Graduate Program in Molecular and Cellular
Pharmacology, State University of New York at Stony Brook, Stony
Brook, New York 117941; Howard Hughes
Medical Institute,4 Cold Spring Harbor
Laboratory,2 Cold Spring Harbor, New York
11724; and Howard Hughes Medical Institute, Department of
Biochemistry, Robert Wood Johnson Medical School, University of
Medicine and Dentistry of New Jersey, Piscataway, New Jersey
088543
Received 6 November 1998/Returned for modification 3 December
1998/Accepted 14 December 1998
RNA polymerase II transcribes the mRNA-encoding genes and the
majority of the small nuclear RNA (snRNA) genes. The formation of a
minimal functional transcription initiation complex on a TATA-box-containing mRNA promoter has been well characterized and
involves the ordered assembly of a number of general transcription factors (GTFs), all of which have been either cloned or purified to
near homogeneity. In the human RNA polymerase II snRNA promoters, a
single element, the proximal sequence element (PSE), is sufficient to
direct basal levels of transcription in vitro. The PSE is recognized by
the basal transcription complex SNAPc. SNAPc,
which is not required for transcription from mRNA-type RNA polymerase
II promoters such as the adenovirus type 2 major late (Ad2ML) promoter,
is thought to recruit TATA binding protein (TBP) and nucleate the assembly of the snRNA transcription initiation complex, but little is known about which GTFs other than TBP are required. Here we show
that the GTFs IIA, IIB, IIF, and IIE are required for efficient RNA
polymerase II transcription from snRNA promoters. Thus, although the factors that recognize the core elements of RNA polymerase II mRNA
and snRNA-type promoters differ, they mediate the recruitment of
many common GTFs.
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INTRODUCTION |
In the past several years, all of
the factors required for basal RNA polymerase II transcription
from TATA-containing RNA polymerase II mRNA promoters have been
identified and purified and most of them have been cloned (61,
70). In vivo, several of these factors may be recruited to
promoters as part of large, RNA polymerase II-containing complexes,
some of which contain all the factors required for activated
transcription in vitro and are referred to as holoenzymes (9, 39,
42, 54). In vitro, however, the assembly of an RNA polymerase II
transcription initiation complex on a TATA box can be divided into
several steps. TATA binding protein (TBP) or the TBP-containing complex
TFIID binds to the TATA box in an association that is greatly
stabilized by the subsequent binding of TFIIB, which contacts both TBP
and the DNA. The presence of TFIIB allows the recruitment of a
TFIIF-RNA polymerase II complex and then of TFIIE and TFIIH. Another
general transcription factor (GTF), TFIIA, can join the initiation
complex at any stage of assembly. Like TFIIB, TFIIA greatly stabilizes the association of TBP with the TATA box (61, 70).
The role of the various transcription factors in directing
transcription initiation is the subject of intense studies. While TBP and TFIIB play central roles in the nucleation of the
transcription initiation complex, TFIIF, TFIIE, and TFIIH play roles at
later steps. TFIIF interacts directly with RNA polymerase II and
TFIIB and is required for stable assembly of RNA polymerase II with the
TATA-TBP-TFIIB complex (11, 20). It also inhibits
nonspecific binding of RNA polymerase II to nonpromoter sequences
(10, 37) and stimulates the rate of transcription elongation
(4, 6, 21, 31, 36, 68). TFIIE incorporation into the
TATA-TBP-TFIIB-RNA polymerase II-TFIIF complex is required for
subsequent assembly of TFIIH (19). TFIIE and TFIIH are
involved in promoter melting and promoter clearance (15, 28,
65-67, 82). TFIIE regulates the activities of TFIIH
(50), which possesses both ATP-dependent helicase activities
and a kinase activity capable of phosphorylating the C-terminal domain
of RNA polymerase II (14, 16-18, 50, 71, 74-77). The
helicase activity is thought to be involved in promoter melting
(27, 29). The C-terminal domain kinase activity may be
involved in promoter clearance and transcription elongation (1,
32, 44). In addition, TFIIE plays a direct role in promoter
melting, perhaps by binding to the single-stranded region and
thereby stabilizing the melted region of the promoter (29), and has been shown to help recruit TBP and TFIIA to the TATA box (93).
TFIIA is required for activation of transcription (see, for example,
references 13, 38, 40, 51, 62, 64, 81, and
94). In addition, TFIIA plays a role in basal
transcription, although this role varies with the precise in vitro
transcription system used. Thus, when transcription reaction mixtures
are reconstituted with TBP, addition of TFIIA has no effect (12,
52, 81). However, when transcription reaction mixtures are
reconstituted with TFIID, addition of TFIIA is stimulatory
(12, 94). This may be attributed in part to the
ability of TFIIA to counteract the activities of repressors such as
Dr1, Mot1 (also known as TAF-172), and Dr2 (also known as PC3 and
topoisomerase 1) (2, 8, 30, 43, 51, 58).
However, TFIIA is also capable of stimulating transcription when very
pure preparations of TFIID are used (51, 81). This may
reflect the ability of TFIIA to counteract the inhibitory effect of
TBP-associated factors in TFIID on TFIID binding (41, 63).
Many mRNA promoters lack TATA boxes altogether. In several of these
promoters, basal transcription is directed by an initiator (Inr)
element (79). The Inr is recognized by some of the TFIID TBP-associated factors (35, 55, 96). In particular,
Drosophila TAFII150, or its recently cloned
human homolog, CIF150 or hTAFII150, is required for
TFIID-dependent, Inr-directed transcription (34, 56, 85,
86). In addition, fractions referred to as TIC-1, TIC-2, and
TIC-3, as well as the GTF TFIIA, are required (56). Other
GTFs, namely TFIIB, TFIIF, TFIIE, and TFIIH, are assumed to be
required, and in the case of the TATA-less DNA polymerase
promoter,
which can be transcribed with TBP rather than TFIID, this has been
shown directly (90).
The human small nuclear RNA (snRNA) gene family consists of RNA
polymerase II and RNA polymerase III genes. Both of the human RNA
polymerase II and III snRNA promoters contain a distal
sequence element, which serves as a transcriptional enhancer. The
basal RNA polymerase II snRNA promoters contain a single
essential element, the proximal sequence element (PSE), which is
sufficient to nucleate the assembly of an RNA polymerase II
transcription initiation complex and to direct basal RNA polymerase II
transcription in vitro. The basal RNA polymerase III snRNA
promoters contain, in addition to the PSE, a TATA box, which in this
context determines the RNA polymerase III specificity of the promoter
(25, 47).
The PSE is recognized by a complex named SNAPc
(73) or PTF (60), which is composed of five
subunits (24). The TATA box in the RNA polymerase III
snRNA promoters is recognized by TBP (48, 72, 78, 88).
TBP is also required for transcription of the TATA-less RNA polymerase
II snRNA genes but not as part of the TBP-containing complexes
TFIID or TFIIB (73, 95). Thus, in this case, it is not clear
how TBP is recruited to the promoter. The other factors required for
assembly of the RNA polymerase II and III snRNA initiation
complexes are not well characterized. Most notably, it is not known
whether transcription from RNA polymerase II snRNA promoters relies
on the same GTFs as those used in transcription from mRNA promoters.
Here we compare the requirements of RNA polymerase II snRNA and
mRNA promoters for various GTFs. We find that basal RNA
polymerase II transcription from snRNA promoters requires TFIIA, TFIIB, TFIIF, and TFIIE. These results suggest that snRNA promoters and TATA-containing mRNA promoters use different
pathways to recruit many of the same general transcription factors.
They also point to a different function for TFIIA in basal
transcription from snRNA promoters and TATA-containing mRNA promoters.
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MATERIALS AND METHODS |
Sources of proteins.
TBP, TFIIA, TFIIB, TFIIE, and TFIIF
were expressed in Escherichia coli and purified as described
previously (53). RNA polymerase II and TFIIH were purified
from HeLa nuclear extracts also as described previously
(53). In some cases, TBP was purchased from Promega and
TFIIB was expressed in E. coli BL21 (DE3) cells as a
glutathione S-transferase (GST) fusion protein with the T7 expression system (80). The GST-TFIIB fusion protein was
purified by chromatography on glutathione-agarose beads (Sigma). TFIIB was released from GST, which remained bound to the beads, by cleavage with thrombin and was dialyzed against buffer D100 (20 mM
HEPES [pH 7.9], 100 mM KCl, 0.2 mM EDTA, 20% glycerol, 3 mM
dithiothreitol [DTT], 0.5 mM phenylmethylsulfonyl fluoride, 0.05%
Tween 20). Protein concentration was determined by sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and staining with
Coomassie blue, with bovine serum albumin as a standard.
