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Molecular and Cellular Biology, November 2006, p. 7846-7857, Vol. 26, No. 21
0270-7306/06/$08.00+0 doi:10.1128/MCB.00568-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
Received 31 March 2006/ Returned for modification 17 May 2006/ Accepted 14 August 2006
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Considerable experimental data have established that agonist-bound steroid receptors directly recruit the SRC/p160 family coactivators, which subsequently recruit secondary coactivators, including the E1A binding protein p300 and its homolog, the cyclic AMP-response element binding protein (CREB)-binding protein (CBP), as well as the coactivator-associated arginine methyltransferase 1 (CARM1) (5). Many of these coactivators contain intrinsic enzymatic activities. For instance, p300/CBP contain potent histone acetyltransferase (HAT) activity (28), whereas SRC-1 and SRC-3/ACTR exhibit relatively weak HAT activity (6, 31). CARM1 and PRMT1 (5, 38) have histone methyltransferase activity, and SWI/SNF complexes possess ATP-dependent nucleosome remodeling activity (3, 17). It has been generally accepted that following recruitment to the promoter, these coactivators can modify local chromatin structure and increase DNA accessibility to the basal transcription machinery (26).
Recent studies indicated that coactivator recruitment to estrogen receptor-bound promoters is a cyclical and ordered process involving multiple rounds of coactivator assembly and disassembly (27, 30). SRC-3 coactivator phosphorylation has been shown to affect coactivator complex assembly (40). However, the mechanisms by which coactivator complex disassembly is regulated have not been well established. In this study, we provide in vitro and in vivo evidence that SRC-3/AIB1 is methylated by CARM1 during estrogen signaling and that this modification promotes dissociation of the SRC-3/CARM1 coactivator complex, thereby attenuating the transcriptional response and completing a dynamic equilibrium of receptor-mediated coactivator assembly and disassembly at the promoter.
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Me [
1171-1238]) were created by use of the double-PCR
strategy. Sequencing confirmed all mutations. pSG5-HA-CARM1 was kindly
provided by Michael R. Stallcup (University of Southern California).
The ERE-Luc reporter has been previously described
(44).
Recombinant proteins and siRNA.
Recombinant ER
and PR-A
proteins were generously provided by Dean Edwards (Baylor College of
Medicine). Recombinant SRC-1 protein was a gift from Steven Nordeen
(University of Colorado). SRC-2 and SRC-3 recombinant proteins were
generated by the Bac-to-Bac baculoviral system (Invitrogen). SRC-2 and
SRC-3 were doubly tagged, with an N-terminal His tag and a C-terminal
Flag tag, to ensure production of full-length SRC proteins. After 3
rounds of amplification, the baculoviruses were used to infect
log-phase Sf9 cells maintained in Grace's medium containing 10% fetal
calf serum (FCS) for 48 h. SRC-2 and SRC-3 proteins were
purified with a Ni-nitrilotriacetic acid column (QIAGEN) followed by
purification using anti-Flag-M2 affinity gel (Sigma). Wild-type CARM1
protein was purchased from Upstate, and CARM1 (E267Q) protein with an
N-terminal Flag tag was expressed by using the Bac-to-Bac system and
purified as described above. All GST fusion proteins were expressed in
BL21 cells (Stratagene) and purified using glutathione Sepharose
according to the manufacturer's protocol (Amersham Bioscience). p300
baculovirus was obtained from W. Lee Kraus (Cornell University) and
purified with a Ni-nitrilotriacetic acid column (QIAGEN). HeLa core
histones were prepared as previously described
(38). Small interfering
RNA (siRNA) of CARM1 used in the knockdown experiments was SMART pool
siRNA from Dharmacon. CARM1 siRNA was used at 20 nM in each
sample.
Cell culture, transfection, and luciferase assay. CARM1 wild-type and knockout mouse embryonic fibroblasts (MEFs) were kindly provided by Mark Bedford (M.D. Anderson Cancer Center) (43). MCF7, CV-1, SRC-3/ MEFs, and HEK293T cells were maintained in Dulbecco's modified Eagle medium supplemented with 10% FCS. For estradiol-induced experiments, cells were maintained in phenol red-free medium containing 5% charcoal-dextran-stripped FCS until hormone addition. Fugene 6 transfection reagent (Roche) was used for all of the transient transfections. Transfected cells were treated with 10 nM estradiol 24 h after transfection and harvested after another 24-h incubation. Luciferase activity was determined with the Promega luciferase assay kit according to the manufacturer's protocols. Three independent experiments were done, and the most representative results were shown.
