345 Review resulting in p65 Lys310 acetylation and optimal p65 transactivation activity [64,65]. Different signaling pathways can interfere with one another by modulating the availability of HATs or HDACs for a particular transcription complex. For example, p65 and p53 directly compete for CBP or p300 [63], and this competition is responsible for their cross-repression. After IKKa-mediated CBP phosphorylation, the CBP–p65 interaction increases, whereas the CBP–p53 interaction decreases [63]. A consequence of the functional relationship between p53 and p65 is the ability of p65 to facilitate p53-induced cell death, probably because p53 converts NFkB to a repressor of antiapoptotic gene expression. Glycogen synthase kinase 3b (GSK3b), a constitutively active downstream kinase in the phosphoinositide 3-kinase (PI 3kinase) pathway, regulates the NF-kB-mediated inflammatory response by affecting the amount of nuclear CBP that is complexed with p65 or CREB. Indeed, GSK3b phosphorylates and inactivates CREB, thereby disrupting the CREB–CBP interaction. Thus, GSK3b inactivation releases CREB repression, promotes CREB–CBP interaction and, as a consequence, reduces CBP access to NFkB, thereby dampening NF-kB transcriptional potential [66]. PPARg is a nuclear receptor in the peroxisome proliferator-activated receptor (PPAR) family that inhibits inflammatory responses by repressing NF-kB-mediated gene expression [67]. It is likely that PPARg suppresses Eotaxin (an NF-kB target) gene expression by direct inhibition of p65-associated HAT activity, for example, by competing with p65 for limited amounts of CBP and/or by recruiting HDAC to the p65–HAT complex [67]. Acetylation and deacetylation events regulate the interactions between NF-kB and other transcription factors, including the glucocorticoid receptor (GR) and STAT1 (signal transducer and activator of transcription 1). Recent studies indicate that the GR acetylation status modulates its interaction with NF-kB [68], which is probably responsible for the inhibitory effect on inflammatory and immune genes by glucocorticoids, the most effective class of antiinflammatory agents [69]. More specifically, HDAC-2mediated deacetylation of the GR, which is acetylated after ligand binding, enables GR–p65 interaction and the subsequent attenuation of NF-kB-mediated, but not GRmediated, gene transcription [68]. This mechanism could provide a molecular explanation for the repression of NFkB-mediated IL-8 transcription induced by GR-associated steroid receptor coactivator-2 (SRC-2), a member of the p160 family of coactivators [70]. Indeed, when tethered to DNA by protein–protein interactions, GR-associated SRC2 represses transcription via its unique corepression surface; by contrast, GR interaction with SRC-2 at glucocorticoid response elements (GREs) results in transcriptional activation [70]. Thus, because the GR acetylation status regulates GR–NF-kB binding, HDAC-2 might be crucially involved in regulating the SRC-2 coactivator– corepressor switch. Similarly to GR acetylation, direct acetylation of STAT1, which is a mediator of interferon signaling, modulates its ability to regulate NF-kB activity [71]. Interferon-a-induced STAT1 acetylation, within its DNA-binding domain, enables its interaction with p65. As a consequence, the level 346 Trends in Biochemical Sciences Vol.33 No.7 of nuclear p65 strongly decreases and NF-kB–DNA binding is inhibited, thereby leading to the downregulation of antiapoptotic NF-kB target genes [71]. These findings offer an explanation for the induction of apoptosis observed in a human melanoma cell line after a combined treatment with HDAC inhibitors and interferon a [71]. Interference between signaling modules also can terminate signal-induced gene expression. Indeed, although activating protein-1 (AP-1)-mediated histone H4 acetylation is required for NF-kB–DNA binding at promoters with regulated and late NF-kB accessibility [60] (Figure 3), AP-1 also can be recruited to