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Laboratory of Biochemistry and Molecular Biology, The Rockefeller
University, 1230 York Avenue, New York, NY 10021
Contributed by Robert G. Roeder, October 31, 2000
Transcription factor IIIB (TFIIIB) is directly involved in
transcription initiation by RNA polymerase III in eukaryotes. Yeast contain a single TFIIIB activity that is comprised of the TATA-binding protein (TBP), TFIIB-related factor 1 (BRF1), and TFIIIB'', whereas two
distinct TFIIIB activities, TFIIIB- In the yeast
Saccharomyces cerevisiae, all genes transcribed by RNA
polymerase III depend on essential promoter elements that are localized
downstream of the transcription initiation site. These promoter
elements are recognized by the multisubunit transcription factor IIIC
(TFIIIC) (or by TFIIIA and TFIIIC) and the resulting complex in turn
recruits TFIIIB. Yeast TFIIIB activity has been assigned to the
TATA-binding protein (TBP), TFIIB-related factor 1 (BRF1), and the
TFIIIB'' component (1-3). These three components have been shown to be
necessary and sufficient for reconstitution of yeast tRNA and U6 RNA
gene transcription in appropriate cell-free systems (reviewed in refs.
4 and 5).
In human cells, two generally distinct types of promoters direct RNA
polymerase III transcription. The promoters of tRNA, VA RNA, and 5S RNA
genes are internal to the gene and consist of either A- and B-boxes
(tRNA and VA RNA) or A- and C-boxes (5S RNA). In contrast, the
promoters of U6 and 7SK RNA genes lie upstream of the transcription
initiation site and consist of the distal sequence element, the
proximal sequence element (PSE), and a TATA-box. Gene-internal
promoters are recognized by TFIIIC (or by TFIIIA and TFIIIC in the case
of the 5S RNA gene; reviewed in ref. 6), whereas the gene-external
promoters are recognized by Oct-1 and the PSE transcription factor
(reviewed in ref. 7). As a consequence, two distinct TFIIIB activities,
designated hTFIIIB- Here we report the identification, cloning, and characterization
of TFIIIB50, a protein with sequence homology to TFIIB and TFIIIB90. A
complex of TFIIIB50 and four tightly associated factors constitutes,
together with TBP and TFIIIB150, the complete TFIIIB- Plasmids.
ph7SK and ptRNA have been described (6, 13).
Reconstituted in Vitro Transcription System.
cEDF 0.2 and cEDF 1 M KCl fractions were obtained by chromatography of
the phosphocellulose P11 0.6 fraction (fraction C) over
EMD-DEAE-Fractogel (EDF; Merck) and elution with 200 mM and 1 M KCl,
respectively, in BC buffer (20 mM Hepes, pH 7.9/10% glycerol/3mM DTT/0.2 mM PMSF). Of the known RNA polymerase III transcription factor activities, the cEDF 0.2 fraction contains TFIIIC0, TFIIIC1 (14,
15), and the TFIIIB50 complex described here, whereas the cEDF 1 M
fraction contains the PSE transcription factor (16), TFIIIC2, and RNA
polymerase III itself (6). Expression and purification of rhTBP and
TFIIIIB150 were as described (ref. 17; unpublished observations).
Purification of the FLAG/Hemagglutinin (HA)-hTFIIIB50 Complex.
The generation of a HeLa cell line that stably expresses FLAG- and
HA-tagged hTFIIIB50 was as described (13). The complex was purified
essentially as described (13) except that 500 mM KCl was used for
incubation of the extracts with M2 agarose and for subsequent wash
steps. The complex was eluted from M2 agarose by incubation with 200 ng/µl FLAG peptide in BC buffer containing 60 mM KCl for 30 min at room temperature.
Peptide Sequences.
