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B-Mediated Gene Transcription through Methylation of Histone H3 at Arginine 17
Gonda Diabetes Center, Beckman Research Institute of City of Hope, Duarte, California 91010
Address all correspondence and requests for reprints to: Dr. Rama Natarajan, Gonda Diabetes Center, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, California 91010. E-mail: RNatarajan{at}coh.org.
| ABSTRACT |
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B (NF-
B) and enhance NF-
B activity in a CBP (p300)-dependent manner. This enhancement in 293T cells was abolished by cotransfection with a specific short hairpin RNA targeted to knockdown CARM1. Chromatin immunoprecipitation demonstrated CARM1 recruitment in vivo to the promoters of NF-
B p65-regulated genes along with CBP and steroid receptor coactivator-1. This was accompanied by an increase in histone H3-R17 methylation as well as H3-K9 and H3-K14 acetylation, and a decrease in H3-citrulline. Immunoprecipitation with anti-p65 antibody revealed that CARM1 physically interacts with NF-
B p65. Furthermore, we demonstrated the physiological significance by observing that similar events occurred when THP-1 monocytic cells were stimulated with TNF-
or with S100b, a ligand for the receptor of advanced glycation end products, both of which are associated with diabetic complications and also known inducers of NF-
B and inflammatory genes in monocytes. These results demonstrate that CARM1 participates in NF-
B-mediated transcription through H3-R17 methylation and support a nonnuclear receptor-associated function for CARM1. They also demonstrate for the first time that CARM1 occupancy, histone H3-R17 methylation, and citrullination are regulated at the promoters of inflammatory genes in monocytes, thereby suggesting a novel role for histone arginine modifications in inflammatory diseases. | INTRODUCTION |
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B (NF-
B) is an inducible transcription factor that plays a pivotal role in cellular responses by regulating the expression of a variety of genes involved in various cellular processes ranging from proliferation, immune responses, inflammation, and cell survival (1, 2, 3). Although NF-
B consists of homo- or heterodimers of different subunits such as p50, p52, p65/RelA, RelB, and c-Rel, it is predominantly a heterodimeric complex of p65/RelA and p50. In most cells, p65/RelA and p50 exist in an inactive form in the cytoplasm bound to an inhibitory protein, I
B-
. Phosphorylation of the inhibitory I
B-
subunit by an I
B kinase complex results in ubiquitination and degradation of I
B-
and translocation of the p50-p65 dimer to the nucleus, where it binds to cognate
B enhancer elements on gene promoters and modulates their expression. A major negative feedback mechanism to down-regulate the activated NF-
B is the NF-
B-dependent expression of the I
B-
gene. Newly synthesized I
B-
shuttles between the cytoplasm and the nucleus and sequesters NF-
B from the promoters, thus facilitating the return of the NF-
B-I
B
complex to the cytoplasm and terminating the NF-
B transcriptional response (4, 5).
NF-
B-dependent gene expression involves various coactivators that function by facilitating, modifying, recruiting or bridging the sequence-specific activators to the basal transcriptional machinery and altering chromatin structure. The p65 component of NF-
B can bind to the coactivator, cAMP response element binding protein-binding protein (CBP), and its structural homolog p300 (6, 7, 8). Phosphorylation of p65 by protein kinase A has been shown to stimulate NF-
B-dependent gene expression by enhancing p65 association with CBP (8, 9). CBP-associated protein p/CAF is also a component of the NF-
B coactivator complex (10). Additionally, NF-
B-dependent gene expression involves a second class of transcriptional coactivators, namely steroid receptor coactivator-1 (SRC-1) and nuclear receptor coactivator-1 that interact with p50 and potentiate NF-
B-mediated transactivation (10, 11).
