1: BMC Evol Biol. 2005 Feb 13;5(1):15. 

The architecture of mammalian ribosomal protein promoters.

Perry RP.

Fox Chase Cancer Center Philadelphia, PA 19111, USA. RP_Perry@fccc.edu

BACKGROUND: Mammalian ribosomes contain 79 different proteins encoded by widely
scattered single copy genes. Coordinate expression of these genes at
transcriptional and post-transcriptional levels is required to ensure a roughly
equimolar accumulation of ribosomal proteins. To date, detailed studies of only
a very few ribosomal protein (rp) promoters have been made. To elucidate the
general features of rp promoter architecture, I made a detailed sequence
comparison of the promoter regions of the entire set of orthologous human and
mouse rp genes. RESULTS: A striking evolutionarily conserved feature of most rp
genes is the separation by an intron of the sequences involved in
transcriptional and translational regulation from the sequences with protein
encoding function. Another conserved feature is the polypyrimidine initiator,
which conforms to the consensus (Y)2C+1TY(T)2(Y)3. At least 60 % of the rp
promoters contain a largely conserved TATA box or A/T-rich motif, which should
theoretically have TBP-binding capability. A remarkably high proportion of the
promoters contain conserved binding sites for transcription factors that were
previously implicated in rp gene expression, namely upstream GABP and Sp1 sites
and downstream YY1 sites. Over 80 % of human and mouse rp genes contain a
transposable element residue within 900 bp of 5' flanking sequence; very little
sequence identity between human and mouse orthologues was evident more than 200
bp upstream of the transcriptional start point. CONCLUSIONS: This analysis has
provided some valuable insights into the general architecture of mammalian rp
promoters and has identified parameters that might coordinately regulate the
transcriptional activity of certain subsets of rp genes.

PMID: 15707503 [PubMed - in process]


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2: Biochem J. 2005 Jul 1;389(Pt 1):37-46. 

In vivo DNase I-mediated footprinting analysis along the human bradykinin B1
receptor (BDKRB1) gene promoter: evidence for cell-specific regulation.

Angers M, Drouin R, Bachvarova M, Paradis I, Bissell B, Hiromura M, Usheva A,
Bachvarov D.

Unite de Recherche en Genetique Humaine et Moleculaire, Research Centre, Hopital
St-Francois d'Assise, Centre Hospitalier Universitaire de Quebec, 10 de
l'Espinay Street, QC, G1L 3L5, Canada.

By applying in vivo dimethyl sulphate and UV light type C-footprinting analysis,
we previously showed that specific DNA sequences in the -1349/+42 core promoter
region of the inducible human BDKRB1 (bradykinin B1 receptor) gene correlated
with its transcriptional activity. In the present study we used the highly
sensitive DNase I in vivo footprinting approach to delineate more precisely the
functional domains of the BDKRB1 gene promoter in human SMCs (smooth muscle
cells). Human lymphocytes that do not express a functional BDKRB1 were also
studied as a reference using dimethyl sulphate, UV light type C and DNase I
treatments. An obvious difference was found in the DNase I-footprinting patterns
between cellular systems that express a functional BDKRB1 (SMCs) in comparison
with human lymphocytes, where randomly distributed nucleosome-like footprinting
patterns were found in the bulk of the core promoter region studied. Gel-shift
assays and expression studies pointed to the implication of the YY1 and a
TBP/TFIIB (TATA-box-binding protein/transcription factor IIB) transcription
factor in the regulation of BDKRB1 gene expression in SMCs and possible YY1
involvement in the mechanisms of nuclear factor kappaB-mediated regulation of
the receptor expression. No significant changes in the promoter foot-printing
pattern were found after treatment with interleukin-1beta or serum (known BDKRB1
gene inducers), indicating that definite regulatory motifs could exist outside
the BDKRB1 gene core promoter region studied.

PMID: 15705059 [PubMed - in process]


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3: Biol Reprod. 2004 Jun;70(6):1701-9. Epub 2004 Feb 11. 

Transcription factor expression patterns in bovine in vitro-derived embryos
prior to maternal-zygotic transition.

Vigneault C, McGraw S, Massicotte L, Sirard MA.