Proteins were blotted onto poly(vinylidene difluoride) membrane after
SDS/4-20% PAGE, excised, and digested with LysC. The following
internal peptide sequences were obtained: p30 (calcyclin-binding protein), PAAVVAPITTGYTVK; p40, (S)YADSYYYEDGGMK and
(D)LEQQDCEIAQEIQEK; p50 We showed previously that whereas anti-hTFIIIB90 antibodies
deplete VA, tRNA, 5S, U6, and 7SK transcription activity from nuclear
extracts, readdition of rhTFIIIB90 is able to restore transcription
from VA, tRNA, and 5S genes but not U6 or 7SK genes (18). This finding
led us to search for a protein that was depleted by anti-hTFIIIB90
antibodies and was required for U6/7SK transcription. For this
purpose, we established a 7SK transcription system comprised of
partially purified fractions (Materials and Methods) and
determined by immuno-depletion which fraction contained such a factor.
Anti-hTFIIIB90 Antibodies Deplete an Activity from the cEDF 0.2 Fraction That Is Essential for 7SK Transcription.
The cEDF 0.2 fraction was found to contain a factor that is essential
for 7SK transcription and that could be specifically depleted by
anti-hTFIIIB90 antibodies but not by control antibodies (Fig.
1, compare lanes 3-5). The corresponding
Western blot showed that the cEDF 0.2 fraction does not contain any
detectable hTFIIIB90 (Fig. 2A,
lane 1), suggesting that a protein different from hTFIIIB90 was
depleted from the cEDF 0.2 fraction. This surprising finding led us to
search for the protein(s) that had been depleted by the anti-hTFIIIB90
antibodies and that were required for 7SK transcription. Antibodies
against hTFIIIB90 predominantly and specifically retained proteins of
30 and 40 kDa as well as a doublet of 50-kDa proteins from the cEDF 0.2 fraction, and these proteins could be eluted with 0.1 M glycine, pH 2.6 (Fig. 2B; data not shown). Of these proteins, only a
40-kDa polypeptide was recognized by anti-hTFIIIB90 antibodies in a
Western blot analysis (Fig. 2A, lane 3). Although this protein band appears irrelevant for 7SK/U6 transcription (below), its recognition by anti-hTFIIIB90 antibodies has been confirmed in experiments with the corresponding recombinant protein (data not shown). Moreover, although anti-hTFIIIB90 antibodies apparently recognize and coimmunoprecipitate a TFIIIB90-related 50-kDa
protein in the cEDF 0.2 fraction (below), they do not appear to
recognize this protein after denaturation and Western blot analysis
(Fig. 2A).
Biochemistry
A stable complex of a novel transcription factor IIB- related
factor, human TFIIIB50, and associated proteins mediate selective
transcription by RNA polymerase III of genes with upstream
promoter elements
Abstract
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Abstract
Introduction
Materials and Methods
Results
Discussion
References
and TFIIIB-
, have been described in human cells. Human TFIIIB- is required for
transcription of genes with internal promoter elements, and contains
TBP, a TFIIIB'' homologue (TFIIIB150), and a BRF1 homologue (TFIIIB90), whereas TFIIIB- is required for transcription of genes with promoter elements upstream of the initiation site. Here we describe the identification, cloning, and characterization of TFIIIB50, a novel homologue of TFIIB and TFIIIB90. TFIIIB50 and tightly associated factors, along with TBP and TFIIIB150, reconstitute human TFIIIB- activity. Thus, higher eukaryotes, in contrast to the yeast
Saccharomyces cerevisiae, have evolved two distinct
TFIIB-related factors that mediate promoter selectivity by RNA
polymerase III.
Introduction
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
and hTFIIIB-, function with TFIIIC-bound
internal promoters or PSE transcription factor-bound external
promoters, respectively (8). Human TFIIIB- (hTFIIIB-) has
been reconstituted from recombinant human (rh)TBP, rhTFIIIB90 (related
in sequence to TFIIB), and rhTFIIIB150 that is related to the yeast
TFIIIB'' component (unpublished observations), whereas hTFIIIB- is
less well characterized. The hTFIIIB- activity isolated by DEAE
chromatography was shown to support U6, but not VA1, transcription in
crude reconstituted systems (8). It then was demonstrated that this
hTFIIIB- activity could be replaced either by S. cerevisiae TFIIIB'' (9) or its human homologue rhTFIIIB150
(unpublished observations). These studies also showed that hTFIIIB-
activity is not stably associated with TBP (8) and that it does not
contain hTFIIIB90 (9). In agreement, it was reported that hTFIIIB90 is
dispensable for, or even represses, U6 or 7SK transcription (ref. 10;
unpublished observations). Recently, McCulloch and colleagues (11)
reported the identification of a differentially spliced variant of
hTFIIIB90 (BRF2) that was reported, as part of a poorly characterized
immunopurified complex, to reconstitute U6 transcription in a nuclear
extract that had been depleted with anti-BRF2 antibodies. This result
suggested that BRF2 might be the TFIIB-related protein that is required for RNA polymerase III transcription of genes with upstream promoter elements.