Methylation assays. Methylation assays were performed as previously described (11). In brief, 0.5 µg recombinant SRC family proteins or other proteins (see Fig. 1) were incubated with recombinant CARM1 (0.2 µg for each reaction) in a reaction mixture containing 20 mM Tris-HCl (pH 8.0), 4 mM EDTA, 1 mM phenylmethylsulfonyl fluoride, 0.5 mM dithiothreitol, and 1 µl [3H]AdoMet (13.3 Ci/mM; Perkin Elmer) for 1 h at 30°C. Reactions were stopped by the addition of 6x sodium dodecyl sulfate (SDS) loading buffer, and proteins were separated in a 4 to 15% SDS-polyacrylamide gel electrophoresis (PAGE) gel. Following staining with Coomassie blue, gels were treated with autoradiography Amplify reagent (Amersham Biosciences) for 20 min, dried, and exposed to X-ray films. For peptide competition assay, different concentrations of unmodified or methylated peptide were added to reactions containing Flag-tagged SRC-3 (see Fig. 5).
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FIG. 1. SRC
family proteins are methylated by CARM1 in vitro. (A)
Recombinant p300, SRC-1, SRC-3, ER , and PR-A were incubated
with recombinant CARM1 in the presence of [3H]AdoMet for
1 h at 30°C. Products were analyzed by Coomassie blue
staining and fluorography. Arrowheads indicate the positions of
full-length proteins. (B) SRC-2 is methylated by CARM1 in
vitro. Recombinant SRC-2 and SRC-3 (0.5 µg) were methylated by
recombinant CARM1. (C) SRC-3 is a preferred substrate for
CARM1 in vitro. Four micrograms of HeLa core histone protein was
incubated in the absence () or presence (+) of 0.2
µg of SRC-3 protein in the methylation assay. (D)
CARM1 is responsible for methylation of SRC-3 in vitro. SRC-3 protein
(0.5 µg) was incubated with either wild-type CARM1 or an
inactive mutant (E267Q). The positions of protein size standards (in
kilodaltons) are indicated beside each
panel.
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FIG. 5. Mutation
of SRC-3 methylation sites increases its coactivator function in
cell-free transcription assays. (A) Analysis of in
vitro-assembled chromatin by partial digestion with MNase. Twenty-five
microliters of assembled chromatin was digested with 3 U, 1 U, and 0.3
U of MNase (lanes from left to right, respectively). Ladders of
nucleosomal bands were visualized by ethidium bromide staining in a 1%
agarose gel. (B) Recombinant proteins used in the in vitro
transcription assay. Purity was determined by Coomassie blue staining.
(C) The schematic in the upper right corner shows the plasmid
pERE-E4 that was assembled into chromatin and transcribed. Triangles
indicate 20 or 60 ng of SRC-3 protein and 50 or 150 ng of CARM1 protein
employed in the different transcription reactions for which results are
shown in the bottom panel. The relative amount of E4 transcript was
determined by real-time RT-PCR. Error bars shown throughout Fig.
5 represent standard
deviations. (D) A similar experiment was performed as for
panel C, except that 20 ng of SRC-3 protein and 50 ng of wild-type or
mutated CARM1 was added to the mixture individually or sequentially.
+, present; ,
absent.
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(Santa
Cruz Biotechnology).
Chromatin assembly and analysis.
Chromatin was
assembled using the pERE-E4 plasmid DNA template (a gift from W. Lee
Kraus, Cornell University), HeLa core histones, an ATP-regenerating
system, and S190 extract derived form postblastoderm Drosophila
melanogaster embryos (0 to 6 h), as
previously described
(25). Untreated rabbit
reticulocyte lysate (Promega) was added into the assembly reaction
mixture to potentiate the transcription activity of ER
(33). Assembly reaction
mixtures (100 µl) were incubated at 27°C for
4 h before further experiments, such as chromatin structure
analysis or in vitro transcription, were performed. The quality of
assembled chromatin was analyzed by partial digestion with micrococcal
nuclease (MNase). After MNase digestion for 10 min at room temperature,
assembled chromatin was treated with RNase A and proteinase K, followed
by phenol-chloroform extraction. Precipitated DNA was separated by
agarose gel electrophoresis, and ladders of nucleosomal bands were
visualized by ethidium bromide
staining.