Centre de Recherche en Biologie de la Reproduction, Departement des Sciences
Animales, Universite Laval,Quebec, Canada G1K 7P4.

Maternal-zygotic transition (MZT) is a complex phenomenon characterized by the
initiation of transcription in the embryo and the replacement of maternal mRNA
with embryonic mRNA. In order for this to occur, transcriptional activation
requires various factors and conditions. Our hypothesis is that the lack of
transcription in the bovine pre-MZT embryo is due, in part, to an incomplete or
dormant transcriptional apparatus. Therefore, in accordance with this
hypothesis, functioning transcriptional mechanisms should appear in the
eight-cell bovine embryo to facilitate embryonic transcription during the MZT.
With this in mind, we examined the presence of selected transcription factors
during preimplantation embryo development to establish how their transcript
levels change in bovine pre-MZT embryos. To achieve this goal, real-time reverse
transcription-polymerase chain reaction was used to quantify the mRNA level of
several different transcription factors (YY1, HMGA1, RY-1, P300, CREB, YAP65,
HMGN1, HMGB1, NFAR, OCT-4, TEAD2, ATF-1, HMGN2, MSY2, and TBP) in germinal
vesicle (GV) and metaphase II (MII) bovine oocytes and in two-, four-,
eight-cell, and blastocyst stage embryos produced in vitro. Our results
demonstrate that all genes examined can be grouped into five different
categories according to their mRNA expression patterns at the developmental
stages observed. To summarize, all transcription factors studied were present in
pre-MZT embryos and the expression pattern of many of them suggest a potential
role in MZT.

PMID: 14960490 [PubMed - indexed for MEDLINE]


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4: J Biol Chem. 2001 Oct 19;276(42):38665-72. Epub 2001 Aug 20. 

YY1 is a positive regulator of transcription of the Col1a1 gene.

Riquet FB, Tan L, Choy BK, Osaki M, Karsenty G, Osborne TF, Auron PE, Goldring
MB.

Beth Israel Deaconess Medical Center, Division of Rheumatology, and New England
Baptist Bone & Joint Institute, Harvard Institutes of Medicine, Boston,
Massachusetts 02115, USA.

Both cell-specific and ubiquitous transcription factors in fibroblasts have been
identified as critical for expression of the Col1a1 gene, which encodes the
alpha1 chain of type I collagen. Here, we report that Yin Yang 1 (YY1) binds to
the Col1a1 promoter immediately upstream of the TATA box, and we examine the
functional implications of YY1 binding for regulation of Col1a1 gene expression
in BALBc/3T3 fibroblasts. The Col1a1 promoter region spanning base pairs (bp)
-56 to -9 bound purified recombinant YY1 and the corresponding binding activity
in nuclear extracts was supershifted using a YY1-specific antibody. Mutation of
the TATA box to TgTA enhanced YY1 complex formation. Mutation analysis revealed
two YY1 core binding sites at -40/-37 bp (YY1A) and, on the reverse strand, at
-32/-29 bp (YY1B) immediately adjacent to the TATA box. In transfections using
Col1a1-luciferase constructs, mutation of YY1A decreased activity completely
(wild-type p350 (p350wt), -222/+113 bp) or partially (p130wt, -84 bp/+13 bp),
whereas mutation of YY1B blocked the expression of both promoter constructs.
Cotransfection with pCMV-YY1 increased p350wt and p130wt activities by as much
as 10-fold, whereas antisense YY1 decreased constitutive expression and blocked
the increased activity due to pCMV-YY1 overexpression. The mTgTA constructs were
devoid of activity, arguing for a requirement for cognate binding of the TATA
box-binding protein (TBP). Electrophoretic mobility shift assays performed under
conditions permitting TBP binding showed that recombinant TBP/TFIID and YY1
could bind to the -56/-9 bp fragment and that YY1B was the preferred site for
YY1 binding. Our results indicate that YY1 binds to the Col1a1 proximal promoter
and functions as a positive regulator of constitutive activity in fibroblasts.
Although YY1 is not sufficient for transcriptional initiation, it is a required
component of the transcription machinery in this promoter.

PMID: 11514536 [PubMed - indexed for MEDLINE]


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5: Oncogene. 1999 Nov 18;18(48):6810-7. 