activity that
is required for transcription of U6 or 7SK genes in vertebrates. During
preparation of this manuscript, Hernandez and colleagues (12) reported
the cloning of a factor, designated BRFU, that is identical to
hTFIIIB50 (12).
Materials and Methods
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Abstract
Introduction
Materials and Methods
Results
Discussion
References
(elongation factor 1),
XGDAAIVDMVP(G)K; and p50 (hTFIIIB50), RPASPALLLPPCMLK.
Results
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Abstract
Introduction
Materials and Methods
Results
Discussion
References
View larger version (24K):
[in a new window]
Fig. 1.
Inhibition of 7SK transcription by anti-hTFIIIB90 antibodies.
Transcription reactions in lanes 1-5 were reconstituted with 24 ng
rhTFIIIB150 and 40 ng rhTBP. The following protein fractions were added
to individual reactions: lanes 1 and 3-5, 1.5 µl cEDF 1 M; lanes 2 and 3, 20 µl cEDF 0.2; lane 4, 20 µl flow-through (FT) from
anti-hTFIIIB90 antibodies that had been incubated with a cEDF 0.2 fraction; and lane 5, 20 µl flow-through from nonrelevant antibodies
that had been incubated with a cEDF 0.2 fraction. Immuno-depletion is
described in Materials and Methods. Transcription
reactions were performed as described (13).
View larger version (17K):
[in a new window]
Fig. 2.
Purification of hTFIIIB50 from HeLa cells and expression of the
recombinant protein in E. coli. (A)
Western blot with anti-hTFIIIB90 antibodies. The following fractions
were separated by SDS/12.5% PAGE: lane 1, 10 µl cEDF 0.2; lane 2, 10 µl flow-through (FT) from the anti-hTFIIIB90 antibody column, onto
which a cEDF 0.2 fraction had been loaded; lane 3, 10 µl eluate from
the anti-hTFIIIB90 antibody depletion; lane 4, 1.5 µl cEDF 1 M; and
lane 5, 2.5 ng rhTFIIIB90. cEDF fractions and rhTFIIIB90 were purified
as described (Materials and Methods; ref. 18).
SDS/PAGE and Western blot procedures were essentially as described
(8). (B) SDS/12.5% PAGE. Ten microliters of protein
fractions that were retained from a cEDF 0.2 fraction by the
anti-hTFIIIB90 antibody column and eluted with 0.1 M glycine, pH 2.6 was neutralized and separated by SDS/PAGE and stained with
Coomassie brilliant blue (8). (C) SDS/10%
PAGE. Two micrograms of recombinant Ni-NTA agarose purified hTFIIIB50
was separated by SDS/PAGE. Purification of the recombinant protein
and SDS/PAGE were as described (8).
Identification of hTFIIIB50.
We obtained internal protein sequences of tryptic peptides from
the four major protein bands that could be eluted from anti-hTFIIIB90 immunoprecipitates and that were identified on SDS/PAGE
(Materials and Methods). Peptide sequences from the
30-kDa protein (p30) matched the sequence of the calcyclin-binding
protein (CACYBP; GenBank accession no. GI7656952), those of the
40-kDa protein (p40) matched expressed sequence tags coding for a
protein of unknown function (p40; GenBank accession nos. AA101892,
AI111898, AI180527, and AA835673), and those from one of the 50-kDa protein bands matched translation elongation factor 1 (EF1; GenBank accession no. GI1070665). However, neither the corresponding recombinant proteins (CACYBP, p40, and EF1) nor the cognate
antibodies showed any effect on, and appear to be irrelevant to,
in vitro transcription of the 7SK/U6 genes (data not shown).