Generation of anti-peptide antibodies for TFIIB.
Synthetic peptides corresponding to TFIIB amino acids 1 to 18 (peptide CSH505), 50 to 66 (peptide CSH506), and 300 to 316 (peptide
CSH508) were coupled to keyhole limpet hemocyanin (Pierce) as described
previously (23) and injected into rabbits to generate the
polyclonal anti-peptide antibodies
-IIB/1,
-IIB/2, and
-IIB/4, respectively.
Constructs.
The constructs pU1*G
, p119MLP(C2A),
pSBM13+VAI, and pU6/Hae/RA.2 have been described previously
(46, 49, 73). The construct pU1*G
Oct
, in which the
octamer sequence in pU1*G
was mutated into a BamHI site,
was constructed by oligonucleotide-directed PCR mutagenesis
(Stratagene) with the following oligonucleotides: U1mOctFd, with the
sequence 5'-GGACAGGGCGACTTCTGGGATCCAGAGGCAGCGCAGAGG-3', and
U1mOctRv, with the sequence
5'-CCTCTGCGCTGCCTCTGGATCCCAGAAGTCGCCCTGTCC-3'.
Immunodepletions.
Normal rabbit serum, immune sera directed
against the various RNA polymerase II GTFs, or, in the experiments
whose results are shown in Fig. 2, preimmune sera were incubated with
protein A-agarose beads (Boehringer Mannheim) for 1 h at room
temperature, washed in phosphate-buffered saline, and cross-linked as
described previously (23) except in the experiments whose
results are shown in Fig. 2, 3, and 5A and B, where the antibodies were
not cross-linked to the beads. The antibody beads were washed in buffer D50 (20% glycerol, 20 mM HEPES [pH 7.9], 50 mM KCl, 0.2 mM EDTA, 3 mM DTT, 0.05% Tween 20, 0.5 mM phenylmethylsulfonyl
fluoride), and used for depletions. Whole-cell or nuclear extracts
(approximately 30 or 20 µg/µl, respectively) were subjected to two
successive incubations with antibody beads, each for 25 min at room
temperature with agitation. The beads-to-extract ratios indicated in
the figure legends reflect the total amounts of beads used in the two
successive incubations. For example, two successive incubations with
beads-to-extract ratios of 1:1 are indicated as a beads-to-extract
ratio of 2:1. After the second incubation, the supernatants were used
for in vitro transcription reactions and depletions were monitored by immunoblotting.
In vitro transcriptions.
Transcriptions from the pU1*G
construct, which contains U1 promoter sequences in front of a G-less
cassette, were performed in a total volume of 40 µl containing 45 to
50 mM KCl, 12 mM HEPES (pH 7.9), 5 mM MgCl2, 1 mM
spermidine trihydrochloride (Sigma), 1 mM DTT, 400 µM ATP, 400 µM
UTP, 0.625 µM (1.5 to 2 µl) [
-32P]CTP (20 µCi),
1.2 mM 3'-O-methyl-GTP (Pharmacia), 12% glycerol, 0.01%
Tween 20, 0.1 mM EDTA, 2% polyethylene glycol 8000, 4.5 U of RNase
T1, and 0.5 to 1.0 µg of pU1*G
template (73)
or, in the experiments whose results are shown in Fig. 8 and 9, pU1*G
that had been linearized with HindIII. In addition,
reaction mixtures included approximately 360 µg of whole-cell extract
or 160 µg of nuclear extract and similar amounts of mock-depleted or
depleted extracts. The reaction mixtures were incubated for 90 min at
30°C and stopped by addition of 270 µl of stop buffer containing
0.3 M sodium acetate, 0.5% SDS, 2.5 mM EDTA, 50 µg of tRNA per ml, and 80 µg of proteinase K. After further incubation for 30 min to
1 h at 37°C, the reaction mixtures were extracted with phenol and the nucleic acids were precipitated with ethanol and fractioned on
a 4.5% polyacrylamide-urea gel. The dried gels were quantitated with
a phosphorimager (Fuji) and exposed to film.
Transcriptions from the p119MLP(C2A) construct, which contains the
adenovirus type 2 major late (Ad2ML) promoter in front of a G-less
cassette, were performed under the same conditions as those described
above except that the total reaction volume was 25 µl and the
reaction mixtures contained 10 mM MgCl2, no Tween 20, 0.5 µg of the p119MLP(C2A) template (49), 90 to 120 µg of
whole-cell extract or 50 µg of nuclear extract, and similar amounts
of mock-depleted or depleted extracts. In the experiments whose results
are shown in Fig. 8 and 9, p119MLP(C2A) was first linearized with
Eco0109I.
VAI transcription reactions were performed as described previously
(49) in a total volume of 20 µl containing 250 ng of pSBM13+VAI supercoiled template, 20 to 30 µg of
whole-cell or nuclear extract, and similar amounts of mock-depleted or
depleted extract.
U6 transcription reactions were performed as described previously
(49) in a total volume of 20 µl containing 400 ng of the pU6/Hae/RA.2 supercoiled template, approximately 90 to 150 µg of
whole-cell extract or 35 µg of nuclear extract, and similar amounts
of mock-depleted or depleted extract.
Immunoblots.
Whole-cell or nuclear extract and extracts
treated with antibody beads were fractionated by SDS-PAGE on 12.5%
polyacrylamide gels. Purified protein preparations and Rainbow markers
(Amersham) were used as markers (not shown). The proteins were
transferred to nitrocellulose, and the membranes were probed with the
antibodies indicated in the figures.
 |
RESULTS |
To assess the roles of various RNA polymerase II GTFs in
transcription from RNA polymerase II snRNA promoters, we
immunodepleted each of these GTFs from extracts and tested the depleted
extracts for their ability to direct transcription from four types of
promoters, whose structures are illustrated in Fig.
1A; the Ad2ML promoter, a typical
mRNA-type RNA polymerase II promoter, the RNA polymerase II U1 and RNA
polymerase III U6 snRNA promoters, and the Ad2 VAI promoter, a
typical RNA polymerase III promoter with gene-internal A and B boxes.
In those cases where transcription was reduced by the immunodepletion,
we then tested whether addition of the factor against which the
antibody had been raised restored transcription. All of these factors
except for RNA polymerase II and TFIIH were recombinant proteins
expressed in bacteria, and Fig. 1B shows their polypeptide
compositions. Both TBP (lane 1) and TFIIB (lane 3) migrated close to
their calculated molecular masses of 38 and 33 kDa, respectively. TFIIA
is composed of three subunits,
,
, and
, two of which (
and
) are derived from a single gene, probably by protein processing
(61). The recombinant TFIIA used here contains a 56-kDa
polypeptide corresponding to fused
and
subunits as well as the
14-kDa
subunit (lane 2). Lanes 4 and 5 show the 56- and 34-kDa
subunits of TFIIE and the RAP74 and RAP30 subunits of TFIIF,
respectively, while lane 6 shows highly purified human RNA
polymerase II.

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FIG. 1.
(A) Basal promoter elements in the Ad2ML, U1
snRNA, U6 snRNA, and VAI promoters. Pol II and III, RNA
polymerases II and III, respectively. (B) Polypeptide compositions
of recombinant (TBP, TFIIA, TFIIB, TFIIE and TFIIF) or
highly purified (RNA polymerase II) factors.
The proteins were fractionated by SDS-PAGE and stained with silver.
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TFIIB is required for RNA polymerase II snRNA
transcription.