Nmi protein interacts with regions that differ between MycN and Myc and is
localized in the cytoplasm of neuroblastoma cells in contrast to nuclear MycN.

Bannasch D, Weis I, Schwab M.

Division of Cytogenetics-H0400, Deutsches Krebsforschungszentrum, Heidelberg,
Germany.

Myc family proteins play an important role in cellular processes such as
proliferation, differentiation, apoptosis and transformation. A number of
interaction partners of Myc have been identified, such as Max, p107, TBP, YY1,
Miz-1, AP-2 and Nmi. Both Max and Nmi also bind to MycN. In contrast to the well
defined binding of Max to Myc family proteins the interaction of Nmi with Myc or
MycN is only poorly characterized. By employing the yeast two-hybrid system we
have mapped the regions of MycN and Myc responsible for binding to Nmi. For MycN
exclusively a central region mediates binding to Nmi. In contrast, for Myc a
C-terminal portion of the protein, and possibly also a central part, is involved
in Nmi interaction. Nmi does not interact with Max and has no transactivation
capabilities in yeast, suggesting that Nmi alone is not a transcriptional
activator in mammalian cells. Immunofluorescence demonstrates that both in 293
embryonic kidney cells and in Kelly neuroblastoma cells all detectable
ectopically expressed Nmi is localized in the cytoplasm, in part in a punctate,
granular pattern. MycN, which is highly expressed in Kelly cells consequent to
amplification, appears to be localized exclusively in the nuclei. This directly
demonstrates that in the same cell at least the major proportion of MycN and Nmi
is localized in different cellular compartments. This result is confirmed by the
finding that endogenous Nmi, which is expressed in Kelly cells only after
stimulation with interferon gamma, is detected exclusively in the cytoplasm of
these cells. Therefore only a very small amount of MycN and Nmi is likely to be
involved in MycN/Nmi interaction in vivo.

PMID: 10597290 [PubMed - indexed for MEDLINE]


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6: Gene. 1999 Aug 20;236(2):197-208. 

Unlocking the mechanisms of transcription factor YY1: are chromatin modifying
enzymes the key?

Thomas MJ, Seto E.

Molecular Oncology Program, H. Lee Moffitt Cancer Center & Research Institute,
University of South Florida, Tampa, FL 33612, USA.

The transcription factor YY1 is a complex protein that is involved in repressing
and activating a diverse number of promoters. Numerous studies have attempted to
understand how this one factor can act both as a repressor and an activator in
such a wide set of different contexts. The fact that YY1 interacts with a number
of key regulatory proteins (e.g. TBP, TFIIB, TAFII55, Sp1, and E1A) has
suggested that these interactions are important for determining which particular
function of YY1 is displayed at a specific promoter. Two groups of proteins,
previously known to function as corepressors and coactivators, that now seem
likely to modulate YY1's functions, are the histone deacetylases (HDAC) and
histone acetyltransferases (HAT). These two groups of enzymes modify histones,
and this modification is proposed to alter chromatin structure. Acetylated
histones are typically localized to active chromatin while deacetylated histones
colocalize with transcriptionally inactive chromatin. When these enzymes are
directed to a promoter through a DNA binding factor such as YY1, that promoter
can be activated or repressed. This review will discuss the recent work dealing
with the different proteins that interact with YY1, with particular emphasis on
ones that modify chromatin, and how they could be involved in regulating YY1's
activities.

Publication Types:
    Review
    Review, Tutorial

PMID: 10452940 [PubMed - indexed for MEDLINE]


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7: Genes Cells. 1998 Aug;3(8):549-65. 

AMY-1, a novel C-MYC binding protein that stimulates transcription activity of
C-MYC.

Taira T, Maeda J, Onishi T, Kitaura H, Yoshida S, Kato H, Ikeda M, Tamai K,
Iguchi-Ariga SM, Ariga H.

Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12 Nishi 6,
Kita-ku, Sapporo 060 Japan.