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hTFIIIB50 Is Specifically Required for RNA Polymerase III Transcription of Genes with Upstream Promoter Elements. Because antibodies against hTFIIIB90 depleted hTFIIIB50 from the cEDF 0.2 fraction (Fig. 3A, lane 3) and at the same time depleted 7SK gene transcription activity from this fraction (Fig. 1, lane 4), we determined whether anti-hTFIIIB50 antibodies were similarly able to deplete 7SK gene transcription activity from the cEDF 0.2 fraction. As shown in Fig. 4, depletion of hTFIIIB50 from a cEDF 0.2 fraction severely inhibited transcription of the 7SK gene (Upper, compare lanes 2 and 3 and lanes 4 and 5). In contrast, depletion of hTFIIIB50 from the same cEDF 0.2 fraction did not inhibit, but instead slightly stimulated, tRNA transcription in a system reconstituted with partially purified transcription factors (Fig. 4 Lower, compare lanes 2 and 3 and lanes 4 and 5). This result clearly indicates a specific requirement for hTFIIIB50 in transcription of genes with upstream promoter elements by RNA polymerase III.
|
A Complex of hTFIIIB50 and Stably Associated Factors Is Required for 7SK/U6 Transcription. We next tested the ability of increasing amounts of bacterially expressed and affinity-purified rhTFIIIB50 to restore 7SK transcription activity to the reconstitution system that had been depleted of hTFIIIB50. Surprisingly, rhTFIIIB50 alone was not able to restore 7SK gene transcription activity to the immuno-depleted reconstitution system (Fig. 5C, lanes 4-8). Because modification of hTFIIIB50 or stable association with additional transcription factors were possible explanations for the inability of rhTFIIIB50 to restore transcription, we generated HeLa S cell lines that stably express epitope-tagged hTFIIIB50. We were able to purify a complex of hTFIIIB50 and associated factors from a cell line stably expressing N-terminally FLAG- and HA-tagged hTFIIIB50 (fHA-B50). fHA-B50 was retained by M2 agarose (containing anti-FLAG antibody) from extracts of HeLa cells stably expressing fHA-B50 and could be specifically eluted by FLAG peptide (Fig. 5 A and B, lane 2), but no hTFIIIB50 was retained by (or eluted from) M2 agarose with extracts from nontransfected HeLa cells (Fig. 5 A and B, lane 1). In addition to fHA-B50, proteins of 54, 48, 42, and 40 kDa were selectively retained by and eluted with FLAG peptide from M2 agarose that had been incubated with extracts from HeLa cells that stably express fHA-B50. These proteins were not present in M2 agarose-bound and eluted fractions from control cells not expressing fHA-B50 (Fig. 5A, compare lanes 1 and 2). The complex of fHA-B50 and associated factors then was analyzed for its ability to reconstitute transcription in a system of partially purified fractions that had been immuno-depleted of hTFIIIB50. The fHA-B50 complex, but not a preparation from a control cell line, was able to fully restore 7SK transcription in this reconstitution system (Fig. 5D, compare lanes 7 and 8 with lanes 9 and 10).
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activity for transcription of U6/7SK genes in humans.
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Discussion |
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Abstract
Introduction
Materials and Methods
Results
Discussion
References
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Gene selectivity through structural variations in the general
transcription machinery was first evident from identification of
functionally distinct nuclear RNA polymerases with common, related, and
distinct subunits (19), and subsequently extended through the
demonstration of TBP-related factors (20) and TFIIB-related factors
(21) with altered specificity within the same organism. The distinct
hTFIIIB activities (hTFIIIB- and hTFIIIB-) that were described
earlier (8) are now understood at the molecular level and reflect,
minimally, the presence of distinct TFIIB-related proteins from
distinct genes. Thus, it is clear that the evolution from yeast to
humans of promoter elements within the genes transcribed by RNA
polymerase III has been accompanied by the coevolutionary appearance of
an additional TFIIB-related factor. The diversified set of promoter
elements and the corresponding increase in complexity of DNA-binding
transcription factors (Introduction) might allow or require the
utilization of distinct TFIIB-related factors for achieving a more
sophisticated regulation of RNA polymerase III transcription in
vertebrates than in the unicellular eukaryote S. cerevisiae.