NF-
B and nuclear receptors exhibit certain key similarities with respect to their specific requirements for p160 coactivators and their acetyltransferase functions (10). Both NF-
B activity and nuclear receptor-dependent gene expression require a coactivator complex with the p160 family members. These coactivators contain the consensus LXXLL motif that is important for the interaction of the coactivators with both nuclear receptors and CBP (12, 13, 14). This suggests that LXXLL-mediated interactions between the p160 family members and CBP underlie the assembly of both the NF-
B and the nuclear receptor coactivator complexes. Furthermore, the histone acetyl transferase (HAT) activity of p/CAF was implicated in the activation of NF-
B-dependent gene expression and nuclear receptor activation (15), suggesting that both have the same selectivity in the type of HAT activity required for their function. However, it is not clear whether NF-
B and nuclear receptors use the same HAT-containing complexes. Furthermore, the extent of similarity between these two complexes is also unclear.
Coactivator-associated arginine methyltransferase-1 (CARM1) was originally isolated by a yeast two-hybrid screen while evaluating proteins that interact with the p160 family member glucocorticoid receptor interacting protein 1 (16). It enhances nuclear receptor function in a p160-dependent manner (17), although its activity reached a maximum only in the presence of the p160 and p300/CBP coactivators (17, 18, 19). The catalytic activity of CARM1 methyltransferase, as assessed by methylation of arginine (R) 17 of histone H3 (H3-R17), is required for nuclear receptor transactivation and this has been associated with gene activation (20, 21). The fact that CARM1 and CBP/p300 could cooperate to increase the transcriptional activity of the estrogen receptor (16, 17, 18, 19) indicated a potential cross talk between lysine (K) acetylation and H3-R17 methylation (22). In vitro, the CARM1 methylation activity was most effective on preacetylated histone, suggesting that CARM1 acts downstream of the histone acetylation (19, 22).
CBP/p300 and p160-dependent CARM1 coactivator functions have been mainly investigated among nuclear receptors. However, because CBP/p300 and p160 are also coactivators of NF-
B-dependent transcription (10), it can be speculated that CARM1 could be involved in NF-
B mediated transcription. Very recently, Covic et al. (23) reported that the expression of a subset of NF-
B-dependent genes in response to TNF-
or lipopolysaccharide stimulation is impaired in CARM1 knockout mouse embryo fibroblasts. By comparing CARM1 knockout cells with wild-type cells, they concluded that CARM1 can function as a promoter-specific regulator of NF-
B. In our current study, by using expressed short hairpin RNAs (shRNAs) targeted to knockdown CARM1, we provide novel evidence that CARM1 is required for NF-
B-mediated gene expression and that it enhances these NF-
B effects in a CBP (p300)-dependent manner. Using chromatin immunoprecipitation (ChIP) assays, we showed that, in response to TNF-
stimulation, there is increased recruitment of CARM1 to the promoters of NF-
B-dependent genes along with increased H3-R17 methylation and simultaneously decreased H3-citrulline. These were associated with other events related to the activation of NF-
B-mediated gene transcription such as recruitment of p65, CBP, SRC-1, and histone H3-K9/14 acetylation at these promoters. We further demonstrated for the first time the physiological relevance and implication of this histone arginine modification by showing that this H3-R17 methylation and citrulline connection occurs during TNF-
stimulation of human THP-1 monocytic cells. Furthermore, CARM1 occupancy at the TNF-
promoter was also increased in THP-1 cells by S100B, a ligand for the receptor for advanced glycation end products (RAGE), and a known inducer of NF-
B-dependent inflammatory genes in monocytes.
| RESULTS |
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promoter (295TNF-
Luc, which includes the NF-
B response element), along with CBP, SRC-1, and CARM1 expression plasmids and various amounts of the p65 expression vector. Figure 1A
promoter in the presence of CBP and SRC-1 especially at lower concentrations of p65. The optimal p65 vector input range for maximal CARM1 coactivator effects in our system was between 10 and 20 ng. We then tested potential synergy among various coactivators by cotransfection of 293T cells with various combinations of p65, CBP (p300), SRC-1, and CARM1 expression vectors (Fig. 1B
B-mediated transcription in the presence of CBP (p300) alone (third set of bars), although the maximal luciferase activity was observed when p65, CBP (p300), SRC-1, and CARM1 were all cotransfected together (fourth bar set). Interestingly, it has been shown that, in nuclear receptor-mediated transcription, CARM1 acts as coactivator in which synergistic effects between CARM1 and p300 depends on p160 (17). The current observation reveals that CBP(p300) is the primary coactivator in NF-
B-mediated transcription. This is in contrast to nuclear receptor-mediated transcription, which uses p160 as the primary coactivator (17).