In vitro transcription.
Each
transcription reaction mixture consisted of 10 µl of assembled
chromatin, 3 ng of ER
, 100 nM of estradiol, 20 to 60 ng of
SRC-3 proteins, and 50 to 150 ng of CARM1, if applicable. After
incubation with coactivators for 5 min at room temperature, HeLa
nuclear extract (50 µg per reaction) was added, followed by a
20-min incubation to form transcriptional initiation complexes.
Transcription was initiated by the addition of recombinant nucleoside
triphosphates (0.625 mM final) in a 40-µl final reaction
mixture. Templates were transcribed at 30°C for 45 min, and the
synthesized RNA was extracted using Tri-reagent (Molecular Research
Center) according to the manufacturer's protocol. DNA-free reagent
(Ambion) was used to remove any residual DNA in the RNA preparation
before further quantitative analysis of E4 gene transcripts by
real-time reverse transcription (RT)-PCR. The sense primer of the E4
gene for quantitative PCR was
5'-CGCTGTGGAAGCGCTGTAT-3', and
the antisense primer was
5'-AAAAACCCTCCTGCCTAGGC-3'. The
sequence of the probe was
5'-6-carboxyfluorescein-TTGTTCTGGAGCGGGAGGGTGCT-6-carboxy-tetramethyl
rhodamine-3'. Quantitative PCR was
performed using the TaqMan one-step RT-PCR master mix and processed on
an ABI 7500 real-time PCR system (Applied Biosystems). Each sample was
duplicated, and three independent experiments were done to show the
most representative results. As a control, reactions lacking RT failed
to give signal above the background (data not
shown).
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, and PR-A were incubated with
recombinant CARM1 protein in the presence of [3H]AdoMet
(S-adenosyl-L-[methyl-3H]methionine),
and the products were separated by SDS-PAGE and analyzed by
autofluorography. In agreement with previous reports, p300 was
methylated by
CARM1 (Fig. 1A). Both SRC-1 and
SRC-3 also were methylated by CARM1, and the methylation efficiency
appeared comparable to that of p300 (Fig.
1A, compare lanes 6, 7,
and 8). The other SRC family member, SRC-2 could also be methylated by
CARM1 in vitro (Fig. 1B).
Neither ER
nor PR-A could be methylated by CARM1 in this
assay, indicating that the SRC family proteins and p300 are relatively
specific substrates for CARM1. Since histone H3 is a well-characterized CARM1 substrate and methylation of histone H3 contributes to CARM1's coactivator function (5), we compared CARM1's substrate preference for core histones versus SRC-3. The addition of equal amounts of purified SRC-3 recombinant protein dramatically decreased histone H3 methylation by CARM1 in vitro (Fig. 1C), indicating that SRC-3 is a preferred substrate for CARM1 in comparison to histone H3.
To confirm that CARM1, and not some other copurifying methylase, is solely responsible for methylation of the SRC proteins in our in vitro assays, we generated a methylation-defective CARM1 protein by mutating its substrate binding site (E267Q) and produced and purified it from a baculovirus expression system. This mutation has been reported previously to completely abolish CARM1 methylase activity (22). As expected, the mutant could not methylate SRC-3 (Fig. 1D), indicating that CARM1 is a bona fide methyltransferase for SRC family proteins in vitro.
SRC-3 is a substrate for CARM1 in vivo. Having demonstrated that SRC-3 could be methylated by CARM1 in vitro, we next asked whether this modification occurred in vivo. MEFs derived from wild-type and CARM1 knockout mice (43) were used for detection of endogenous SRC-3 methylation. An antibody that specifically recognizes mono- or dimethylated arginine was used to immunoprecipitate methylated proteins from cellular extracts derived from the wild-type and CARM1/ MEFs, and the presence of SRC-3 or p300 was detected by Western blotting. Methylated SRC-3 and methylated p300 were observed following immunoprecipitation from wild-type cells but not from the CARM1 knockout cells (Fig. 2A). SRC-3 methylation also was detected in a reciprocal immunoprecipitation experiment in which an SRC-3 antibody was used for immunoprecipitation (Fig. 2B). Taken together, these data demonstrate that SRC-3 is a substrate for CARM1 in vivo. Interestingly, methylated SRC-3 was not detected in the MCF7 breast cancer cell line, despite the fact that SRC-3 protein level is much higher in these cells (Fig. 2B, compare lanes 1 and 2), suggesting that the methylation of SRC-3 by CARM1 might be under tight regulation in MCF7 cells.