Complete hTFIIIB- Activity Is Composed of TBP, hTFIIIB150, and a
Complex of hTFIIIB50 and Associated Proteins.
In this report, we describe the molecular composition of hTFIIIB-
activity, as it appears to be required for in vitro
transcription of 7SK and U6 genes. The data confirm, at the molecular
level, the existence of two distinct hTFIIIB activities as previously shown (8). According to data presented here, the complete
hTFIIIB- activity is composed of TBP, hTFIIIB150 (related to the
S. cerevisiae TFIIIB''), and a complex containing both a
novel TFIIB-related factor (hTFIIIB50) and at least four stably
associated proteins. The nature of the reconstitution system used in
earlier studies of the hTFIIIB- activity (8, 9) only monitored the
hTFIIIB150 activity, because all of the other components of complete
hTFIIIB- also were provided by the reconstituted transcription
system. Nevertheless, the originally purified hTFIIIB- fractions
also contain hTFIIIB50 in addition to hTFIIIB150 (data not shown). Whether they also contain the hTFIIIB50-associated factors described here is not yet known. However, the association of TBP with hTFIIIB- activity appears to be weak, and it has not been clarified which source
of TBP is required for transcription of U6/7SK genes in vivo. Recently, a complex of TBP and TFIIA has been described that
could have such a function (22).
TFIIIB50 Forms a Stable Complex with Associated Factors in HeLa
Cells.
hTFIIIB- and TFIIIB- activities contain TBP, hTFIIIB150, and a
specific TFIIB-related factor, and are thus generally conserved in
structure from yeast to human. The individual TFIIB-related factors
(hTFIIIB90 and hTFIIIB50) specific to hTFIIIB- versus hTFIIIB-
are likely involved in conferring promoter specificity to RNA
polymerase III, but also might depend on associated factors for doing
so. In HeLa cells, hTFIIIB90 forms an extremely stable complex with
TBP, whereas other proteins (e.g. TFIIIB150) seem to be either
transiently or loosely associated with hTFIIIB90 (data not shown). In
sharp contrast, hTFIIIB50 forms a highly stable complex with four
associated proteins, and this complex is stable to immuno-purification
in the presence of high salt (500 mM KCl; Fig. 5A, lane 2).
Furthermore, immuno-depletion of hTFIIIB50 from the cEDF 0.2 fraction
in the presence of 2 M urea with polyclonal anti-hTFIIIB50 antibodies
abolishes transcription of the 7SK gene, and restoration of
transcription activity is not mediated by rhTFIIIB50 but requires the
complex of hTFIIIB50 and associated factors (data not shown). One
explanation for these observations is that the hTFIIIB50 complex is
very stable and resists dissociation by incubation with high salt or
2 M urea. Alternatively, it might be that antibody treatment
disrupts the complex of hTFIIIB50 and associated factors under certain
circumstances and that the complex is unable to reform upon subsequent
addition of rhTFIIIB50. Whatever the explanation, rhTFIIIB50 alone is
unable to restore transcription of the 7SK/U6 gene under our assay conditions.
The Proteins Associated with hTFIIIB50.
The cDNAs encoding the proteins that form a complex with hTFIIIB50
have not yet been cloned. Hence we do not know whether these proteins
are completely distinct or potentially related. The fact that the
smaller (42 and 40 kDa) polypeptides appear to be substoichiometric may
reflect derivitization (e.g., by proteolysis) from larger components,
differential staining properties, or differential cellular levels of
these proteins. We originally had identified hTFIIIB50 by an
immuno-purification procedure with anti-hTFIIIB90 antibodies that also
yielded proteins of 30 kDa (calcyclin-binding protein), 40 kDa, and 50 kDa (elongation factor 1). However, these proteins were not detected
in the fHA-hTFIIIB50-complex by Western blot analyses (data not shown),
consistent with their failure to show any effects on 7SK gene transcription.