some activated NF-kB target promoters at a later time in induction and can inhibit transcription by recruiting a specific HDAC complex to modify local histone acetylation patterns [72]. AP-1mediated HDAC recruitment to specific NF-kB target promoters represses only the promoters containing AP1-binding sites and, because most AP-1 transcription factors are synthesized after activation of the transcriptional response, this mechanism also provides a sufficient time delay for transcriptional termination [72]. In conclusion, NF-kB activity is regulated at multiple levels by acetylation and deacetylation events that occur in the NF-kB-activation pathway or regulate the crosstalk between the NF-kB pathway and other signaling pathways. Concluding remarks and future perspectives NF-kB was discovered in 1986 [73]; ten years later, CBP and p300 were demonstrated to possess HAT activity [5]. Shortly thereafter, NF-kB-dependent transcription was shown to require multiple coactivators that possess HAT activity, including CBP and p300. The interactions between NF-kB and these HATs indicated the existence of a link between histone acetylation and NF-kB-mediated transactivation. It is now well established that lysine acetylation plays a crucial part in regulating NF-kB-dependent gene transcription. Indeed, interactions between several members of the NF-kB pathway with HATs and/or HDACs, direct acetylation of NF-kB family members, and acetylation and deacetylation events regulating the crosstalk between the NF-kB pathway and other signaling pathways, modulate NF-kB activation and transcriptional potential both at the chromatin level and at the non-histone protein level. The specificity of these regulatory events depends on the inducer, the promoter and the cell line considered. An important issue for future investigations is to further elucidate how this specificity is achieved, and how it relates to what we have termed the ‘NF-kB-signaling code’. Much remains to be learned about the role of nonhistone protein acetylation in the NF-kB pathway. Indeed, the specific role of p50 Lys431, Lys440 and Lys441 acetylation in addition to the acetylation target site(s) in p52 remain undefined. Moreover, future studies will probably identify acetylation-dependent regulation of other members of the NF-kB pathway. In this regard, we have reported that TSA prolongs TNFa-induced IKK activity, thus suggesting that unidentified acetylation events regulate IKK activity [27,74]. Because temporal control of NF-kB activation can direct specific gene-expression Review patterns [75], stimulus-specific temporal control of IKK activity could promote distinct biological responses and could introduce an additional level of complexity to the known intricate regulation of the NF-kB-activating pathway. To gain a complete understanding of the multi-level and multi-dimensional network that regulates NF-kB activation and activity in a given cell type in response to a given inducer will be a huge challenge in the coming years. Abnormal NF-kB activation is observed in several inflammatory diseases, neurodegenerative disorders and cancers [76]. However, molecules that block NF-kB activation have shown weak clinical efficacy, and their lack of specificity causes side effects by interfering with NF-kB physiological roles in immunity, inflammation and cellular homeostasis [76]. One of the major challenges in clinical research is to develop a series of NF-kB inhibitors aimed at treating different diseases, based on their ability to target specific pathways or cells, thereby avoiding the risk of undesired side effects. To this end, it is important to investigate the molecular mechanisms that govern the differential association of NF-kB with coactivator and corepressor proteins that have profound consequences on many cellular processes and are at least partially responsible for NF-kB response specificity. Several HDAC inhibitors have been developed by the pharmaceutical industry and are promising