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FIG. 2. SRC-3
is methylated by CARM1 in vivo. (A) Cell extracts of CARM1
wild-type and knockout MEFs were immunoprecipitated with an antibody
against mono- or dimethylated arginine ( -mArg), followed by
Western blotting with specific antibodies against p300 or SRC-3 (upper
panel). Input lanes (lower panel) represent 5% of the total amount of
SRC-3 used for immunoprecipitation (IP). (B) Cell extracts of
MCF7 or CARM1 wild-type and knockout MEFs were immunoprecipitated with
antibody against SRC-3 ( -SRC-3), followed by Western blotting
with an antibody against mono- or dimethylated arginine. The amount of
immunoprecipitated SRC-3 is also shown (upper panel). The lower panel
shows the amount of CARM1 protein in 5% of the immunoprecipitation
input from the three different cell line extracts. (C) SRC-3
methylation is induced by estrogen signaling. MCF7 cells were cultured
in medium containing 5% charcoal-dextran-stripped FCS for 3 days before
the addition of estradiol (10 nM), followed by different incubation
times prior to harvesting. Cell lysates were immunoprecipitated with an
antibody against methylated arginine, followed by Western blotting (IB)
with antibody against SRC-3. The amount of ER , CARM1, and
SRC-3 in different samples was determined by Western blotting. In all
panels, ß-actin serves as a loading control. (D)
CARM1 is responsible for SRC-3 methylation in response to estrogen
signaling. The same experiment was done as for panel C except that the
MCF7 cells were transfected with 20 nM scramble siRNA or siRNA against
CARM1 for 3 days prior to hormone
induction.
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We next wanted to see if CARM1 is responsible for E2-induced SRC-3 methylation in vivo. We used siRNA to knockdown CARM1 in MCF7 cells and examined E2-induced SRC-3 methylation by immunoprecipitation-Western analysis. siRNA against CARM1 efficiently reduced the CARM1 protein level in MCF7 cells (Fig. 2D). Consequently, SRC-3 methylation in response to E2 treatment was significantly reduced (Fig. 2D). The results confirmed that CARM1 is responsible for E2-induced SRC-3 methylation in MCF7 cells and that it likely acts as the only arginine methyltransferase for SRC-3 in vivo.
Identification of a key SRC-3 methylation site in its Q-rich region. Since there is no consensus CARM1 substrate sequence, we initially identified the region of SRC-3 that was methylated by deletion mapping. GST fusion proteins containing five different functional domains of SRC-3 were purified and subjected to methylation by CARM1 in the in vitro methylation assay (Fig. 3A). Strong methylation was observed on the C-terminal domain of SRC-3, comprising residues 1081 to 1417 (Fig. 3A, lane 5) and indicating that the majority of CARM1 methylation occurs in this region. After additional deletion mapping (Fig. 3B), a small fragment containing 74 amino acids in the Q-rich domain of SRC-3 appeared to be the major target for CARM1 (Fig. 3B, lane 3).
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FIG. 3. Identification
of SRC-3 methylation sites. (A) Mapping regions on SRC-3 that
are methylated by CARM1. Five fragments of SRC-3 representing different
functional domains were generated as GST fusion proteins. The amount of
each protein (1 µg) used in the methylation assay was
determined by Coomassie blue staining (middle panel). Arrowheads
indicate the positions of full-length proteins. The incorporation of
[3H]methyl into the proteins is shown on the bottom panel.
(B) Deletion mapping further defines the region of SRC-3 that
is methylated. The C-terminal region of SRC-3 from 1041 to 1417 was
further divided into three fragments and fused with GST. These protein
fragments contain 5, 8, and 3 arginine residues, respectively (upper
panel). Full-length proteins are indicated by arrowheads, and the
incorporation of [3H]methyl into the proteins is shown on
the bottom panel. (C) Primary sequence alignment of the
methylation region of SRC-3 compared to the other SRC family proteins.
Highly conserved regions are shadowed. (D) Site-directed
point mutagenesis (arginine-to-alanine) of the SRC-3 methylation region
further refines which arginine residues serve as methylation acceptor
sites. Eight methylation mutants were generated, and their activities
were compared
with the wild-type protein in the CARM1 methylation assay. Arrowheads
indicate the positions of full-length proteins. (E) Confirmation of
methylation sites in the content of full-length SRC-3 protein.