BACKGROUND: The c-myc proto-oncogene has been suggested to play key roles in
cell proliferation, differentiation, transformation and apoptosis. A variety of
functions of C-MYC, the product of c-myc, are attributed to protein-protein
interactions with various cellular factors including Max, YY1, p107, Bin1 and
TBP. Max and YY1 bind to the C-terminal region of C-MYC, while p107, Bin1 and
TBP bind to the N-terminal region covering myc boxes. The N-terminal region is
involved in all the biological functions of C-MYC, and different proteins are
therefore thought to interact with the N-terminal region of C-MYC to display
different functions. RESULTS: We cloned two cDNAs which encode a novel
C-MYC-binding protein of 11 kDa, designated AMY-1 (Associate of C-MYC). The two
cDNAs, AMY-1L and AMY-1S, derived from alternative usage of polyadenylation
signals, code for the same protein of 11 kDa. AMY-1 was bound via its C-terminal
region to the N-terminal region of C-MYC (amino acids nos 58-148) corresponding
to the transactivation domain. AMY-1 was localized in the cytoplasm in cells
expressing c-myc at low levels, but in the nucleus in the cells of a high c-myc
expression in transiently transfected cells. A similar difference in endogenous
AMY-1 localization was observed during the cell cycle: AMY-1 translocated from
cytoplasm to nucleus during the S phase when c-myc expression was increased.
AMY-1 by itself did not recognize the E-box element, the MYC/Max binding
sequence, nor did it transactivate via the element, but stimulated the
activation of E-box-regulated transcription by MYC/Max. FISH analyses revealed
that the amy-1 gene was located at 1p32.2-1p33 in human genome. CONCLUSIONS:
AMY-1 is a 11 kDa protein which binds to the N-terminal region of C-MYC and
stimulates the activation of E-box-dependent transcription by C-MYC. AMY-1,
which mostly localizes in the cytoplasm, translocates into the nucleus in the S
phase of the cell cycle upon an increase of c-myc expression, and may thus
control the transcriptional activity of C-MYC.

PMID: 9797456 [PubMed - indexed for MEDLINE]


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8: Nucleic Acids Res. 1997 Jul 1;25(13):2661-71. 

Identification and characterization of the human XIST gene promoter:
implications for models of X chromosome inactivation.

Hendrich BD, Plenge RM, Willard HF.

Department of Genetics and Center for Human Genetics, Case Western Reserve
University School of Medicine, Cleveland, OH 44106-4955, USA.

The XIST gene in both humans and mice is expressed exclusively from the inactive
X chromosome and is required for X chromosome inactivation to occur early in
development. In order to understand transcriptional regulation of the XIST gene,
we have identified and characterized the human XIST promoter and two repeated
DNA elements that modulate promoter activity. As determined by reporter gene
constructs, the XIST minimal promoter is constitutively active at high levels in
human male and female cell lines and in transgenic mice. We demonstrate that
this promoter activity is dependent in vitro upon binding of the common
transcription factors SP1, YY1 and TBP. We further identify two cis -acting
repeated DNA sequences that influence reporter gene activity. First, DNA
fragments containing a set of highly conserved repeats located within the 5'-end
of XIST stimulate reporter activity 3-fold in transiently transfected cell
lines. Second, a 450 bp alternating purine-pyrimidine repeat located 25 kb
upstream of the XIST promoter partially suppresses promoter activity by
approximately 70% in transient transfection assays. These results indicate that
the XIST promoter is constitutively active and that critical steps in the X
inactivation process must involve silencing of XIST on the active X chromosome
by factors that interact with and/or recognize sequences located outside the
minimal promoter.

PMID: 9185579 [PubMed - indexed for MEDLINE]


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9: Mol Cell Biol. 1997 Jun;17(6):2973-84. 

Accurate positioning of RNA polymerase II on a natural TATA-less promoter is
independent of TATA-binding-protein-associated factors and initiator-binding
proteins.

Weis L, Reinberg D.

Department of Biochemistry, Robert Wood Johnson Medical School, University of
Medicine and Dentistry of New Jersey, Piscataway 08854-5635, USA.