In experiments where anti-TFIIB monoclonal
antibodies were added to an extract, transcription from both the U1 and
Ad2ML promoters was inhibited and could then be restored by the
addition of recombinant TFIIB (5). These results were
consistent with TFIIB being required for RNA polymerase II
snRNA gene transcription, but because TFIIB was not depleted
from the extracts, it remained possible that the anti-TFIIB monoclonal
antibodies cross-reacted with another factor required for U1
transcription. Upon addition of recombinant TFIIB, such a factor might
have been released from the antibodies and thus become available again
to participate in U1 transcription. We therefore tested whether RNA
polymerase II transcription from snRNA genes requires TFIIB
by depleting a whole-cell extract with anti-TFIIB antibodies
(
-IIB/2) bound to protein A-agarose beads. Figure
2A shows the effects of such depletion on
transcription from various promoters. Treatment of the extract with
anti-TFIIB antibodies inhibited transcription from the Ad2ML promoter
much more than treatment with preimmune beads, as expected (compare lanes 4 and 5 with lanes 2 and 3 in the top gel). Significantly, the
anti-TFIIB depletion also inhibited transcription from the RNA
polymerase II U1 snRNA promoter but not from the RNA
polymerase III U6 snRNA and VAI promoters (Fig. 2A, compare
lanes 4 and 5 to lanes 2 and 3 in the second, third, and fourth gels).
An immunoblot analysis of the extracts, shown in Fig. 2B, indicated
that the anti-TFIIB depletion had been efficient.

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FIG. 2.
TFIIB is required for RNA polymerase II
snRNA transcription from the U1 promoter. (A) Parallel in vitro
transcription reactions were performed with the Ad2ML, U1 snRNA, U6
snRNA, and VAI promoters with untreated whole-cell extract (WCE;
lane 1), WCE treated with increasing amounts of preimmune antibody
beads (Pre-I; lanes 2 and 3), or WCE-treated with increasing amounts of
anti-TFIIB antibody beads ( -IIB/2; lanes 4 and 5) at
beads-to-extract ratios of 2:1 (lanes 2 and 4) and 2.5:1 (lanes 3 and
5). The locations of correctly initiated transcripts are indicated at
left, and an asterisk marks readthrough transcripts (73).
(B) Immunoblot analysis of the extracts used in the experiments whose
results are shown in panel A. The membrane was probed with the
-IIB/4 antibody. Eight microliters of each extract was loaded per
lane. (C) In vitro transcription reactions were performed with WCE
supplemented with SNAPc (lane 1), WCE supplemented with
SNAPc and treated with preimmune antibody beads (lanes 2 and 7), or WCE supplemented with SNAPc and treated with
-IIB/1 (lanes 3 to 6) or -IIB/2 (lanes 8 to 11) antibody beads at
a beads-to-extract ratio of 0.5:1. In lanes 4 to 6 and 9 to 11, 40, 200, and 400 ng, respectively, of E. coli-expressed TFIIB
was added back to the TFIIB-depleted reaction mixtures. An asterisk
marks readthrough transcripts. (D) Immunoblot analysis of the extracts
used in the experiments whose results are shown in panel C. The
membrane was probed with the -IIB/4 antibody. Eight microliters of
each extract was loaded per lane.
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To determine whether the inhibition of transcription from the U1
snRNA promoter was indeed due to removal of TFIIB rather than, for
example, removal of a TFIIB-associated factor, we tested whether
addition of recombinant TFIIB to depleted extracts could restore U1
transcription. For this experiment, we first complemented a whole-cell
extract with biochemically purified SNAPc to ensure that
SNAPc would not be limiting. As shown in Fig. 2C, treatment of the extract with preimmune beads diminished transcription but much
less so than treatment with the
-IIB/2 antibody beads (compare lanes
7 and 8) or beads coupled to another anti-TFIIB antibody,
-IIB/1 (compare lanes 2 and 3). Both of these antibodies
depleted TFIIB efficiently, as determined by immunoblotting (Fig. 2D). Importantly, in both cases, addition of increasing amounts of recombinant full-length TFIIB restored efficient U1 transcription (lanes 4 to 6 and 9 to 11). Addition of just the C-terminal core domain
of TFIIB, which is sufficient for association with a TBP-TATA box
complex but cannot sustain basal RNA polymerase II mRNA
transcription (see reference 61 for a review), did
not restore U1 transcription (data not shown). Together, these results
strongly suggest that TFIIB is required for snRNA gene
transcription by RNA polymerase II.
TFIIA is required for efficient basal RNA polymerase II
transcription from the U1 snRNA promoter.
In in vitro
transcription systems that are reconstituted wtih TFIID, but not with
TBP, TFIIA is required for basal transcription from RNA
polymerase II mRNA-type promoters (12, 52, 81, 94).
This finding probably reflects the ability of TFIIA to counteract the
effects of factors that interfere with the binding of TBP to the TATA
box and that are associated with TFIID or may be present in
TFIID fractions (2, 8, 30, 41, 43, 51, 58, 63).
We used polyclonal antibodies directed against the
and
subunits
of TFIIA coupled to protein A-agarose beads to deplete extracts and
tested the depleted extracts for transcription from the four model
promoters. As shown in Fig. 3, treatment
with anti-TFIIA antibodies had only a small effect on transcription
from the Ad2ML promoter (compare lanes 2 and 3), even though most of
the TFIIA present in the extract was removed by such treatment (data
not shown, but see Fig. 4B below). Addition of increasing amounts of
TFIIA restored transcription from the Ad2ML promoter to levels that
were slightly higher than starting levels (compare lanes 4 to 6 with
lane 2). Since the role of TFIIA in basal transcription from mRNA-type
RNA polymerase II promoters is mainly to counteract inhibitors
that disrupt association of TBP with the TATA box, addition of
excess recombinant TBP to depleted extracts should overcome the
need for TFIIA. Indeed, addition only of recombinant TBP to the
TFIIA-depleted extract achieved levels of transcription that were
higher than those observed in the mock-depleted extract (lane 7) and
that were not increased further by addition of TFIIA (lanes 8 and 9).
In contrast, when highly purified TFIID was added, transcription could
be further enhanced by addition of TFIIA (data not shown). Together,
these results indicate that TFIIA has a small positive effect on basal
transcription from the Ad2ML promoter in this system but that
this effect is not apparent in the presence of added recombinant TBP.
This is consistent with a role for TFIIA in counteracting
repressors that inhibit the binding of TFIID to the TATA box.

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FIG. 3.
TFIIA is required for efficient RNA polymerase
II snRNA transcription from the U1 promoter in vitro. In vitro
transcription reactions were performed with untreated nuclear extract
(NE; lane 1), NE treated with control (nonimmune) antibody beads (lane
2), or NE treated with antibody beads directed against the and subunits of TFIIA ( -IIA; lanes 3 to 9) at a 1:1 beads-to-extract
ratio. Two, 4, and 6 µl of E. coli-expressed TFIIA was
added to the reaction mixtures in lanes 4 to 6. Recombinant TBP (3 ng)
was added to the reaction mixture in lane 7 and a combination of 3 ng
of TBP and 2 and 6 µl of TFIIA was added to the reaction mixtures in
lanes 8 and 9, respectively. The asterisk marks RNA polymerase
III transcripts that are produced in U1 transcription reactions when
TBP is added. The signals corresponding to correct transcription
initiation in each panel were quantitated with a phosphorimager, the
background was subtracted, and the numbers were normalized for the
signal obtained in lane 2, which was set at 1. Ctr., control.
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We then tested the same extracts for transcription from the RNA
polymerase II U1 snRNA promoter and observed strikingly
different results. Depletion with anti-TFIIA antibody beads
reduced transcription much more efficiently than depletion with
control antibody beads (Fig. 3, compare lanes 2 and 3 in the second
panel). Addition of increasing amounts of TFIIA reproducibly restored
only a low level of U1 transcription, below that observed in
mock-immunodepleted extract (lanes 4 to 6). Unlike with transcription
from the Ad2ML promoter, where the requirement for TFIIA was
obviated by addition of excess recombinant TBP, addition only of
recombinant TBP to the U1 reaction mixtures restored only a low level
of transcription (lane 7), which could be increased to
levels that were higher than starting levels by further
addition of increasing amounts of TFIIA (compare lanes 8 and 9 to lane
2). The combined effect of TBP and TFIIA could not be achieved by
simply increasing the amounts of added TBP indeed, this
resulted only in stimulation of transcription from an aberrant start
site (Fig. 3, asterisk) which is directed by RNA polymerase III
(data not shown).
For TATA-containing mRNA promoters, TFIIA is much more important for
activated transcription than for basal transcription. To ensure that
the signal derived from the U1 promoter reflected basal
transcription, we repeated the experiment using a U1 template with a mutated distal sequence element. As shown in Fig.