Wild-type and methylation mutants of SRC-3 were expressed and purified
from a baculoviral system and tested in the CARM1 methylation assay.
The amount of protein (0.3 µg) used in each assay was
determined by Coomassie blue
staining.
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To confirm the identity
of the methylation sites in the context of the full-length protein, we
expressed full-length SRC-3 proteins bearing these corresponding
mutations in a baculoviral system and purified them to homogeneity
(Fig. 3E). The in vitro
methylation assay revealed that all proteins containing the R1171A
mutation exhibited decreased methyl incorporation, further confirming
that R1171 was a major substrate site for CARM1 modification (Fig.
3E, lanes 2, 4, and 5).
Similar to the GST fusion mutants, the R1177 mutant showed compromised
methylation compared with the wild-type protein, but methyl
incorporation in the R1171/1177A double mutant was not further
decreased compared to the R1171A single mutation (Fig.
3E, compare lanes 2 and
4), providing additional evidence that R1177 may play only a regulatory
role. Although the R1225A mutant displayed reduced methylation in the
context of the truncated SRC-3 GST fusion, the R1225/1227A double
mutant of the full-length protein incorporated the same level of
methylation as the wild-type protein (Fig.
3E, compare lanes 1 and
6). The data suggest that R1225 is not a preferred methylation site for
CARM1. Similarly, a 68-amino-acid deletion mutant
(
Me/
residues 1171 to 1238) eliminating all 8
arginines was generated and tested in the methylation assay. No
detectable methylation was observed for the deletion mutant (Fig.
3E, lane 7), indicating
that this region either contains all major methylation sites or, less
likely, is required for methylation on another region of in SRC-3. In
summary, we mapped the methylation of SRC-3 by CARM1 to a 68-amino-acid
Q-rich region of SRC-3, and within this region, we identified R1171 as
the major methylation site.
SRC-3 proteins defective for methylation have increased coactivator activity in vivo.
Having demonstrated
that SRC-3 can be methylated by CARM1 in vitro and in vivo, we next
asked whether this modification has any effect on SRC-3 coactivator
function. We compared the SRC-3 methylation mutants R1171A and
Me with wild-type SRC-3 for their ability to facilitate
transcriptional activation by ER
in a transient-transfection
assay in CV-1 cells. Although SRC-3 methylation mutants showed
coactivator activity comparable to that of wild-type SRC-3 in the
absence of CARM1, they exhibited 1.5-fold-higher activity
when CARM1 was coexpressed (Fig.
4A). We reasoned that the relatively mild effect seen with the methylation
mutants could be due to endogenous wild-type SRC-3 masking, at least to
some extent, the effect of the SRC-3 methylation mutants. Therefore, we
performed the same experiment in SRC3/
MEFs instead of CV-1 cells. As shown in Fig.
4B, the SRC-3 methylation
mutants, in the presence of CARM1, exhibited about threefold-higher
activity than wild-type SRC-3 in these cells. Our results suggest that
methylation of SRC-3 by CARM1 antagonizes SRC-3 coactivator activity in
ER-mediated transcriptional activation.
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FIG. 4. Mutation
of SRC-3 methylation sites increases its coactivator function in vivo.
(A) SRC-3 methylation site mutants, when coexpressed with
CARM1, display higher coactivation activity for ER -mediated
transcription. CV-1 cells were transiently transfected with 200 ng of
ERE-Luc reporter, 6 ng of pCR3.1-ER , 100 ng of pSG5-HA-CARM1,
and 100 ng of pSG5-Flag-SRC3 wild type (WT) or indicated mutant in each
well of a 12-well plate. Ten nanomolar estradiol (E2) was added
24 h after transfection, and luciferase activity was measured
at 48 h posttransfection. Luciferase activity was normalized
for protein content. t test was performed, and the statistical
significance compared with wild-type SRC-3 (n = 4) was
shown as follows:
*,
P value of <0.05;
**,
P value of <0.01. (B) A similar experiment
was performed as for panel A, except that
SRC-3/ MEFs were used. (C and D) The same
experiments were carried out as for panel B, except that a mouse
mammary tumor virus-luciferase reporter was used, and PR-B or GR was
cotransfected instead of ER . (E) SRC-3 methylation
mutants display higher coactivation activity on an endogenous promoter.