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B-mediated gene expression.
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B-mediated gene transcription in response to TNF-
stimulation. This was performed by testing the effects of CARM1 shRNA in luciferase assays as illustrated in Fig. 2B
-stimulated luciferase activity not only when p65, p300, SRC-1, and CARM1 were added together (Fig. 2B
B-dependent transcription need additional CBP and SRC-1 due to limited endogenous cellular levels of these coactivators. On the other hand, the knockdown of CARM1 directly affects p65-mediated transcription, and this is not dependent on added exogenous CBP and SRC-1. Both these data support an essential role for CARM1 in p65 mediated gene transcription and also provide additional evidence that CARM1 participates in TNF-
-stimulated NF-
B-dependent transcription.
To evaluate the effect of CARM1 in p65-mediated gene expression, 293T cells were transfected with Scrambled, CARM1 shRNA, and CARM1 expression vectors as indicated in Fig. 3A
, and treated with or without TNF-
. Total RNA was then prepared for relative RT-PCR analyses of several known NF-
B-regulated genes. CARM1 knockdown by the shRNA led to clearly reduced CARM1 levels, although it was not a complete inhibition. Interestingly, when CARM1 levels were reduced by its shRNA, there was a marked reduction in TNF-
-induced expression of IL-8, and a partial reduction of TNF-
and interferon-inducible protein 10 (IP-10). We also confirmed these results by performing quantitative real-time PCR (Fig. 3B
), which shows that TNF-
-induced expression of IL-8, IP-10, and TNF-
were all significantly reduced by the CARM-1 shRNA (P < 0.01) but not by control Scr vector. On the other hand, overexpression of CARM1, however, did not seem to increase the expression of these genes. Among the genes shown in Fig. 3A
, the expressions of TP53 and IL-6 were not affected by CARM1 or CARM1 shRNA. This was somewhat surprising because evidence shows that CARM1 can strongly enhance TP53 transcription in vitro (26). Overall, these results demonstrate that a reduction in the levels of endogenous CARM1 can impair the responses to TNF-
on a subset of inflammatory genes that are known to be regulated by NF-
B.
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and IL-8 promoter regions around the NF-
B binding sites. Figure 4
and IL-8 in 293T cells is associated with several key in vivo nuclear chromatin events including the recruitment of p65, CBP, and SRC-1 to their promoters, and acetylation of histone H3 at K9 and K14. When the 293T cells were cotransfected with p65, CBP, and CARM1 (lanes 2, 5), or with p65, CBP, SRC-1, and CARM1 (lanes 3 and 6), the factor occupancy at these promoters and histone modifications representing transcriptional activation events were all clearly augmented compared with those with only p65 (lanes 1 and 4). Cotransfection of p65 along with CBP, SRC-1, and CARM1 showed the maximum effects including that of CARM1 accumulation at the TNF-
and IL-8 promoters. Importantly, at the same time, the methylation of histone H3 at R17 was also increased simultaneously as assessed by the ChIP assays. Combined with the synergistic coactivator role of CARM1 in p65-mediated TNF-
promoter transcription (Fig. 1B
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in 293T cells and performed ChIPs with the abovementioned antibodies as well as an antibody that recognizes H3-citrulline followed by ChIP-PCR analyses with primers amplifying the TNF-
, IL-8, and IP-10 promoter regions containing NF-
B binding sites. These three genes were selected due to their reduction by CARM1 shRNA in response to TNF-
stimulation (Fig. 3
stimulation have very similar patterns. TNF-
stimulation clearly increased the recruitment of p65, CBP, SRC-1, and CARM1 at all three promoters, and these events also coincided with marked increases in lysine (K9 and K14) acetylation and arginine 17 methylation of HH3. Overall, histone H3 K9/14 acetylation and R17 methylation are increased in frame with CBP, SRC-1, and CARM1 recruitment, respectively. Although H3-R17 methylation might appear to slightly precede CARM1 recruitment at the IL-8 promoter, it could be due to the fact that some CARM1 prebound at the promoter may induce some methylation. Furthermore, the antibody that we used (anti-dimethyl H3-R17, Upstate 07-214) can also recognize mono-methyl H3-R17, albeit to a much lower degree, and H3-R17 may be mono- or dimethylated to some extent even before TNF-
stimulation. The lowest panel shows amplification of control input DNA.