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Acknowledgements |
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This work has been supported by National Institutes of Health Grant CA42567 to R.G.R. and postdoctoral fellowships from the Deutsche Forschungsgemeinschaft (DFG) and the Leukemia Research Foundation to M.T.
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Abbreviations |
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TBP, TATA-binding protein; TF, transcription factor; hTF, human TF; rh, recombinant human; EDF, EMD-DEAE-Fractogel; cEDF, EDF fraction C; HA, hemagglutinin; fHA, FLAG-HA.
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Footnotes |
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* To whom reprint requests should be addressed. E-mail: roeder{at}rockvax.rockefeller.edu.
Data deposition: The sequence reported in this paper has been deposited in the GenBank database (accession no. AF206673).
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Introduction
Materials and Methods
Results
Discussion
References
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 S. Weser, J. Riemann, K. H. Seifart, and W. Meissner Assembly and isolation of intermediate steps of transcription complexes formed on the human 5S rRNA gene Nucleic Acids Res., May 1, 2003; 31(9): 2408 - 2416. [Abstract] [Full Text] [PDF]
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Y. Huang, E. McGillicuddy, M. Weindel, S. Dong, and R. J. Maraia The fission yeast TFIIB-related factor limits RNA polymerase III to a TATA-dependent pathway of TBP recruitment Nucleic Acids Res., April 15, 2003; 31(8): 2108 - 2116. [Abstract] [Full Text] [PDF]
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 S. Jin, M. Kalkum, M. Overholtzer, A. Stoffel, B. T. Chait, and A. J. Levine CIAP1 and the serine protease HTRA2 are involved in a novel p53-dependent apoptosis pathway in mammals Genes & Dev., February 1, 2003; 17(3): 359 - 367. [Abstract] [Full Text] [PDF]
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P. Hu, S. Wu, Y. Sun, C.-C. Yuan, R. Kobayashi, M. P. Myers, and N. Hernandez Characterization of Human RNA Polymerase III Identifies Orthologues for Saccharomyces cerevisiae RNA Polymerase III Subunits Mol. Cell. Biol., November 15, 2002; 22(22): 8044 - 8055. [Abstract] [Full Text] [PDF]
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B. Ma and N. Hernandez Redundant Cooperative Interactions for Assembly of a Human U6 Transcription Initiation Complex Mol. Cell. Biol., November 15, 2002; 22(22): 8067 - 8078. [Abstract] [Full Text] [PDF]
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L. Schramm and N. Hernandez Recruitment of RNA polymerase III to its target promoters Genes & Dev., October 15, 2002; 16(20): 2593 - 2620. [Full Text] [PDF]
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P. Cabart and S. Murphy Assembly of Human Small Nuclear RNA Gene-specific Transcription Factor IIIB Complex de Novo On and Off Promoter J. Biol. Chem., July 19, 2002; 277(30): 26831 - 26838. [Abstract] [Full Text] [PDF]
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A. Ishiguro, G. A. Kassavetis, and E. P. Geiduschek Essential Roles of Bdp1, a Subunit of RNA Polymerase III Initiation Factor TFIIIB, in Transcription and tRNA Processing Mol. Cell. Biol., May 15, 2002; 22(10): 3264 - 3275. [Abstract] [Full Text] [PDF]
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W. Meissner, R. Thomae, and K. H. Seifart The Activity of Transcription Factor IIIC1 Is Impaired during Differentiation of F9 Cells J. Biol. Chem., February 22, 2002; 277(9): 7148 - 7156. [Abstract] [Full Text] [PDF]
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P. Cabart and S. Murphy BRFU, a TFIIB-like Factor, Is Directly Recruited to the TATA-box of Polymerase III Small Nuclear RNA Gene Promoters through Its Interaction with TATA-binding Protein J. Biol. Chem., November 9, 2001; 276(46): 43056 - 43064. [Abstract] [Full Text] [PDF]
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