4A, depletion with anti-TFIIA antibodies
again severely and specifically decreased U1 transcription (lanes 2 and
3) and addition of either TFIIA or TBP alone did not reconstitute
efficient transcription (lanes 4 and 5). However, as before, addition
of both TFIIA and TBP reconstituted high levels of U1 transcription
(lane 6). The immunoblot in Fig. 4B shows that TFIIA depletion was
efficient. Together, these results indicate that TFIIA plays a role in
basal transcription from the U1 snRNA promoter that is different
from its role in transcription from the Ad2ML promoter. Indeed, whereas
with the Ad2ML promoter addition of recombinant TBP circumvents the
need for TFIIA, recombinant TBP cannot be used by the U1 snRNA
promoter unless TFIIA is present.

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FIG. 4.
TFIIA is required for basal transcription from the
U1 snRNA promoter. (A) In vitro transcription
reactions were performed with the pU1*G Oct template and untreated
whole-cell extract (WCE; lane 1) or WCE treated with either control
(nonimmume) antibody beads (lane 2) or beads coupled to antibodies
directed against the and subunits of TFIIA ( -IIA; lanes 3 to
6) at a 1:1 beads-to-extract ratio. Six microliters of E. coli-expressed TFIIA was added to the reaction mixtures in lanes 4 and 6, and recombinant TBP (3 ng) was added to the reaction mixtures in
lanes 5 and 6. The signals corresponding to correct transcription
initiation were quantitated with a phosphorimager, the background was
subtracted, and the numbers were normalized for the signal obtained in
lane 2, which was set at 1. (B) Immunoblot analysis of the extracts
used in the experiment whose results are shown in panel A with a
polyclonal antibody directed against the subunit of TFIIA. WCE (5 µl) was loaded in lane 1, and control depleted extract (10 µl) and
-IIA depleted extract (10 µl) were loaded in lanes 2 and 3, respectively. The location of the -subunit is indicated at left.
Ctr., control.
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TFIIA is not essential for RNA polymerase III transcription
from the U6 snRNA promoter in vitro.
TFIIA has been reported
to be required for or to stimulate RNA polymerase III
transcription from the U6, VAI, tRNA, and 5S promoters (57,
87). These results contrast with the finding that, unlike RNA
polymerase II transcription, RNA polymerase III transcription is unaffected in extracts from Saccharomyces
cerevisiae cells carrying temperature-sensitive mutations in the
TFIIA subunits (33) and with the recent observation that
depletion of TFIIA from a nuclear extract has no effect on VAI
transcription (8).
The same depleted extracts tested as described above for RNA
polymerase II transcription were also tested for their ability to direct RNA polymerase III transcription. As shown in Fig. 3, treatment with anti-TFIIA antibody beads had no effect on VAI transcription, even though TFIIA had been efficiently depleted as
judged from immunoblots (data not shown), suggesting that TFIIA is not
required for transcription from RNA polymerase III tRNA-type promoters (compare lanes 2 and 3, bottom panel). In sharp contrast, however, U6 snRNA transcription was significantly reduced in
extracts immunodepleted of TFIIA compared to transcription in
mock-immunodepleted extracts (lanes 2 and 3, third panel). Addition of
recombinant TFIIA had no significant effect (lanes 4 to 6), but U6
transcription could be reconstituted to levels higher than starting
levels by addition of recombinant TBP (lane 7). These levels could not
be increased by further addition of TFIIA (lanes 8 and 9).
To confirm that TFIIA is dispensable for U6 RNA polymerase III
transcription in the presence of exogenous TBP, we supplemented the
extracts with recombinant TBP before treatment with the beads. As shown
in Fig. 5A and B, treatment with
anti-TFIIA antibody beads depleted TFIIA much more efficiently than
treatment with control antibody beads (Fig. 5B, compare lanes 7 to 11 with lanes 2 to 6), yet in this case, depletion of TFIIA had no
specific deleterious effect on transcription from either the Ad2ML
promoter, as expected, or the U6 promoter (Fig. 5A, compare lanes 7 to
11 with lanes 2 to 6). These results suggest that in the presence of
excess exogenous TBP, TFIIA is not required for U6 transcription in
vitro.

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FIG. 5.
TFIIA is not required for efficient RNA
polymerase III snRNA transcription from the U6 promoter in
vitro. (A) Parallel in vitro transcription reactions from the Ad2ML and
U6 snRNA promoters. Whole-cell extract (WCE) was supplemented with
TBP (lane 1) and then treated with increasing amounts of control
(nonimmune) antibody beads (lanes 2 to 6) or -IIA antibody beads
directed against the and subunits of TFIIA (lanes 7 to 11) at
beads-to-extract ratios of 0.5:1, 1:1, 1.5:1, 2:1, and 2.5:1,
respectively. (B) Immunoblot analysis of the extracts used in the
experiment whose results are shown in panel A with the antibody
directed against the and subunits of TFIIA. WCE plus TBP (4 µl) was loaded in lane 1, and the depleted extracts (6 µl) were
loaded in lanes 2 to 11. The location of the subunit is indicated
at left. (C) Addition of TFIIA to TFIIA-depleted extracts does not
stimulate U6 transcription in vitro in the presence of limiting amounts
of recombinant TBP. Nuclear extract (NE) was treated with control
(nonimmune) (lane 2) or anti-TFIIA (lanes 3 to 18) antibody beads at a
1:1 beads-to-extract ratio. E. coli-expressed TFIIA (2 µl)
and TBP (amounts are indicated in nanograms) were added to the reaction
mixtures as indicated above the lanes (lanes 4 to 18). The signals
corresponding to correct transcription initiation were quantitated with
a phosphorimager, the background was subtracted, and the numbers were
normalized for the signal obtained in lane 3, which was set at 1. Ctr.,
control.
|
|
It remained possible, however, that TFIIA helped to recruit
limiting amounts of TBP to the U6 promoter. To test this
possibility, we supplemented an extract treated with anti-TFIIA
antibody beads with decreasing amounts of TBP, with or without TFIIA.
As shown in Fig. 5C, addition of TFIIA alone had little effect on U6
transcription (compare lanes 4, 7, 10, 13, and 16 to lane 3). Addition
of 3.3 ng of TBP restored transcription to levels higher than those
observed in the extract depleted with preimmune antibody beads (lane
18), but this level was not changed by further addition of TFIIA (lane 17). As lower levels of TBP were added, U6 transcription decreased but
in no case did addition of TFIIA significantly improve transcription (compare lanes 5 and 6, 8 and 9, 11 and 12, and 14 and 15). Thus, even
at levels of TBP too low to restore efficient U6 transcription, addition of TFIIA did not have a stimulatory effect. These results suggest that TFIIA is not required for basal U6 transcription in vitro,
even when limiting amounts of TBP are added to the extract. They do not
exclude, however, that TFIIA performs a role in U6 transcription in vitro.
TFIIF is required for RNA polymerase II snRNA gene
transcription in vitro.
TFIIF complexed with RNA
polymerase II interacts directly with TFIIB and is thus
essential for the recruitment of RNA polymerase II to mRNA-type
RNA polymerase II promoters. To determine if TFIIF participates
in RNA polymerase II snRNA gene transcription, we depleted
a nuclear extract using polyclonal antibodies directed against the
RAP75 subunit of TFIIF. As shown in Fig.
6A, treatment of the extract with the
anti-TFIIF antibody beads specifically inhibited transcription from
both the Ad2ML and U1 snRNA promoters but had no specific effect on
RNA polymerase III transcription from the VAI or U6 snRNA
promoters (compare lanes 5 to 7 with lanes 2 to 4). Figure 6B shows an
immunoblot of these reactions that confirms that most of the TFIIF
RAP74 and RAP30 subunits had been depleted.

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FIG. 6.