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B-mediated gene expression.
CARM1 Interacts with p65 during Transcription
CARM1 was originally isolated as a protein interacting with p160 (16), and evidence shows that it also directly interacts with CBP/p300 (17, 18, 19). The results in Figs. 1
and 2
suggest that there could be an interaction between CARM1 and p65 through either CBP or SRC-1 or both. To evaluate this further, we carried out immunoprecipitation with an anti-p65 antibody in 293T cells in which we overexpressed relevant expression vectors and then examined by Western blotting whether the p65 immunoprecipitates contain CARM1. Figure 6A
shows that CARM1 is not detectable in the p65 immunoprecipitates in the basal state (lane 3). However, when the 293T cells were cotransfected with p65 along with CARM1, CARM1 was present in the p65 immunoprecipitates (lane 4), which provides evidence that CARM1 physically associates with p65 during transcription. Lane 5 shows that CARM1 is also present in the p65 immunoprecipitates in cells that were also cotransfected with CBP and SRC-1. The positive control (input) is seen in the first lane (lane 1), whereas negative control and control for specificity with IgG alone is seen in lane 2.
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Histone H3-R17 Methylation Plays a Role in NF-
B-Regulated Inflammatory Gene Expression in Human Monocytes
NF-
B-mediated gene expression in human monocytes has been extensively investigated due to the important physiological and pathological roles of inflammatory genes in these cells and relevance to several human diseases (29, 30). Our experiments in Figs. 16![]()
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clearly demonstrate that CARM1 and arginine modifications (methylation and citrullination) play important roles in inflammatory gene expression and regulation in 293T cells that can be transfected with high efficiency. To demonstrate the physiological relevance, we investigated these events in THP-1 monocytes. We recently demonstrated the role of histone lysine acetylation in NF-
B-dependent inflammatory gene expression in response to TNF-
and diabetic conditions in these cells (31). We now investigated for the first time the potential involvement of histone R17 methylation in NF-
B-dependent effects in these cells. We performed ChIP analysis to examine events at TNF-
and IL-8 promoters in human monocytic THP-1 cells. Figure 7A
shows that, after TNF-
treatment, CARM1 is recruited and H3-R17 methylation is increased in a time-dependent fashion at the TNF-
and IL-8 promoters in THP-1 cells treated with TNF-
. In parallel, there was a concomitant decrease in histone H3 arginine citrullination at these promoter regions. These results are similar to those obtained with the 293T cell line (Fig. 5
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expression in monocytes, including THP-1 cells (32, 33), we further evaluated the relevance of our findings in THP-1 cells treated with S100b. S100b, a specific ligand for RAGE and a member of a multigenic family of Ca2+-regulated proteins of the EF-hand type, is associated with inflammatory properties (34, 35). We used S100b because it can mimic diabetic conditions and also induce a variety of proinflammatory events through the RAGE receptor such as the activation of NF-
B and its target genes including vascular cell adhesion molecule-1, TNF-
, IL-6, and cyclooxygenase-2 (32, 33, 34, 35, 36). The ChIP assays in Fig. 7B
promoter similar to those occurring when THP-1 cells or 293T cells were stimulated with TNF-
as shown in Figs. 4| DISCUSSION |
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B-mediated gene regulation has been extensively studied, several new discoveries (37, 38) have revealed that NF-
B-mediated transactivation is far more complicated than anticipated. Beyond the fact that new coactivators and mediators have been implicated, the role of factors that covalently modify tails of core histone in chromatin is now becoming evident. The recent rapid advances in deciphering the histone code and functional roles of histone modifications have now changed the classic concept of chromatin structure from a static carrier to an active platform that mediates dynamic changes in gene function and expression. In particular, histone methylation events at key lysine residues by various specific methylases, and at arginine by protein arginine methyltransferases and CARM1 have elicited enormous interest recently due to increasing evidence that they provide an additional layer in the control of chromatin remodeling and gene expression (39, 40, 41, 42, 43).