agents for cancer treatment [77]. However, NF-kB provides a strong protective role against HDAC-inhibitormediated apoptosis; thus, a combined molecular strategy that inhibits both NF-kB and HDAC activities might lead to the design of an efficient anticancer therapy [78]. Thus, further investigation of the underlying molecular mechanisms of HAT- and HDAC-mediated NF-kB-pathway regulation, and the identification of additional specific NF-kB and HDAC inhibitors should provide us with new therapeutic opportunities. Acknowledgements We thank the reviewers for helpful comments on this manuscript and we apologize to those whose work could not be cited directly because of space limitations. We acknowledge grant support from the Belgian Fund for Scientific Research (FRS-FNRS, Belgium), the Télévie-Program of the FRS-FNRS, the Action de Recherche Concertée du Ministère de la Communauté Française (Université Libre de Bruxelles, ARC program no. 04/09–309), the Internationale Brachet Stiftung, the Fondation contre le Cancer, the Interreg III program (Intergenes project), the Région Wallonne (Program WALEO2 616295) and the Theyskens-Mineur Foundation. M.C. is a fellow of the Belgian Fonds pour la Recherche dans l’Industrie et l’Agriculture. A.D. and C.V.L. are Chargé de Recherches and Directeur de Recherches of the FRS- FNRS, respectively. References 1 Viatour, P. et al. (2005) Phosphorylation of NF-kB and IkB proteins: implications in cancer and inflammation. Trends Biochem. Sci. 30, 43– 52 2 Hayden, M.S. and Ghosh, S. (2008) Shared principles in NF-kB signaling. Cell 132, 344–362 3 Strahl, B.D. and Allis, C.D. (2000) The language of covalent histone modifications. Nature 403, 41–45 4 Sterner, D.E. and Berger, S.L. (2000) Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev. 64, 435– 459 5 Yang, X.J. and Seto, E. (2007) HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention. Oncogene 26, 5310–5318 Trends in Biochemical Sciences Vol.33 No.7 6 Viatour, P. et al. (2003) Cytoplasmic IkBa increases NF-kBindependent transcription through binding to histone deacetylase (HDAC) 1 and HDAC3. J. Biol. Chem. 278, 46541–46548 7 Aguilera, C. et al. (2004) Recruitment of IkBa to the hes1 promoter is associated with transcriptional repression. Proc. Natl. Acad. Sci. U. S. A. 101, 16537–16542 8 Yamamoto, Y. et al. (2003) Histone H3 phosphorylation by IKK-a is critical for cytokine-induced gene expression. Nature 423, 655–659 9 Verma, U.N. et al. (2004) Nuclear role of IkB kinase-g/NF-kB essential modulator (IKKg/NEMO) in NF-kB-dependent gene expression. J. Biol. Chem. 279, 3509–3515 10 Zhong, H. et al. (1998) Phosphorylation of NF-kB p65 by PKA stimulates transcriptional activity by promoting a novel bivalent interaction with the coactivator CBP/p300. Mol. Cell 1, 661–671 11 Vanden Berghe, W. et al. (1999) The nuclear factor-kB engages CBP/ p300 and histone acetyltransferase activity for transcriptional activation of the interleukin-6 gene promoter. J. Biol. Chem. 274, 32091–32098 12 Sheppard, K.A. et al. (1999) Transcriptional activation by NF-kB requires multiple coactivators. Mol. Cell. Biol. 19, 6367–6378 13 Mittal, R. et al. (2006) Acetylation of MEK2 and IkB kinase (IKK) activation loop residues by YopJ inhibits signaling. Proc. Natl. Acad. Sci. U. S. A. 103, 18574–18579 14 Hu, J. and Colburn, N.H. (2005) Histone deacetylase inhibition downregulates cyclin D1 transcription by inhibiting nuclear factor-kB/p65 DNA binding. Mol. Cancer Res. 3, 100–109 15 Deng, W.G. et al. (2006) Melatonin suppresses macrophage cyclooxygenase-2 and inducible nitric oxide synthase expression by inhibiting p52 acetylation and binding. Blood 108, 518–524 16 Furia, B. et al. (2002) Enhancement of nuclear factor-kB acetylation by coactivator p300 and HIV-1 Tat proteins. J. Biol. Chem. 277, 4973– 4980 17 Deng, W.G. and Wu, K.K. (2003) Regulation of inducible nitric oxide synthase expression by p300 and p50 acetylation. J. Immunol. 