Depletion of TFIIF inhibits RNA polymerase II
snRNA transcription from the U1 promoter. (A) In vitro
transcription reactions with the Ad2ML, U1 snRNA, U6 snRNA, and
VAI promoters. Transcription reactions were performed with
untreated nuclear extract (NE; lane 1), NE treated with increasing
amounts of control (nonimmune) antibody beads (lanes 2 to 4), or NE
treated with increasing amounts of -RAP74 antibody beads (lanes 5 to
7) at beads-to-extract ratios of 0.5:1, 1:1, and 2:1, respectively. (B)
Immunoblot analysis of the extracts used to obtain the results shown in
panel A with -RAP74 and -RAP30 antibodies. Ten microliters
of every extract was loaded per lane. Ctr., control.
|
|
Attempts to reconstitute transcription by addition only of recombinant
TFIIF were unsuccessful (data not shown). We reasoned that the
anti-TFIIF depletion had probably removed other associated factors such
as RNA polymerase II. In preliminary experiments, we therefore
supplemented depleted extracts with a mixture of TFIIF and the GTFs
TFIIA, TFIIB, TFIIE, TFIIH, and RNA polymerase II or with every
possible mixture of all but one of these GTFs (data not shown). Figure
7 shows the results of an experiment in
which we supplied only the factors we had identified as necessary for
reconstitution of transcription. Addition of a mixture containing TFIIF, RNA polymerase II, and TFIIB reconstituted
transcription from both the Ad2ML and U1 snRNA promoters in
an extract treated with anti-TFIIF antibody beads (Fig. 7A, lanes 3 and
4). However, a mixture lacking TFIIF did not reconstitute transcription
efficiently (lane 5). Thus, TFIIF is not only required for RNA
polymerase II transcription from the Ad2ML promoter but also
essential for efficient transcription from the U1 snRNA promoter.

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FIG. 7.
TFIIF is required for U1 transcription in vitro. (A)
Parallel transcription reactions were performed with the Ad2ML and U1
promoters as templates and untreated nuclear extract (NE; lane 1), NE
treated with control (nonimmune) antibody beads (lane 2), or NE treated
with anti-RAP74 ( -RAP74) antibody beads (lanes 3 to 7) at a 1:1
beads-to-extract ratio. Recombinant TFIIF (1 µl), purified RNA
polymerase II (pol II; 1.5 µl), and recombinant TFIIB (2 µg) were added to the reaction mixture in lane 4. In lanes 5 to
7, the same combination of factors was added except for the factor
indicated above each lane. (B) Immunoblot analysis of the extracts used
in the experiment whose results are shown in panel A with
-RAP74 and -RAP30 antibodies, anti-C-terminal domain
antibodies directed against the largest subunit of RNA
polymerase II, and anti-TFIIB antibodies. Ten microliters of
extract was loaded per lane. Ctr., control.
|
|
When the TFIIF-depleted extract was complemented with a mixture
containing TFIIF and TFIIB but lacking RNA polymerase II, we
observed little or no transcription from both the Ad2ML and the U1
promoter (Fig. 7A, lane 6). This result suggests that depletion with
the anti-TFIIF antibodies also removed RNA polymerase II. Indeed, consistent with the known association of TFIIF with RNA polymerase II, the amounts of both factors were severely
reduced in extracts treated with anti-TFIIF antibody beads as
determined by immunoblotting (Fig. 7B). More surprisingly, a mixture
lacking TFIIB did not restore U1 transcription even though it restored transcription from the Ad2ML promoter efficiently (Fig. 7A, lane 7). As shown in the bottom gel of Fig. 7B, the amounts of TFIIB were reduced in the TFIIF-depleted extract, although much less so than
the amounts of either TFIIF or RNA polymerase II. These results
indicate that the Ad2ML and U1 promoters differ in their requirements
for TFIIB. One possibility is that transcription from the U1 promoter
simply requires higher levels of TFIIB. Indeed, even different mRNA
promoters require different concentrations of TFIIB for optimal
transcription. Thus, at concentrations of TFIIB that still stimulate
transcription of the Drosophila Krüppel and
Jockey promoters, transcription from the
Drosophila alcohol dehydrogenase and Ad2E4 promoters is
repressed, probably by a squelching effect (89).
TFIIE stimulates transcription from the RNA polymerase II
snRNA U1 promoter.
TFIIE regulates the activity of TFIIH,
plays a direct role in promoter melting, and can help recruit TFIIA and
TBP to the TATA box of mRNA promoters (61, 93). To determine
if TFIIE is involved in RNA polymerase II snRNA gene
transcription, we depleted nuclear extracts using polyclonal
antibodies directed against the p34 subunit of TFIIE. Because
both TFIIE and TFIIH requirements are more apparent with linear
templates than with supercoiled templates (66, 83), we
linearized the templates by digestion with a restriction enzyme. As
shown in Fig. 8, treatment of the extract
with the anti-TFIIE antibody beads depleted TFIIE from the extracts
(Fig. 8B) and inhibited transcription from linearized templates
containing the Ad2ML or the U1 promoter (Fig. 8A, compare lanes 5 to 7 with lanes 2 to 4). We then tested the effect of adding back TFIIE. As
shown in Fig. 9A and B, treatment with
anti-TFIIE antibody beads inhibited transcription (Fig. 9A, lane 3) and
efficiently depleted TFIIE (Fig. 9B, lane 3), as expected, and for both
the Ad2ML promoter and the U1 snRNA promoter, addition of
recombinant TFIIE resulted in recovery of a significant but low level
of transcription (Fig. 9A, lanes 4 to 6). These results suggested
that other factors required for U1 transcription had been depleted
along with TFIIE. Indeed, as shown in Fig. 9C, addition of RNA
polymerase II and all of the GTFs (excluding TBP) to the
TFIIE-depleted extract restored full levels of transcription from the
Ad2ML and U1 promoters (compare lanes 3 and 4). Importantly, addition
of these same GTFs without TFIIE resulted in much lower levels of
transcription (lane 5). Together, these results suggest that TFIIE is
involved in RNA polymerase II transcription of snRNA genes.

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FIG. 8.
Depletion of TFIIE inhibits RNA polymerase II
transcription from the Ad2ML and the U1 snRNA promoters. (A) In
vitro transcription reactions from linearized templates were performed
with untreated nuclear extract (NE; lane 1) or NE treated with
increasing amounts of control (nonimmune) antibody beads (lanes 2 to 4)
or with increasing amounts of anti-TFIIE antibody beads directed
against the p34 subunit of TFIIE ( -IIEp34; lanes 5 to 7) at
beads-to-extract ratios of 0.1:1, 1:1, and 2:1, respectively. (B)
Immunoblot analysis of the extracts used to obtain the results shown in
panel A with antibodies directed against the p34 and p56 subunits
of TFIIE. The locations of the TFIIE subunits are indicated at the
left. Ten microliters of extracts was loaded per lane. Ctr., control.
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|

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FIG. 9.
TFIIE stimulates transcription from the RNA
polymerase II snRNA U1 promoter. (A) Addition of E. coli-expressed TFIIE to TFIIE-depleted extract. Nuclear extract
(NE) was treated with control (nonimmune) antibody beads (lane 2) or
anti-TFIIE antibody beads directed against the p34 subunit of TFIIE
( -IIEp34; lanes 3 to 6) at a 2:1 beads-to-extract ratio and used in
transcription reactions with linearized Ad2ML and U1 templates. In
lanes 4 to 6, 0.5, 1.5, and 3 µl of E. coli-expressed
TFIIE was added to the reaction mixtures. (B) Immunoblot analysis of
the extracts used to obtain the results shown in panel A with
antibodies directed against the p34 and p56 subunits of TFIIE. (C)
Addition of GTFs to TFIIE-depleted extracts. Nuclear extract was
treated with control (nonimmune) antibody beads (lane 2) or
-TFIIEp34 antibody beads (lanes 3 to 10) at a 1:1 beads-to-extract
ratio and used in parallel transcription reactions with linearized
Ad2ML and U1 templates. In the reaction whose results are shown in lane
4, a combination of recombinant TFIIE (1 µl), purified RNA
polymerase II (pol II; 1.5 µl), recombinant TFIIA (1 µl),
recombinant TFIIB (2 µg), recombinant TFIIF (1 µl), and purified
TFIIH (2 µl) was added. In lanes 5 to 10, the same combination of
GTFs was added except for the factor indicated above each lane. (D)
Immunoblot analysis of the extracts used to obtain the results shown in
panel C with antibodies directed against the p34 and p56 subunits of
TFIIE, the largest subunit of RNA polymerase II, and TFIIB. Ten
microliters of extract was loaded per lane. Ctr., control.
|
|
Figure 9D shows the levels of the two TFIIE subunits, the largest RNA
polymerase II subunit, and TFIIB, present in the extracts treated with the anti-TFIIE antibodies. As expected, both TFIIE subunits were efficiently depleted (lane 3). In addition, however, there were small decreases in the amounts of the largest RNA
polymerase II subunit and TFIIB. Consistent with these small
decreases, omission of RNA polymerase II or TFIIB from the
combination of GTFs had a deleterious effect on transcription from the
Ad2ML and U1 promoters (Fig. 9C, lanes 6 and 8). Notably, however,
omission of RNA polymerase II was more detrimental to
transcription from the Ad2ML promoter than to transcription from the U1
promoter, whereas the reverse was true for omission of TFIIB. Thus, as
observed above for TFIIF-depleted extracts, the Ad2ML and the
U1 promoters have different quantitative requirements for
various factors, in particular TFIIB.
 |
DISCUSSION |
Which of the GTFs are required for RNA polymerase II
transcription of snRNA genes is not known. Here we show that
efficient transcription from the human U1 snRNA promoter requires
TFIIA, TFIIB, TFIIF, and TFIIE.