HEK293T cells were transiently transfected with 100 ng of
pCR3.1-ER and 400 ng of pSG5-Flag-SRC-3 wild type or indicated
mutants. Forty-eight hours after transfection, cells were treated with
10 nM E2 overnight to induce endogenous gene transcription. The amount
of pS2 gene expression was determined by real-time RT-PCR, and the
relative induction is shown. The expression of cyclophilin was used for
normalization. +, present; ,
absent.
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We next asked whether the SRC-3 methylation mutants
exhibit enhanced coactivation of an estrogen-induced endogenous gene.
Induction of the pS2 gene was examined by real-time RT-PCR in the
presence of exogenously expressed wild-type or methylation site-mutated
SRC-3 in HEK293T cells. Both the R1171A and
Me mutants showed
increased ability to activate the endogenous pS2 gene (Fig.
4E), further confirming
that the loss of methylation of SRC-3 increased its coactivator
function.
SRC-3 proteins defective for methylation have increased coactivator activity in vitro.
To further assess the coactivation
activity of the methylation-defective SRC-3 mutants, we took advantage
of an ER
-mediated in vitro transcription assay system. In this
assay, a reporter plasmid containing the adenoviral E4 gene with 4
estrogen-responsive elements (ERE) was assembled into chromatin by
using a Drosophila embryo S190 extract, followed by sequential
addition of purified ER
and coactivators. The transcriptional
activity of the coactivator was measured by quantifying transcription
from the reporter gene by real-time RT-PCR. To confirm the high quality
of the assembled chromatin, partial digestion with MNase was performed
(Fig.
5A). In agreement with the results obtained from the ERE-Luc reporter assay
conducted in cultured cells, the SRC-3 methylation mutants (Fig.
5C) showed higher
coactivation activity than wild-type SRC-3 in the chromatin-based in
vitro transcription assay; this effect appeared to be dosage dependent
(Fig. 5C). Thus, assaying
different transcription readout systems, we substantiated that
methylation site mutations enhanced the ability of SRC-3 to function as
a steroid receptor coactivator.
Next, a CARM1 E267Q mutant, in which the mutation eliminates the methyltransferase activity, was tested in the same assay. As shown in Fig. 5D, the CARM1 mutant showed consistently higher activity than the wild type in the presence of SRC-3. This can be explained by our model that, as a dual-function coactivator, CARM1 exerts both positive and negative effects on ER-mediated transcription. The luciferase readout is the combination of the dual effects. Alternatively, since CARM1 has been shown to contain a methylation activity-independent coactivator function, the E267Q mutation may retain the secondary coactivator function.
SRC-3 methylation modulates the interaction between SRC-3 and CARM1.
We next performed experiments to
understand the mechanisms by which SRC-3 methylation mutants exhibit
stronger coactivator activity toward ER
. The methylation
region of SRC-3 locates within the interaction region between the SRC
family proteins and CARM1
(4). This finding prompted
us to test whether methylation would affect the association between
SRC-3 and CARM1. We transfected Flag-tagged SRC-3 and methylation
mutants into 293T cells and analyzed their interaction with CARM1 by
coimmunoprecipitation. Following immunoprecipitation of SRC-3 with
anti-Flag antibody, endogenous CARM1 associated with the wild type or
methylation site SRC-3 mutants was compared. SRC-3 methylation mutants
displayed a decreased capacity to bind to CARM1, indicating that R1171
plays a critical role in mediating the association between SRC-3 and
CARM1 (Fig.
6A). These results suggest that methylation of SRC-3 on R1171 could modulate
the association between SRC-3 and CARM1. To test this hypothesis, we
synthesized two peptides containing residues R1171 and R1177. One
peptide (P2) contains asymmetrically dimethylated R1171 to mimic the
methylated form of SRC-3, whereas the other one (P1) is unmodified
(Fig. 6B, upper panel). We
then investigated which peptide could effectively inhibit the
methylation of SRC-3 by CARM1 in a competitive methylation assay.
Interestingly, P1 peptide strongly inhibited the methylation of SRC-3,
while the P2 peptide showed little inhibitory activity (Fig.
6B, bottom panel),
suggesting that only the unmodified peptide can bind to and sequester
functional CARM1 from SRC-3.
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FIG. 6. SRC-3
methylation dissociates CARM1 from the coactivator complex.