Two promoter elements, the TATA element and initiator (Inr), are capable of
directing specific transcription initiation of protein-encoding genes by RNA
polymerase II (RNAPII). Although binding to the TATA element by the TATA-binding
protein (TBP) has been shown to be the initial recognition step in transcription
complex formation in vitro, the mechanism through which the basal machinery
assembles into a functional complex on TATA-less promoters is controversial.
Evidence supporting numerous models of Inr-mediated transcription complex
formation exists, including the nucleation of a complex by Inr-binding proteins,
a component of the TFIID complex, or a specific upstream activator common to
many TATA-less promoters, Sp1. Using various techniques, we have undertaken a
systematic analysis of the natural TATA-less human DNA polymerase beta
(beta-pol) gene promoter. Although the beta-pol promoter contains upstream Sp1
elements and a functional Inr that binds YY1, neither of these factors is
essential for Inr-mediated transcription complex formation. A complex containing
TBP, TFIIB, TFIIF, and RNAPII (DBPolF complex) is capable of forming on the
promoter in an Inr-dependent manner. A single point mutation within the Inr that
affects DBPolF complex formation diminishes beta-pol transcriptional activity.

PMID: 9154795 [PubMed - indexed for MEDLINE]


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10: Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13577-82. 

Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator.

Houbaviy HB, Usheva A, Shenk T, Burley SK.

Laboratory of Molecular Biophysics, Rockefeller University, New York, NY
10021-6399, USA.

Ying-Yang 1 protein (YY1) supports specific, unidirectional initiation of
messenger RNA production by RNA polymerase II from two adjacent start sites in
the adeno-associated virus P5 promoter, a process which is independent of the
TATA box-binding protein (TBP). The 2.5-A resolution YY1-initiator element
cocrystal structure reveals four zinc fingers recognizing a YY1-binding
consensus sequence. Upstream of the transcription start sites protein-DNA
contacts involve both strands and downstream they are virtually restricted to
the template strand, permitting access to the active center of RNA polymerase II
and ensuring specificity and directionality. The observed pattern of protein-DNA
contacts also explains YY1 binding to a preformed transcription bubble, and YY1
binding to a DNA/RNA hybrid analog of the P5 promoter region containing a
nascent RNA transcript. A model is proposed for YY1-directed, TBP-independent
transcription initiation.

PMID: 8942976 [PubMed - indexed for MEDLINE]


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11: Mol Cell Biol. 1996 Feb;16(2):503-12. 

The major histocompatibility complex class II Ea promoter requires TFIID binding
to an initiator sequence.

Bellorini M, Dantonel JC, Yoon JB, Roeder RG, Tora L, Mantovani R.

Dipartimento di Genetica e Biologia dei Microrganismi, Universita di Milano,
Italy.

The major histocompatibility complex (MHC) class II Ea promoter is dependent on
the presence of conserved upstream X and Y boxes and of initiator (Inr)
sequences. In vitro transcription analysis of the Inr region with
linker-scanning mutants pinpoints a functionally essential element that shows
homology to the terminal deoxynucleotidyltransferase (TdT) Inr; contrary to the
TdT Inr and other Inrs identified so far, the key sequence, between positions +5
and +12, is located within a transcribed area. Swapping the TdT sequence into
the corresponding Ea position leads to a fivefold increase in transcription
rate, without altering start site selection. Inr-binding proteins LBP-1/CP2 and
TIP--a TdT Inr-binding protein unrelated to YY1--recognize the Ea Inr; they
interact with overlapping yet distinct sequences around the Cap site, but their
binding does not coincide with Ea Inr activity. A good correlation is, rather,
found with binding of immunopurified holo-TFIID to this element. TFIID interacts
both with Ea TATA-like and Inr sequences, but only the latter is functionally
relevant. Unlike TBP, TFIID binds in the absence of TFIIA, indicating a
stabilizing role for TBP-associated factors in Ea promoter recognition. Sequence
comparison with other mouse and human MHC class II promoters suggests a common
mechanism of start site(s) selection for the MHC class II gene family.

PMID: 8552077 [PubMed - indexed for MEDLINE]


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12: J Biol Chem. 1995 Oct 6;270(40):23263-7. 

Transcriptional repression by human adenovirus E1A N terminus/conserved domain 1
polypeptides in vivo and in vitro in the absence of protein synthesis.

Song CZ, Tierney CJ, Loewenstein PM, Pusztai R, Symington JS, Tang QQ, Toth K,
Nishikawa A, Bayley ST, Green M.