TFIIB, including the N-terminal domain, is required for U1
transcription.
On mRNA promoters, a platform for
recruitment of RNA polymerase II is created by the
binding of TBP and TFIIB to the TATA box. TFIIA stabilizes the complex
but is not absolutely required. In contrast, TFIIB is essential because
it then recruits the RNA polymerase II-TFIIF complex through
interactions with both RNA polymerase II and the small subunit
of TFIIF (61). TFIIB is composed of two functional domains,
a protease-resistant C-terminal domain and a protease-sensitive
N-terminal domain. The C-terminal domain is sufficient for association
with TBP bound to a TATA box, but it cannot direct basal RNA
polymerase II transcription (3, 7, 22, 26, 91) or
recruit the RNA polymerase II-TFIIF complex (22).
Our data indicate that U1 transcription requires TFIIB, including the
N-terminal domain, as well as TFIIF. This suggests that TFIIB performs
the same role on both mRNA and RNA polymerase II snRNA
promoters, namely, bridging DNA binding factors with the RNA
polymerase II-TFIIF complex. It is striking, however, that
transcription from the U1 promoter is more sensitive to small decreases
in the TFIIB concentration brought about by the anti-TFIIF and
anti-TFIIE depletions than transcription from the Ad2ML promoter (Fig.
7B and 9D). This suggests that TFIIB recruitment to the U1 promoter may
be less efficient than recruitment to the Ad2ML promoter. The affinity
of TFIIB for various mRNA promoters is determined in part by contacts
with the DNA sequence upstream of the TATA box (45). The
Ad2ML promoter has a good TFIIB binding site, but this may not be the
case for the U1 promoter. In addition, the protein-protein contacts
that mediate TFIIB recruitment to the Ad2ML and U1 promoters are likely
to be different.
TFIIA and TBP are required for U1 transcription.
The RNA
polymerase II core snRNA promoters do not contain a TATA
box. Instead, they consist of the PSE, which recruits
SNAPc and thus presumably nucleates the assembly of
the initiation complex. TBP is required for RNA polymerase II
snRNA gene transcription, but how it is recruited to the
TATA-less RNA polymerase II snRNA promoters is not clear.
Neither TFIID nor TFIIIB can complement a TBP-depleted extract
(73, 95), and recombinant TBP has some activity but fails to
reconstitute efficient transcription (73). In addition, as
shown here, recombinant TBP also fails to reconstitute efficient
transcription in a TFIIA-depleted extract, even though it does
reconstitute efficient transcription from the Ad2ML promoter. Significantly, however, a combination of TBP and TFIIA restores efficient transcription, suggesting that TFIIA somehow allows the
utilization of TBP by the U1 promoter. Together, these data are
consistent with TFIIA playing a much more crucial role in the
recruitment of TBP to basal snRNA promoters than in the
recruitment of TBP to basal TATA-containing mRNA promoters. Because
TFIIB is also required for U1 transcription, it is likely that
SNAPc, TBP, TFIIA, and TFIIB are all involved in the
establishment of the platform that can recruit the RNA
polymerase II-TFIIF complex.
TFIIE and TFIIH in U1 snRNA gene transcription.
In the
stepwise assembly of transcription complexes on mRNA promoters, the
recruitment of the RNA polymerase II-TFIIF complex is
followed by the recruitment of TFIIE and TFIIH. We have shown that
TFIIE is involved in RNA polymerase II transcription of
snRNA genes; however, we were unable to show convincingly that
TFIIH is required. Indeed, although treatment of extracts with
anti-TFIIH antibodies reduced U1 transcription dramatically, we could
restore transcription from linear templates nearly as efficiently with a mixture of GTFs missing TFIIH as with a mixture of GTFs containing TFIIH (data not shown). In contrast, addition of TFIIH was needed to
reconstitute transcription from the Ad2ML promoter. Because we cannot
exclude the presence of trace amounts of TFIIH in the RNA
polymerase II preparation, we can only conclude that in
our assay, U1 transcription either did not require TFIIH or
required much lower levels than transcription from the Ad2ML
promoter. If U1 transcription indeed did not require TFIIH, what would
then be the role of TFIIE? Two of TFIIE's functions are to recruit TFIIH and cooperate with TFIIH to bring about promoter melting, late in
preinitiation complex assembly. However, TFIIE has also been shown to
stimulate basal mRNA transcription from supercoiled templates in the
absence of TFIIH (28, 83, 93). Consistent with this
observation, TFIIE enhances the binding of TBP to the TATA box as
well as the cooperative binding of TFIIA and TBP to the Ad2ML
promoter and the small TFIIE subunit interacts directly with TFIIA
(93). Thus, TFIIE may also play a role early in
preinitiation complex assembly. It is quite possible that for RNA
polymerase II transcription of snRNA promoters, TFIIE helps
in the recruitment of TFIIA, TBP, and/or SNAPc to the promoter.
TFIIB is not involved in RNA polymerase III transcription
from the U6 promoter.
We also tested the roles of many of the GTFs
in RNA polymerase III transcription from both the U6 snRNA
promoter and the VAI promoter. RNA polymerase III transcription
from the VAI promoter and other promoters with gene-internal elements
requires the TBP-containing complex TFIIIB, which in mammalian cells
consists minimally of TBP and the human TFIIB-related factor (BRF)
(59), probably the same protein as another homolog of yeast
BRF referred to as human TFIIIB90 (69). However, we found
that human BRF is not required for transcription from the human U6
promoter in vitro (59). We therefore wondered whether the U6
promoter recruits instead the related protein TFIIB. Our results
clearly indicate that this is not the case, which is consistent with
the idea that recruiment of TFIIB to a promoter is the decisive step
towards specific recruitment of RNA polymerase II.
A role for TFIIA in U6 transcription?
TFIIA has been reported
previously to be required for U6 transcription in vitro, as well as for
transcription from several promoters with gene-internal elements,
including the VAI promoter (57, 87). We were unable to
demonstrate a TFIIA requirement for transcription from the VAI
promoter, consistent with other observations from both yeast and
mammalian systems (8, 33). With the U6 promoter, however,
depletion with anti-TFIIA antibodies severely inhibited transcription
but efficient transcription could be reconstituted by addition of
recombinant TBP. There are at least two possible interpretations for
these results. It is possible that TFIIA plays an antirepressor role
for basal U6 transcription in much the same way as it does for basal
RNA polymerase II transcription from the Ad2ML promoter, for
example, by displacing a repressor such as Mot1. Indeed, Mot1 is
capable of repressing transcription from the human U6 promoter in vitro
(8). Addition of excess recombinant TBP would then relieve
the need for TFIIA. It is also possible that depletion with anti-TFIIA
antibodies removes all of the TBP competent for U6 transcription; some
TBP associates with TFIIA on the anti-TFIIA beads (data not shown),
consistent with the previous observation that endogenous
Drosophila IIA associates with TBP in the absence of DNA
(12, 84, 92). A removal of the TBP competent for U6
transcription by the anti-TFIIA antibodies would imply that all such
TBP is complexed with TFIIA in extracts. This in turn would suggest
either that the TFIIA-TBP complex has to be broken apart to liberate
TBP for U6 transcription or, more likely, that the complex is recruited
as such to the U6 promoter. Thus, although we could not demonstrate a
role for TFIIA in U6 transcription in our assay, it remains possible
that TFIIA is indeed recruited to the U6 promoter in vivo.