(A) HEK293T cells were transfected with the indicated
Flag-SRC-3 constructs. Following immunoprecipitation (IP) with
anti-Flag-M2 ( -Flag) affinity gel, the protein samples were
separated on a 4 to 15% SDS-PAGE gel. Endogenous CARM1
associated with Flag-SRC-3 was examined by Western blotting
(upper panel). The same membrane was also used to probe for SRC-3
(lower panel). (B) R1171 is a bona fide methylation site on
SRC-3. Two peptides, one with an asymmetric dimethylated arginine at
R1171 and the other one without any methyl group, were incubated with
recombinant SRC-3 protein in the CARM1-mediated methylation assay.
Triangles indicate three different peptide concentrations used (1.5
µM, 15 µM, and 150 µM). (C) Peptide
with unmodified R1171 competes with SRC-3 for binding CARM1. Peptide P1
or P2 (150 µM) was incubated together with recombinant
Flag-SRC-3 and CARM1 for 1 h at 30°C. SRC-3
protein was immunoprecipitated with anti-Flag-M2 affinity gel, and the
presence of associated CARM1 was determined by Western blotting.
(D) The methylation region of SRC-3 overlaps with the CARM1
docking region. Wild-type (WT) or methylation site-mutated SRC-3
proteins were incubated with GST or GST-CARM1 for 2 h at
4°C. Glutathione beads were used to pull down GST control and
GST-CARM1 proteins. Associated SRC-3 proteins were determined by
Western blot analysis. (E) A similar experiment was performed
as for panel A, except that ER was also transfected. The
levels of p300 and ER were determined by Western blotting as
well.
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Our results indicated that the methylation region of SRC-3 also serves as a docking site for CARM1. To confirm this deduction, a GST pull-down experiment was performed. Figure 6D showed that GST-CARM1 efficiently pulled down wild-type SRC-3 protein but not the methylation mutants of SRC-3. This result substantiated that the methylation region of SRC-3 overlaps with the protein-protein interacting region between SRC-3 and CARM1 and that the methylation event regulates their interaction.
Methylation of SRC-3 affects its interaction with p300.
As
SRC-3 methylation mutants do not have increased interaction with the
CARM1 coactivator, we wished to further investigate why these mutants
exhibit higher coactivator activity. To this end, we analyzed their
interaction with p300 by coimmunoprecipitation using anti-Flag captured
SRC-3. Interestingly, more p300 was observed to interact with the SRC-3
methylation mutants, whereas no obvious change was detected on
associated ER
(Fig.
6E, lanes 3, 4, and 6).
Thus, the increased coactivator activity of SRC-3 methylation site
mutants may be due, in part, to enhanced association with
p300.
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In addition to modifying the core histones in promoters, p300/CBP and CARM1 also can directly regulate the function of nonhistone transcriptional activators and coactivators by covalent modifications. p300/CBP can acetylate p53, leading to increased DNA binding and coactivator recruitment (2, 14). Androgen receptor and estrogen receptor alpha are also acetylated by p300/CBP (13, 37). In terms of transcriptional coactivator modifications, p300/CBP acetylates lysines preceding the LXXLL motif of SRC-3/ACTR, resulting in dissociation of SRC-3/ACTR from estrogen receptor (7). CARM1 has been reported to methylate various arginines in p300/CBP where methylation of arginines in the KIX domain perturbs CREB binding and affects the interaction between p300/CBP, CREB, and steroid receptors (42). Arginines close to the KIX domain of CBP are also modified and regulate its coactivator function (8). Finally, when the GRIP1 binding region of p300 is methylated, this leads to an attenuated interaction between GRIP1 and p300 (21).
In this study, we provided in vitro and in vivo evidence that SRC-3/AIB1 is a natural substrate for CARM1 and that SRC-3 methylation is induced by estrogen signaling. We identified R1171 of SRC-3 as the major methylation site. This arginine resides in a 12-amino-acid region of SRC-3 that is essential for CARM1 binding and is conserved within the SRC-3/p160 coactivator family. Our in vitro assays demonstrated that SRC-1 and SRC-2 also can be methylated by CARM1, likely through this arginine. CARM1 methylation thus may regulate the coactivator function of all SRC/p160 family proteins. Our SRC-3 data further suggest, along with that published for p300/CBP, that CARM1 regulates hormone-dependent transcription not only by modifying histones to enhance initiation of transcription but also by modifying coactivators to subsequently attenuate transcription. Thus, CARM1, and likely p300/CBP, are dual-function coactivators.