171, 6581–6588 18 Deng, W.G. et al. (2003) Up-regulation of p300 binding and p50 acetylation in tumor necrosis factor-a-induced cyclooxygenase-2 promoter activation. J. Biol. Chem. 278, 4770–4777 19 Chen, L.F. et al. (2001) Duration of nuclear NF-kB action regulated by reversible acetylation. Science 293, 1653–1657 20 Kiernan, R. et al. (2003) Post-activation turn-off of NF-kB-dependent transcription is regulated by acetylation of p65. J. Biol. Chem. 278, 2758–2766 21 Yeung, F. et al. (2004) Modulation of NF-kB-dependent transcription and cell survival by the SIRT1 deacetylase. EMBO J. 23, 2369– 2380 22 Yang, S.R. et al. (2007) Sirtuin regulates cigarette smoke-induced proinflammatory mediator release via RelA/p65 NF-kB in macrophages in vitro and in rat lungs in vivo: implications for chronic inflammation and aging. Am. J. Physiol. Lung Cell. Mol. Physiol. 292, L567–L576 23 Chen, L.F. et al. (2002) Acetylation of RelA at discrete sites regulates distinct nuclear functions of NF-kB. EMBO J. 21, 6539–6548 24 Hoberg, J.E. et al. (2006) IkB kinase a-mediated derepression of SMRT potentiates acetylation of RelA/p65 by p300. Mol. Cell. Biol. 26, 457– 471 25 Chen, L.F. et al. (2005) NF-kB RelA phosphorylation regulates RelA acetylation. Mol. Cell. Biol. 25, 7966–7975 26 Mukherjee, S. et al. (2006) Yersinia YopJ acetylates and inhibits kinase activation by blocking phosphorylation. Science 312, 1211–1214 27 Quivy, V. and Van Lint, C. (2004) Regulation at multiple levels of NFkB-mediated transactivation by protein acetylation. Biochem. Pharmacol. 68, 1221–1229 28 Sapountzi, V. et al. (2006) Cellular functions of TIP60. Int. J. Biochem. Cell Biol. 38, 1496–1509 29 Miao, F. et al. (2006) Coactivator-associated arginine methyltransferase-1 enhances nuclear factor-kB-mediated gene transcription through methylation of histone H3 at Arginine 17. Mol. Endocrinol. 20, 1562–1573 30 Zerfaoui, M. et al. (2008) Nuclear translocation of p65 NF-kB is sufficient for VCAM-1, but not ICAM-1, expression in TNFstimulated smooth muscle cells: differential requirement for PARP-1 expression and interaction. Cell. Signal. 20, 186–194 347 Review 31 Hassa, P.O. et al. (2008) Protein arginine methyltransferase 1 coactivates NF-kB-dependent gene expression synergistically with CARM1 and PARP1. J. Mol. Biol. 377, 668–678 32 Chevillard-Briet, M. et al. (2002) Control of CBP co-activating activity by arginine methylation. EMBO J. 21, 5457–5466 33 Wan, F. et al. (2007) Ribosomal protein S3: a KH domain subunit in NF-kB complexes that mediates selective gene regulation. Cell 131, 927–939 34 Goto, A. et al. (2008) Akirins are highly conserved nuclear proteins required for NF-kB-dependent gene expression in drosophila and mice. Nat. Immunol. 9, 97–104 35 Ashburner, B.P. et al. (2001) The p65 (RelA) subunit of NF-kB interacts with the histone deacetylase (HDAC) corepressors HDAC1 and HDAC2 to negatively regulate gene expression. Mol. Cell. Biol. 21, 7065–7077 36 Zhong, H. et al. (2002) The phosphorylation status of nuclear NF-kB determines its association with CBP/p300 or HDAC-1. Mol. Cell 9, 625–636 37 Zhang, W. and Kone, B.C. (2002) NF-kB inhibits transcription of the H+-K+-ATPase a2-subunit gene: role of histone deacetylases. Am. J. Physiol. Renal Physiol. 283, F904–F911 38 Hong, C.Y. et al. (2003) Expression of MIS in the testis is downregulated by tumor necrosis factor a through the negative regulation of SF-1 transactivation by NF-kB. Mol. Cell. Biol. 23, 6000–6012 39 Hoberg, J.E. et al. (2004) SMRT derepression by the IkB kinase a: a prerequisite to NF-kB transcription and survival. Mol. Cell 16, 245–255 40 Silverman, N. and Maniatis, T. (2001) NF-kB signaling pathways in mammalian and insect innate immunity. Genes Dev. 15, 2321–2342 41 Baek, S.H. et al. (2002) Exchange of N-CoR corepressor and Tip60 coactivator complexes links gene expression by NF-kB and b-amyloid precursor protein. Cell 110, 55–67 42 Schumm, K. et al. (2006) Regulation of p53 tumour suppressor target gene expression by the p52 NF-kB