We thank M. Tanaka and W. P. Tansey for GST-TFIIB expression
vectors; G. Binns for peptide synthesis; and E. Ford, R. W. Henry, B. Ma, V. Mittal, P. S. Pendergast, and C. L. Sadowski
for advice and reagents. We also thank R. Drapkin for providing
reagents and advice in the early stages of this work; D. Ma for
anti-IIA
and -
antibodies and TFIIA; S. Kim for TFIIB; K. P. Kumar for anti-IIEp34 antibodies; and E. Maldonado for TFIIE,
TBP, and anti-RAP74, anti-IIEp56, anti-RAP30, and anti-C-terminal
domain antibodies. The monoclonal ERCC3 antibodies were
characterized by G. Le Roy. We thank V. Mittal for comments on
the manuscript and M. Ockler, J. Duffy, and P. Renna for
artwork and photography.
This work was funded in part by NIH grants GM38810 to N.H. and GM37120
to D.R. N.H and D.R. are supported by the Howard Hughes Medical Institute.
| 1.
|
Akoulitchev, S.,
T. P. Makela,
R. A. Weinberg, and D. Reinberg.
1995.
Requirements for TFIIH kinase activity in transcription by RNA polymerase II.
Nature
377:557-560[Medline].
|
| 2.
|
Auble, D. T.,
K. E. Hansen,
C. G. Mueller,
W. S. Lane,
J. Thorner, and S. Hahn.
1994.
Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism.
Genes Dev.
8:1920-1934[Abstract/Free Full Text].
|
| 3.
|
Barberis, A.,
C. W. Müller,
S. C. Harrison, and M. Ptashne.
1993.
Delineation of two functional regions of transcription factor TFIIB.
Proc. Natl. Acad. Sci. USA
90:5628-5632[Abstract/Free Full Text].
|
| 4.
|
Bengal, E.,
O. Flores,
A. Krauskopf,
D. Reinberg, and Y. Aloni.
1991.
Role of the mammalian transcription factors IIF, IIS, and IIX during elongation by RNA polymerase II.
Mol. Cell. Biol.
11:1195-1206[Abstract/Free Full Text].
|
| 5.
|
Bernues, J.,
K. A. Simmen,
J. D. Lewis,
S. I. Gunderson,
M. Polycarpou-Schwarz,
V. Moncollin,
J.-M. Egly, and I. W. Mattaj.
1993.
Common and unique transcription factor requirements of human U1 and U6 snRNA genes.
EMBO J.
12:3573-3585[Medline].
|
| 6.
|
Bradsher, J. N.,
S. Tan,
H.-J. McLaury,
J. W. Conaway, and R. C. Conaway.
1993.
RNA polymerase II transcription factor SIII.
J. Biol. Chem.
268:25594-25603[Abstract/Free Full Text].
|
| 7.
|
Buratowski, S., and H. Zhou.
1993.
Functional domains of transcription factor TFIIB.
Proc. Natl. Acad. Sci. USA
90:5633-5637[Abstract/Free Full Text].
|
| 8.
|
Chicca, J. J.,
D. T. Auble, and B. F. Pugh.
1998.
Cloning and biochemical characterization of TAF-172, a human homolog of yeast Mot1.
Mol. Cell. Biol.
18:1701-1710[Abstract/Free Full Text].
|
| 9.
|
Cho, H.,
E. Maldonado, and D. Reinberg.
1997.
Affinity purification of human RNA polymerase II complex using monoclonal antibodies against transcription factor IIF.
J. Biol. Chem.
272:11495-11502[Abstract/Free Full Text].
|
| 10.
|
Conaway, J. W., and R. C. Conaway.
1990.
An RNA polymerase II transcription factor shares functional properties with Escherichia coli 70.
Science
248:1550-1553[Abstract/Free Full Text].
|
| 11.
|
Conaway, R. C.,
K. P. Garrett,
J. P. Hanley, and J. W. Conaway.
1991.
Mechanism of promoter selection by RNA polymerase II: mammalian transcription factors and promote entry of polymerase into the preinitiation complex.
Proc Natl. Acad. Sci. USA
88:6205-6209[Abstract/Free Full Text].
|
| 12.
|
Cortes, P.,
O. Flores, and D. Reinberg.
1992.
Factors involved in specific transcription by mammalian RNA polymerase II: purification and analysis of transcription factor IIA and identification of transcription factor IIJ.
Mol. Cell. Biol.
12:413-421[Abstract/Free Full Text].
|
| 13.
|
DeJong, J.,
R. Bernstein, and R. G. Roeder.
1995.
Human general transcription factor TFIIA; characterization of a cDNA encoding the small subunit and requirement for basal and activated transcription.
Proc. Natl. Acad. Sci. USA
92:3313-3317[Abstract/Free Full Text].
|
| 14.
|
Drapkin, R.,
J. T. Reardon,
A. Ansari,
J.-C. Huang,
L. Zawel,
K. Ahn,
A. Sancar, and D. Reinberg.
1994.
Dual role of TFIIH in DNA excision repair and in transcription by RNA polymerase II.
Nature
368:169-172.
|
| 15.
|
Dvir, A.,
K. P. Garrett,
C. Chalut,
J. M. Egly,
J. W. Conaway, and R. C. Conaway.
1996.
A role for ATP and TFIIIH in activation of the RNA polymerase II preinitiation complex prior to transcription initiation.
J. Biol. Chem.
271:7245-7258[Abstract/Free Full Text].
|
| 16.
|
Feaver, W. J.,
O. Gileadi,
Y. Li, and R. D. Kornberg.
1991.
CTD kinase associated with yeast RNA polymerase II initiation factor b.
Cell
67:1223-1230[Medline].
|
| 17.
|
Feaver, W. J.,
J. Q. Svejstrup,
L. Bardwell,
A. J. Bardwell,
S. Buratowski,
K. D. Gulyas,
T. F. Donahue,
E. C. Friedberg, and R. D. Kornberg.
1993.
Dual roles of a multiprotein complex from S. cerevisiae in transcription and DNA repair.
Cell
75:1379-1387[Medline].
|
| 18.
|
Feaver, W. J.,
J. Q. Svejstrup,
N. L. Henry, and R. D. Kornberg.
1994.
Relationship of CDK-activating kinase and RNA polymerase II CTD kinase TFIIH/TFIIK.
Cell
79:1103-1109[Medline].
|
| 19.
|
Flores, O.,
I. Ha, and D. Reinberg.
1990.
Factors involved in specific transcription by mammalian RNA polymerase II. Purification and subunit composition of transcription factor IIF.
J. Biol. Chem.
265:5629-5634[Abstract/Free Full Text].
|
| 20.
|
Flores, O.,
H. Lu,
M. Killeen,
J. Greenblatt,
Z. F. Burton, and D. Reinberg.
1991.
The small subunit of transcription factor IIF recruits RNA polymerase II into the preinitiation complex.
Proc. Natl. Acad. Sci. USA
88:9999-10003[Abstract/Free Full Text].
|
| 21.
|
Flores, O.,
E. Maldonado, and D. Reinberg.
1989.
Factors involved in specific transcription by mammalian RNA polymerase II. Factors IIE and IIF independently interact with RNA polymerase II.
J. Biol. Chem.
264:8913-8921[Abstract/Free Full Text].
|
| 22.
|
Ha, I.,
S. Roberts,
E. Maldonado,
X. Sun,
M. Green, and D. Reinberg.
1993.
Multiple functional domains of human transcription factor IIB. Distinct interactions with two general transcription factors and RNA polymerase II.
Genes Dev.
7:1021-1032[Abstract/Free Full Text].
|
| 23.
|
Harlow, E., and D. Lane.
1988.
Antibodies: a laboratory manual.
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
|
| 24.
|
Henry, R. W.,
V. Mittal,
B. Ma,
R. Kobayashi, and N. Hernandez.
1998.
Assembly of a functional, core promoter complex (SNAPc) shared by RNA polymerase II and III.
Genes Dev.
12:2664-2672[Abstract/Free Full Text].
|
| 25.
|
Hernandez, N.
1992.
Transcription of vertebrate snRNA genes and related genes, p. 281-313.
In
S. L. McKnight, and K. R. Yamamoto (ed.), Transcriptional regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
|
| 26.
|
Hisatake, K.,
R. G. Roeder, and M. Horikoshi.
1993.
Functional dissection of TFIIB domains required for TFIIB-TFIID-promoter complex formation and basal transcription activity.
Nature
363:744-747[Medline].
|
| 27.
|
Holstege, F. C.,
U. Fiedler, and H. T. Timmers.
1997.