In the current study, we have shown that CARM1 functions as a coactivator in NF-
B-mediated gene transcriptional activity in a p300 (CBP)-dependent manner instead of the p160-dependent manner reported in nuclear receptor-mediated transcription. The combination of CBP (p300), SRC-1, and CARM1 showed the highest activity in the luciferase assays. The specific involvement of CARM1 was confirmed by demonstrating that shRNA-mediated knockdown of CARM1 could down-regulate NF-
B transcriptional activity. Notably, we used ChIP assays to demonstrate that CARM1 was recruited to the TNF-
and IL-8 promoters along with p65, CBP, and SRC-1, and these were associated with increased H3-R17 methylation and H3K9 and H3K14 acetylation as well as decreased H3-citrullination. We performed coimmunoprecipitation studies to confirm that p65 directly associates with CARM1 and also showed that the p65 coimmunoprecipitates were associated with CARM1 histone methylation activity. Finally, we extended our study to show the physiological relevance in human monocytic THP-1 cells by demonstrating that TNF-
stimulation also increased the recruitment of CARM1 and H3-R17 methylation while decreasing H3-citrullination around the TNF-
and IL-8 promoters in a similar fashion as in 293T cells. We also showed that similar nuclear chromatin events were induced by treatment of THP-1 cell with S100b, an inflammatory diabetogenic stimulus that binds to the RAGE receptor, suggesting potential relevance to the actions of AGEs and the pathology of diabetes and its complications. Effects of CARM1 shRNA on inflammatory genes in THP-1 cells could not be demonstrated clearly due the low efficiency of transfection of THP-1 cells. Overall, our results demonstrate for the first time that CARM1 recruitment, histone H3-R17 methylation, and citrullination are regulated by inflammatory stimuli in monocytes and could be part of a transcriptional network mediating inflammatory gene expression. Because NF-
B-regulated genes are key modulators of immune, inflammatory, and acute phase responses and are also implicated in the control of cell proliferation and apoptosis (44, 45), our studies suggest that CARM1 actions could confer an additional level of regulation in these important cellular functions, and furthermore, changes in histone H3-R17 modification status may play a role in human inflammatory diseases such as diabetes.
A basic question that arises is what is the role of arginine methylation in this context? One possibility is that CARM1-mediated arginine methylation makes the histone a better substrate for recognition and modification by other cofactors. Another possibility is that the arginine-methylated histones can help in the recruitment of other transcriptional coactivators or antagonize the association of corepressors. Previously, it has been shown that acetylation of histone H3-K18 can augment methylation of H3-R17 in vitro, thus indicating that acetylated H3 is a better substrate for CARM1 (22). The mechanistic implication is that the HAT coactivator CBP (p300) may bind to the promoter first, acetylate histone H3, and then enhance the recruitment of CARM1, which in turn methylates H3-R17. However, it is quite possible that the methylation of H3-R17 can also accelerate specific histone acetylation. Such stepwise histone modifications and cooperative events implicated by the histone code are not yet completely understood and could be essential steps in the initiation of transcription.
Although it is well known that CARM1 functions as a coactivator in nuclear receptor-mediated transcription, recent reports provide evidence that CARM1 can also function as a secondary coactivator in a nonnuclear receptor system. One example is a recent study showing that CARM1 is necessary for muscle differentiation by acting as a secondary coactivator for monocyte enhancer factor-2C-mediated transcription in a SRC-2/glucocorticoid receptor interacting protein 1-dependent manner (46). ChIP assays demonstrated the in vivo recruitment of CARM1 to the endogenous muscle creatine kinase promoter in a differentiation-dependent manner (46). Another example is the very recent study by An et al. which provides compelling evidence that CARM1 and protein arginine methyltransferase 1, another arginine methyltransferase, act as coactivators for p53-mediated transcriptional activation via direct interactions with p53 and CBP (26, 47). Covic et al. (23) and, now, our current study show that CARM1 plays a novel coactivator role in NF-
B-mediated gene expression. In all of these transcription systems, CBP (p300) or SRC-1 plays primary coactivator roles and CARM1 actions occur in a CBP (p300)- or p160-dependent manner. This strongly links CARM1 to CBP (p300)- and p160-mediated gene transcription, and provides clear evidence that CARM1 participates in these transactivation events. Furthermore, apart from histones, evidence shows that CARM1 can also methylate arginines on CBP and p300 coactivators and thereby modulate coactivator transcriptional activity (48, 49). Poly(A) binding protein 1 was identified as another nonhistone protein target of CARM1 (50). A methylation-mediator complex was isolated containing at least eight components of human SWI/SNF complex, and CARM1, which revealed the link between chromatin remodeling and histone arginine methylation (51). In addition, CARM1 knockout embryos are small in size and die during late embryonic development or immediately after birth (52). Taken together, these data indicate that CARM1 has multiple and potentially critical roles in various cellular processes.