subunit. EMBO J. 25, 4820–4832 43 Williams, S.A. et al. (2006) NF-kB p50 promotes HIV latency through HDAC recruitment and repression of transcriptional initiation. EMBO J. 25, 139–149 44 Rocha, S. et al. (2003) p53 represses cyclin D1 transcription through down regulation of Bcl-3 and inducing increased association of the p52 NF-kB subunit with histone deacetylase 1. Mol. Cell. Biol. 23, 4713–4727 45 Campbell, K.J. et al. (2004) Active repression of antiapoptotic gene expression by RelA(p65) NF-k B. Mol. Cell 13, 853–865 46 Rocha, S. et al. (2003) p53- and Mdm2-independent repression of NFkB transactivation by the ARF tumor suppressor. Mol. Cell 12, 15–25 47 Wang, J. et al. (2007) LZAP, a putative tumor suppressor, selectively inhibits NF-kB. Cancer Cell 12, 239–251 48 Rocha, S. and Perkins, N.D. (2005) ARF the integrator: linking NF-kB, p53 and checkpoint kinases. Cell Cycle 4, 756–759 49 Ishinaga, H. et al. (2007) TGF-b induces p65 acetylation to enhance bacteria-induced NF-kB activation. EMBO J. 26, 1150–1162 50 Takada, Y. et al. (2005) Evodiamine abolishes constitutive and inducible NF-kB activation by inhibiting IkBa kinase activation, thereby suppressing NF-kB-regulated antiapoptotic and metastatic gene expression, up-regulating apoptosis, and inhibiting invasion. J. Biol. Chem. 280, 17203–17212 51 Aggarwal, S. et al. (2006) Curcumin (diferuloylmethane) downregulates expression of cell proliferation and antiapoptotic and metastatic gene products through suppression of IkBa kinase and Akt activation. Mol. Pharmacol. 69, 195–206 52 Ho, W.C. et al. (2005) Nuclear factor-kB induced by doxorubicin is deficient in phosphorylation and acetylation and represses nuclear factor-kB-dependent transcription in cancer cells. Cancer Res. 65, 4273–4281 53 Buerki, C. et al. (2008) Functional relevance of novel p300-mediated lysine 314 and 315 acetylation of RelA/p65. Nucleic Acids Res. 36, 1665–1680 54 Johnson, C. et al. (1999) An N-terminal nuclear export signal is required for the nucleocytoplasmic shuttling of IkBa. EMBO J. 18, 6682–6693 55 Arenzana-Seisdedos, F. et al. (1995) Inducible nuclear expression of newly synthesized IkBa negatively regulates DNA-binding and transcriptional activities of NF- kB. Mol. Cell. Biol. 15, 2689–2696 348 Trends in Biochemical Sciences Vol.33 No.7 56 Lubin, F.D. and Sweatt, J.D. (2007) The IkB kinase regulates chromatin structure during reconsolidation of conditioned fear memories. Neuron 55, 942–957 57 Lo, W.S. et al. (2000) Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. Mol. Cell 5, 917–926 58 Gloire, G. et al. (2007) Promoter-dependent Effect of IKKa on NF-kB/ p65 DNA binding. J. Biol. Chem. 282, 21308–21318 59 Horion, J. et al. (2007) Histone deacetylase inhibitor trichostatin A sustains sodium pervanadate-induced NF-kB activation by delaying IkBa mRNA resynthesis: comparison with tumor necrosis factor a. J. Biol. Chem. 282, 15383–15393 60 Saccani, S. et al. (2001) Two waves of nuclear factor kB recruitment to target promoters. J. Exp. Med. 193, 1351–1359 61 Anest, V. et al. (2003) A nucleosomal function for IkB kinase-a in NFkB-dependent gene expression. Nature 423, 659–663 62 Saccani, S. et al. (2002) p38-Dependent marking of inflammatory genes for increased NF-kB recruitment. Nat. Immunol. 3, 69–75 63 Huang, W-C. et al. (2007) Phosphorylation of CBP by IKKa promotes cell growth by switching the binding preference of CBP from p53 to NFkB. Mol. Cell 26, 75–87 64 Saha, R.N. et al. (2007) MAPK p38 regulates transcriptional activity of NF-kB in primary human astrocytes via acetylation of p65. J. Immunol. 179, 7101–7109 65 Liu, Y. et al. (2006) Suberoylanilide hydroxamic acid induces Aktmediated phosphorylation of p300, which promotes acetylation and transcriptional activation of RelA/p65. J. Biol. Chem. 281, 31359– 31368 66 Martin, M. et al. (2005) Toll-like receptor-mediated cytokine production is differentially regulated by glycogen synthase kinase 3. Nat. Immunol. 