Coactivator assembly and disassembly. Coactivator assembly on promoters is an early step in hormone-induced transcriptional activation that is mediated by numerous protein-protein interactions. For instance, the coactivator LXXLL motif is the most common interacting motif bridging the interactions between steroid/nuclear hormone receptor ligand binding domains and a large number of different coactivators (15). Precisely ordered and synergistic folding has been proposed to be the molecular mechanism for functional interactions between the SRC/p160 coactivators and p300/CBP (9, 24). Coactivator assembly also is regulated by signaling pathways. For example, previous work from our laboratory showed that phosphorylation is a major regulator of SRC-3 activation by promoting coactivator assembly (40, 45). Different signaling pathways induce SRC-3 phosphorylation at distinct sites. This differential phosphorylation of SRC-3 in turn leads to differential recruitment of specific transcriptional coactivators at specific transcription factors.
In contrast, the process of disassembling coactivator complexes is not well understood. Prior data suggested that the p23 and Hsp90 molecular chaperones may promote the disassembly of transcriptional regulatory complexes (12). Two other studies, as noted above, suggest that coactivator modification may play a role in this process, especially in the context of attenuating hormone signaling (7, 21, 42). Our current study provides additional mechanistic detail for this process. We show that CARM1 methylates SRC-3 and that this modification, in turn, induces dissociation between CARM1 and SRC-3. Only an unmethylated SRC-3 peptide, but not the methylated peptide, could inhibit CARM1 methylation of SRC-3 by disrupting the SRC-3-CARM1 association. We propose that methylation of the SRC family of coactivators by CARM1 is a molecular switch for further triggering coactivator complex disassembly.
Based on our work and that of others, we propose a model to illustrate the molecular events involved in the assembly and disassembly of SRC-3-containing complexes acting at hormone-responsive genes (Fig. 7). First, SRC-3 activity is modulated by selective phosphorylation of different sites in response to distinct mitogenic signals. The hormone-bound estrogen receptor specifically interacts with promoter/enhancer sequences and recruits the appropriately phosphorylated SRC-3 coactivator to a target gene. SRC-3, in turn, recruits secondary coactivators, such as p300/CBP and CARM1. As a result, CARM1 methylates the core histone H3, while p300/CBP acetylates all core histones. The positive marks resulting from these histone modifications designate transcriptional activation of the target gene. At the same time, as shown by our current study, CARM1 methylates SRC-3 and dismantles the SRC-3-CARM1 coactivator complex. This model is consistent with the kinetics observed when these coactivators are bound and rapidly dissociate from target promoters in estrogen-treated MCF-7 cells (27, 30). In cells, we observe SRC-3 methylation peaking after 1 h of estrogen treatment; disappearance of methylation allows the possibility of another cycle of transcription. It is unclear whether the dissociated p300/CBP and SRC-3 would be rerecruited to the promoter for another round of transcription initiation because it is currently unknown if an arginine demethylase exists for recycling of previously methylated SRC-3. It also is possible that methylated SRC-3 is targeted for proteasome-dependent degradation in a transcription-linked mechanism. In vivo, this cycle is dynamic and leads to cyclic transcription driven by posttranslational coactivator modifications.
![]() View larger version (35K): [in a new window] |
FIG. 7. Model
for coactivator assembly and disassembly on estrogen-responsive
promoters. SRC-3 is phosphorylated at distinct sites by different
kinases induced by various signaling pathways. Dependent upon the
differential phosphorylation patterns, SRC-3 may assemble different
coactivator complexes at regulated target gene promoters. Estrogen
signaling results in estrogen-bound receptors interacting with both
promoter DNA and SRC-3 coactivator complexes. Enzymatic activities
enriched in the complex modify core histones and thereby facilitate
transcription initiation. After one (or limited) round(s) of
transcription initiation and to terminate signaling, p300/CBP and CARM1
modify components within the coactivator complex, leading to
disassembly of the complex and probably also dissociation of receptor
from the promoter DNA. We propose that CARM1, and likely also p300/CBP,
is a dual-function coactivator: it not only activates transcriptional
initiation by modifying core histone tails but also terminates hormone
signaling by disassembling the coactivator complex. It remains unknown
as to how many of the transcriptional coactivators in the complex are
reutilized for another round of transcription initiation or instead
subjected to transcription-linked protein
degradation.
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This work was supported by grants from NIH/NICHD, Welch Foundation, and NIDDK-NURSA (B.W.O.).
Published
ahead of print on 21 August 2006. ![]()
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