Additionally, two very recent papers reveal that PADI4 can act as a histone demethylase and regulate histone arginine methylation levels by converting methyl-arginine to citrulline and releasing methylamine (27, 28). These data have created a new dimension to our understanding of histone arginine methylation. Because evidence indicates that CARM1 has several critical functions, the regulation of arginine demethylation at core histone tails by PADI4 actions may provide a novel cellular mechanism for regulating CARM1 target genes as well as chromatin status. This is supported by data showing that core histone citrullination can block the transcription initiation of pS2 gene (27). It should also be pointed out that PADI4 has recently been identified as a gene associated with susceptibility to rheumatoid arthritis (53), an inflammatory disease. Hence our new data showing the effects of TNF-
and S100b on H3R-citrulline at inflammatory gene promoters may provide additional clues regarding the disease relevance of PADI4 and provide novel new links between CARM1, NF-
B, PADI4, and inflammation, especially in diseases such as diabetes. Additional work is needed to confirm this connection.
Similar to histone lysine methylation, the interest in histone arginine methylation is rapidly increasing (41, 42, 43). Based on current knowledge, the histone modification status of H3-R17 in cells can exist in at least three modes: arginine, methylated arginine, and citrullinated arginine. A mechanism has been proposed to illustrate conversions between these states (27). This is further complicated by the fact that arginine methylation can have mono- and di- levels and that dimethylation of arginine in vitro results in both symmetric and asymmetric NG,NG-dimethylarginine (54). The biological meaning of the three modes or the "H3-R17 code" is slowly emerging but needs more investigation. We have just begun to understand that H3-R17 methylation is associated with gene activation and that H3 arginine citrullination might be associated with repression of nuclear receptor and NF-
B-regulated genes. The well-known connections of nuclear receptors and NF-
B to several human endocrine and inflammatory diseases suggest that the methylation status of H3-R17 could be an important signal that reflects the transcriptional status of key genes or even cellular states. This could provide new information on the connections between the epigenetic characteristics of arginine modifications and human diseases.
| MATERIALS AND METHODS |
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promoter-luciferase construct (295-TNF-
Luc) was from Dr. J. S. Economou (University of California, Los Angeles, CA). p65 expression vector (HA tagged) was from Dr. E. Zandi (University of Southern California, Los Angeles, CA). CBP/p300 and SRC-1 expression vectors were from Dr. B. Forman (Beckman Research Institute, Duarte, CA). CARM1 expression construct was from Dr. M. Stallcup (University of Southern California, Los Angeles, CA). S100b was obtained from Calbiochem (La Jolla, CA). THP-1 cells were from American Type Culture Collection (Manassas, VA).
Transfections and Luciferase Assays
HEK 293T cells were grown in DMEM (Irvine Scientific, Santa Ana, CA) supplemented with 10% fetal calf serum (FCS; Irvine Scientific), 1 mM L-glutamine, 100 U/ml penicillin/ streptomycin, and 25 mM glucose. A total of 2 x 105 cells was placed in six-well culture dishes in RPMI 1640 medium and transfected with combinations of the TNF
Luc construct, p65 and CBP or p300, SRC-1, and CARM1 expression vectors as needed, using Effectene transfection reagent (QIAGEN, Valencia, CA) in 2% FCS-containing medium overnight. Samples were balanced for total DNA content with control plasmid. Cells were then washed once and allowed to recover in DMEM containing 10% FCS for 24 h. The cells were then lysed and luciferase assays performed according to the Promega (Madison, WI) Luciferase Assay System protocol. All assays were performed in triplicate in each experiment.