6, 777–784 67 Nie, M. et al. (2005) Differential regulation of chemokine expression by peroxisome proliferator-activated receptor g agonists: interactions with glucocorticoids and b2-agonists. J. Biol. Chem. 280, 2550–2561 68 Ito, K. et al. (2006) Histone deacetylase 2-mediated deacetylation of the glucocorticoid receptor enables NF-kB suppression. J. Exp. Med. 203, 7–13 69 Barnes, P.J. and Karin, M. (1997) Nuclear factor-kB: a pivotal transcription factor in chronic inflammatory diseases. N. Engl. J. Med. 336, 1066–1071 70 Rogatsky, I. et al. (2002) Alternate surfaces of transcriptional coregulator GRIP1 function in different glucocorticoid receptor activation and repression contexts. Proc. Natl. Acad. Sci. U. S. A. 99, 16701–16706 71 Kramer, O.H. et al. (2006) Acetylation of Stat1 modulates NF-kB activity. Genes Dev. 20, 473–485 72 Kim, T. et al. (2005) Downregulation of lipopolysaccharide response in drosophila by negative crosstalk between the AP1 and NF-kB signaling modules. Nat. Immunol. 6, 211–218 73 Sen, R. and Baltimore, D. (1986) Multiple nuclear factors interact with the immunoglobulin enhancer sequences. Cell 46, 705–716 74 Adam, E. et al. (2003) Potentiation of tumor necrosis factorinduced NF-kB activation by deacetylase inhibitors is associated with a delayed cytoplasmic reappearance of IkBa. Mol. Cell. Biol. 23, 6200–6209 75 Hoffmann, A. et al. (2002) The IkB-NF-kB signaling module: temporal control and selective gene activation. Science 298, 1241–1245 76 Karin, M. (2006) Nuclear factor-kB in cancer development and progression. Nature 441, 431–436 77 Pan, L.N. et al. (2007) HDAC inhibitors: a potential new category of anti-tumor agents. Cell Mol. Immunol. 4, 337–343 78 Mayo, M.W. et al. (2003) Ineffectiveness of histone deacetylase inhibitors to induce apoptosis involves the transcriptional activation of NF-kB through the Akt pathway. J. Biol. Chem. 278, 18980–18989 79 Hayashi, R. et al. (2004) Effects of glucocorticoids on gene transcription. Eur. J. Pharmacol. 500, 51–62 80 Edelstein, L.C. et al. (2005) Chromatin modification and the endothelial-specific activation of the E-selectin gene. J. Biol. Chem. 280, 11192–11202 81 Lee, C.W. et al. (2006) Transcriptional regulation of VCAM-1 expression by tumor necrosis factor-a in human tracheal smooth muscle cells: involvement of MAPKs, NF-kB, p300, and histone acetylation. J. Cell. Physiol. 207, 174–186 Review Trends in Biochemical Sciences 82 Thierry, S. et al. (2004) Cell cycle arrest in G2 induces human immunodeficiency virus type 1 transcriptional activation through histone acetylation and recruitment of CBP, NF-kB, and c-Jun to the long terminal repeat promoter. J. Virol. 78, 12198–12206 83 Lusic, M. et al. (2003) Regulation of HIV-1 gene expression by histone acetylation and factor recruitment at the LTR promoter. EMBO J. 22, 6550–6561 Vol.33 No.7 84 Miao, F. et al. (2004) In vivo chromatin remodeling events leading to inflammatory gene transcription under diabetic conditions. J. Biol. Chem. 279, 18091–18097 85 Na, S-Y. et al. (1998) Steroid receptor coactivator-1 Interacts with the p50 subunit and coactivates nuclear factor kB-mediated transactivations. J. Biol. Chem. 273, 10831–10834 Articles of interest in other Cell Press journals Human Alu RNA Is a Modular Transacting Repressor of mRNA Transcription during Heat Shock Peter D. Mariner,Ryan D. Walters, Celso A. Espinoza, Linda F. Drullinger, Stacey D. Wagner, Jennifer F. Kugel, and James A. Goodrich Molecular Cell February 29, 2008 Molecular Dissection of Mammalian RNA Polymerase II Transcriptional Termination Steven West, Nicholas J. Proudfoot, and Michael J. Dye Molecular Cell March 14, 2008 Poised Polymerases: On Your Mark. . .Get Set. . .Go! David Price Molecular Cell April 11, 2008 Molecular Evolution of RNA Polymerase II CTD Rob D. Chapman, Martin Heidemann, Corinna Hintermair and Dirk Eick Trends in Genetics June 2008 Deciphering the (expanding) RNA polymerase II CTD code Sylvain Egloff and Shona Murphy Trends in Genetics June 2008 349