Three transitions in the RNA polymerase II transcription complex during initiation.
EMBO J.
16:7468-7480[Medline].
|
| 28.
|
Holstege, F. C. P.,
D. Tantin,
M. Carey,
P. C. van der Vilet, and H. T. M. Timmers.
1995.
The requirement for the basal transcription factor IIE is determined by the helical stability of promoter DNA.
EMBO J.
14:810-819[Medline].
|
| 29.
|
Holstege, F. C. P.,
P. C. van der Vliet, and H. T. M. Timmers.
1996.
Opening of an RNA polymerase II promoter occurs in two distinct steps and requires the basal transcription factors IIE and IIH.
EMBO J.
15:1666-1677[Medline].
|
| 30.
|
Inostroza, J. A.,
F. H. Mermelstein,
I. Ha,
W. S. Lane, and D. Reinberg.
1992.
Dr1, a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription.
Cell
70:477-489[Medline].
|
| 31.
|
Izban, M. G., and D. S. Luse.
1992.
The RNA polymerase II ternary complex cleaves the nascent transcript in a 3' to 5' direction in the presence of elongation factor SII.
Genes Dev.
6:1342-1356[Abstract/Free Full Text].
|
| 32.
|
Jiang, Y.,
M. Yan, and J. D. Gralla.
1996.
A three-step pathway of transcription initiation leading to promoter clearance at an activated RNA polymerase II promoter.
Mol. Cell Biol.
16:1614-1621[Abstract].
|
| 33.
|
Kang, J. J.,
D. T. Auble,
J. A. Ranish, and S. Hahn.
1995.
Analysis of the yeast transcription factor TFIIA: distinct functional regions and a polymerase II-specific role in basal and activated transcription.
Mol. Cell. Biol.
15:1234-1243[Abstract].
|
| 34.
|
Kaufmann, J.,
K. Ahrens,
R. Koop,
S. T. Smale, and R. Muller.
1998.
CIF150, a human cofactor for transcription for IID-dependent initiator function.
Mol. Cell. Biol.
18:233-239[Abstract/Free Full Text].
|
| 35.
|
Kaufmann, J., and S. T. Smale.
1994.
Direct recognition of initiator elements by a component of the transcription factor IID complex.
Genes Dev.
8:821-829[Abstract/Free Full Text].
|
| 36.
|
Kephart, D. D.,
B. Q. Wang,
Z. F. Burton, and D. H. Price.
1994.
Functional analysis of Drosophila factor 5 (TFIIF), a general transcription factor.
J. Biol. Chem.
269:13536-13543[Abstract/Free Full Text].
|
| 37.
|
Killeen, M., and J. Greenblatt.
1992.
The general transcription factor RAP30 binds to RNA polymerase II and prevents it from binding nonspecifically to DNA.
Mol. Cell. Biol.
12:30-37[Abstract/Free Full Text].
|
| 38.
|
Kim, T. K., and T. Maniatis.
1997.
The mechanism of transcriptional synergy of an in vitro assembled interferon-beta enhanceosome.
Mol. Cell
1:119-129[Medline].
|
| 39.
|
Kim, Y. J.,
S. Bjorklund,
Y. Li,
H. M. Sayre, and R. d. Kornberg.
1994.
A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II.
Cell
77:599-608[Medline].
|
| 40.
|
Kobayashi, N.,
P. J. Horn,
S.M. Sullivan,
S. J. Triezenberg,
T. G. Boyer, and A. J. Berk.
1998.
DA-complex assembly activity required for VP16C transcriptional activation.
Mol. Cell. Biol.
18:4023-4031[Abstract/Free Full Text].
|
| 41.
|
Kokubo, T.,
M. J. Swanson,
J. I. Nishikawa,
A. G. Hinnebusch, and Y. Nakatani.
1998.
The yeast TAF145 inhibitory domain and TFIIA competitively bind to TATA-binding protein.
Mol. Cell. Biol.
18:1003-1012[Abstract/Free Full Text].
|
| 42.
|
Koleske, A. J., and R. A. Young.
1994.
An RNA polymerase II holoenzyme responsive to activators.
Nature
368:466-469[Medline].
|
| 43.
|
Kretzschmar, M.,
M. Meisterernst, and R. G. Roeder.
1993.
Identification of human DNA topoisomerase I as a cofactor for activator-dependent transcription by RNA polymerase II.
Proc. Natl. Acad. Sci. USA
90:11508-11512[Abstract/Free Full Text].
|
| 44.
|
Kumar, K. P.,
S. Akoulitchev, and D. Reinberg.
1998.
Promoter-proximal stalling results from the inability to recruit transcription factor IIH to the transcription complex and is a regulated event.
Proc. Natl. Acad. Sci. USA
95:9767-9772[Abstract/Free Full Text].
|
| 45.
|
Lagrange, T.,
A. N. Kapanidis,
H. Tang,
D. Reinberg, and R. H. Ebright.
1998.
New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB.
Genes Dev.
12:34-44[Abstract/Free Full Text].
|
| 46.
|
Lobo, S., and N. Hernandez.
1989.
A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter.
Cell
58:55-67[Medline].
|
| 47.
|
Lobo, S. M., and N. Hernandez.
1994.
Transcription of snRNA gene by RNA polymerases II and III, p. 127-159.
In
R. C. Conaway, and J. W. Conaway (ed.), Transcription, mechanisms and regulation. Raven Press, Ltd., New York, N.Y.
|
| 48.
|
Lobo, S. M.,
J. Lister,
M. L. Sullivan, and N. Hernandez.
1991.
The cloned RNA polymerase II transcription factor IID selects RNA polymerase III to transcribe the human U6 gene in vitro.
Genes Dev.
5:1477-1489[Abstract/Free Full Text].
|
| 49.
|
Lobo, S. M.,
M. Tanaka,
M. L. Sullivan, and N. Hernandez.
1992.
A TBP complex essential for transcription from TATA-less but not TATA-containing RNA polymerase III promoters is part of the TFIIIB fraction.
Cell
71:1029-1040[Medline].
|
| 50.
|
Lu, H.,
L. Zawel,
L. Fisher,
J.-M. Egly, and D. Reinberg.
1992.
Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II.
Nature
358:641-645[Medline].
|
| 51.
|
Ma, D.,
I. Olave,
A. Merino, and D. Reinberg.
1996.
Separation of the transcriptional coactivator and antirepression functions of transcription factor IIA.
Proc. Natl. Acad. Sci. USA
93:6583-6588[Abstract/Free Full Text].
|
| 52.
|
Ma, D.,
H. Watanabe,
F. Mermelstein,
A. Admon,
K. Oguri,
S. Sun,
T. Wada,
T. Imai,
T. Shiroya,
D. Reinberg, and H. Handa.
1993.
Isolation of a cDNA encoding the largest subunit of TFIIA reveals functions important for activated transcription.
Genes Dev.
7:2246-2257[Abstract/Free Full Text].
|
| 53.
|
Maldonado, E.,
R. Drapkin, and D. Reinberg.
1996.
Purification of human RNA polymerase II and general transcription factors.
Methods Enzymol.
274:72-100[Medline].
|
| 54.
|
Maldonado, E.,
R. Shiekhattar,
M. Sheldon,
H. Cho,
R. Drapkin,
P. Rickert,
E. Lees,
C. W. Anderson,
S. Linn, and D. Reinberg.
1996.
A human RNA polymerase II complex associated with SRB and DNA-repair proteins.
Nature
381:86-89[Medline].
|
| 55.
|
Martinez, E.,
C. M. Chiang,
H. Ge, and R. G. Roeder.
1994.
TAFs in TFIID function through the initiator to direct basal transcription from a TATA-less class II promoter.
EMBO J.
13:3115-3126[Medline].
|
| 56.
|
Martinez, E.,
H. Ge,
Y. Tao,
C. X. Yuan,
V. Palhan, and R. G. Roeder.
1998.
Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex.
Mol. Cell. Biol.
18:6571-6583[Abstract/Free Full Text].
|
| 57.
|
Meissner, W.,
R. Holland,
R. Waldschmidt, and K. H. Seifart.
1993.
Transcription factor IIA stimulates the expression of classical pol III-genes.
Nucleic Acids Res.
21:1013-1018[Abstract/Free Full Text].
|
| 58.
|
Merino, A.,
K. Madden,
W. S. Lane,
J. Champoux, and D. Reinberg. |