RT-PCR Assays and Real-Time Quantitative PCRs
293T cells were transfected with CARM1 shRNA or scramble control and then treated with or without 20 mM TNF-
for 6 h. Total RNA was isolated by RNA-STAT-60 method (Tel-Test, Friendswood, TX). cDNA was generated with 0.8 µg of RNA using random hexamers and Moloney murine leukemia virus reverse transcriptase using a Gene Amp RNA PCR kit (Applied Biosystems, Foster City, CA). An aliquot was used in multiplex relative RT-PCRs with cytokine-specific primers paired with Quantum RNA 18S internal standards (Ambion, Austin, TX) as described previously (31). PCRs were carried out at 95 C for 2 min followed by 30 cycles at 95 C for 30 sec, 58 C for 30 sec, and 72 C for 45 sec, and a final extension at 72 C for 7 min. PCR primer sequences are shown in Table 1
. Real-time quantitative PCR (50 C for 2 min, 95 C for 10 min, followed by 40 cycles of 95 C for 15 sec, 58 C for 1 min) were performed with an ABI 7300 real-time PCR thermal cycler (Applied Biosystems). SYBR Green PCR Master Mix kit was from Applied Biosystems. All reactions were performed in a 25-µl reaction volume in triplicate. Standard curves were generated using glyceraldehyde-3-phosphate dehydrogenase. Dissociation curves were run to detect nonspecific amplification and we confirmed that single products were amplified in each reaction. Quantitations of the expression of each test gene and 18S RNA were then determined from the standard curve using the Applied Biosystems software. Relative amounts of mRNA of test genes were normalized to 18S mRNA internal control. Primers for real-time PCR are provided in Table 1
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Construction of CARM1 shRNA and Cell Transfections
The shRNA against human CARM1 was constructed according to a recently described method for making shRNAs (24, 25), which uses a rapid PCR method to initially identify the best siRNA accessibility sites on the target gene. The CARM1-specific siRNA sequence under the control of the U6 promoter was prepared by PCR amplification using pTZ/U6+1 containing U6 promoter as a template. The forward primer (5'-CGCGGATCCAAGGTCGGGCAGG-3') was located upstream of the U6 promoter and the reverse primer contained the 21-bp sense sequence (5'-GTCTTTAAGTGCTCAGTGTCC-3'), 9-bp hairpin (5'-TTTGTGTAG-3'), and 21-bp antisense sequence. The PCR products included the U6 promoter sequence, the sense and the antisense sequence with a 9-nucleotide loop in between them, a terminator sequence, and a stuffer tag sequence at the 3' end of the product. We chose one of the PCR products containing the U6+shRNA sequence for the knockdown experiments based on sequence-specific gene silencing with greatest efficiency and this was cloned into the pCR3.1 vector (Invitrogen, San Diego, CA) to obtain the CARM1 shRNA expression vector. As an important control, the sequence 5'-GGATATATCCCGAACTAGACA-3' was used to make a control scrambled nonspecific shRNA. For Western blot analysis of CARM1 levels after shRNA treatments, 293T cells were seeded into 12-well plates at 35 x 105 per well 1 d before transfection. Transfections were carried out using Lipofectamine 2000 reagent according to manufacturers instructions (Invitrogen) and our reported methods (31, 55). Briefly, 48 h after transfection, the cells were washed twice with 1x PBS buffer [137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, 1.4 mM KH2PO4 (pH 7.3)], lysed with 1% sodium dodecyl sulfate (SDS) in 20 mM Tris-HCl buffer (pH 6.8), and about 25 µg of protein was fractionated on a 10% SDS-PAGE gel (56). Immunoblotting was performed with a CARM1-specific antibody (1:2000 dilution) according to our reported procedures (57).
Coimmunoprecipitations
A total of 2 x 106 293T cells were grown in DMEM with 25 mM high glucose and transfected with various combinations of p65, CARM1, CBP, and SRC-1 expression plasmids as described above in Transfections and Luciferase Assays. After 24 h, extracts were prepared by lysing the cells with radioimmunoprecipitation assay buffer [50 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1% Nonidet P-40 (NP-40), 0.5% sodium deoxycholate, 0.1% SDS] and centrifuging for 10 min at 12,000 rpm. The supernatants were incubated with 2 µg of anti-p65 antibody and 30 µl of a 50% suspension of protein A-agarose (Upstate Biotechnology) overnight at 4 C, followed by washing four times with PBS containing 150 mM NaCl. Immunoblotting was performed with an antibody against CARM1. Control for specificity was done with IgG.
ChIP
ChIPs were performed according to Farnham and coworker (58) with some modifications (31). Briefly, 23 x 106 cells were cross-linked with 1% formaldehyde for 3060 min, washed twice with cold PBS, resuspended in lysis buffer [1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.1), 1x protease inhibitor cocktail (Roche Molecular Biochemicals, Basel, Switzerland)], and sonicated one to three times for 30 sec each at 40% maximum setting (Branson Sonifier; model 250) followed by centrifugation for 10 min. One-tenth of total lysate was used for total genomic DNA as "Input DNA" control. Supernatants were collected and diluted in buffer [1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8.1), and 1x protease inhibitor mixture] followed by immunoclearing with 1 µg of sheared salmon sperm DNA, 10 µl of rabbit IgG, and 20 µl of protein A-agarose (Upstate Biotechnology) for 1 h at 4 C. Immunoprecipitation was performed for 15 h at 4 C with 25 µg each of specific relevant antibodies. Precipitates were washed sequentially for 10 min each in TSE I buffer [0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8.1)], TSE II buffer (TSE I with 500 mM NaCl), and TSE III [0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)]. Precipitates were then washed twice with TE buffer [10 mM Tris-HCl (pH 7.5), 1 mM EDTA] and extracted twice with 1% SDS containing 0.1 M NaHCO3. Eluates were pooled and heated at 65 C for at least 6 h to reverse the formaldehyde cross-linking. DNA fragments were purified with QIAGEN Qiaquick spin kits. One microliter of a 40-µl DNA extract was used for PCR. ChIP PCR primers corresponding to sequences within the promoter regions of various genes are listed in Table 1
.
In Vitro Histone Methylation Activity Assay (48)
One microgram of histone H3 (Upstate Biotechnology) was incubated with p65 immunoprecipitates and [3H-Me]S-adenosyl methionine (New England Nuclear, Boston, MA; 80 Ci·mmol1) in buffer containing 50 mM Tris (pH 8.0), 150 mM NaCl, 5 mM EDTA, and 0.5% NP-40 (48) at 30 C for 2 h. Antihistone H3 and protein A agarose beads were added and incubated for 1 h. The samples were spun for 1 min at 2000 rpm and washed four times with the same buffer and then resuspended in 50 µl of water. Five microliters was then taken for liquid scintillation counting.
Data Analyses
Results are expressed as means ± SEM of multiple experiments. Students t tests were used to compare two groups, or ANOVA with Dunnets posttests for multiple groups using Prism software (GraphPad, San Diego, CA). Statistical significance was detected at the 0.05 level.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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F.M., S.L.L., V.C., L.L., and R.N. have nothing to declare.
First Published Online February 23, 2006
Abbreviations: AGE, Advanced glycation end product; CARM1, coactivator-associated arginine methyltransferase-1; ChIP, chromatin immunoprecipitation; CBP, cAMP response element binding protein-binding protein; FCS, fetal calf serum; HAT, histone acetyl transferase; IP-10, interferon-inducible protein 10; NF-
B, nuclear factor-
B; NP-40, Nonidet P-40; PADI4, peptidyl arginine deiminase; RAGE, receptor for advanced glycation end products; SDS, sodium dodecyl sulfate; shRNA, short hairpin RNA; siRNA, small interfering RNA; SRC-1, steroid receptor coactivator-1.
Received for publication September 7, 2005. Accepted for publication February 8, 2006.
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