Institute for Molecular Virology, Saint Louis University School of Medicine,
Missouri, USA.

The human adenovirus E1A 243R protein (243 residues) transcriptionally represses
a set of cellular genes that regulate cellular growth and differentiation. We
describe two lines of evidence that E1A repression does not require cellular
protein synthesis but instead involves direct interaction with a cellular
protein(s). First, E1A 243R protein represses an E1A-repressible promoter in the
presence of inhibitors of protein synthesis, as shown by cell microinjection-in
situ hybridization. Second, E1A 243R protein strongly represses transcription in
vitro from promoters of the E1A-repressible genes, human collagenase, and rat
insulin type II. Repression in vitro is promoter-specific, and an E1A
polypeptide containing only the N-terminal 80 residues is sufficient for strong
repression both in vivo and in vitro. By use of a series of E1A 1-80 deletion
proteins, the E1A repression function was found to require two E1A sequence
elements, one within the nonconserved E1A N terminus, and the second within a
portion of conserved region 1 (40-80). These domains have been reported to
possess binding sites for several cellular transcription regulators, including
p300, Dr1, YY1, and the TBP subunit of TFIID. The in vitro
transcription-repression system described here provides a powerful tool for the
further analysis of molecular mechanism and the possible role of these cellular
factors.

PMID: 7559479 [PubMed - indexed for MEDLINE]


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13: Nucleic Acids Res. 1995 Sep 11;23(17):3473-80. 

TBP binding and the rate of transcription initiation from the human beta-globin
gene.

Antoniou M, de Boer E, Spanopoulou E, Imam A, Grosveld F.

Laboratory of Gene Structure and Expression, National Institute for Medical
Research, London, UK.

DNA-protein interaction studies in vitro revealed several factors binding over
the TATA box and the region of transcription initiation (cap) site of the human
beta-globin promoter; TATA binding protein TBP at -30, Sp1 at -19, GATA-1 at -12
and +5, YY1 at -9 and a novel factor C1 over the site of initiation (-4 to +7).
Point mutants which specifically abolish the binding of each of these proteins
were tested in a beta-globin locus control region (LCR) construct which allows
quantitative comparisons at physiological levels of transcription. Only mutants
which drastically affect the binding of TBP resulted in decreased levels of
transcription. A threshold value of TBP binding of 15-30% of wild type was
sufficient to give normal levels of transcription. This indicates that the
association of TF IID with the TATA box is not limiting in the rate of
initiation of transcription.

PMID: 7567458 [PubMed - indexed for MEDLINE]


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14: Science. 1995 Jan 27;267(5197):531-6. 

Cloning of an intrinsic human TFIID subunit that interacts with multiple
transcriptional activators.

Chiang CM, Roeder RG.

Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New
York, NY 10021.

TFIID is a multisubunit protein complex comprised of the TATA-binding protein
(TBP) and multiple TBP-associated factors (TAFs). The TAFs in TFIID are
essential for activator-dependent transcription. The cloning of a complementary
DNA encoding a human TFIID TAF, TAFII55, that has no known homolog in Drosophila
TFIID is now described. TAFII55 is shown to interact with the largest subunit
(TAFII230) of human TFIID through its central region and with multiple
activators--including Sp1, YY1, USF, CTF, adenoviral E1A, and human
immunodeficiency virus-type 1 Tat proteins--through a distinct amino-terminal
domain. The TAFII55-interacting region of Sp1 was localized to its DNA-binding
domain, which is distinct from the glutamine-rich activation domains previously
shown to interact with Drosophila TAFII110. Thus, this human TFIID TAF may be a
co-activator that mediates a response to multiple activators through a distinct
mechanism.

PMID: 7824954 [PubMed - indexed for MEDLINE]


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15: J Virol. 1994 Aug;68(8):4988-97. 

Identification of linear DNA sequences that specifically bind the
adeno-associated virus Rep protein.

McCarty DM, Pereira DJ, Zolotukhin I, Zhou X, Ryan JH, Muzyczka N.

Department of Microbiology, School of Medicine, University at Stony Brook, New
York 11794.

We have used baculovirus-expressed Rep68 that has been purified to homogeneity
to reexamine the binding properties of the Rep protein. We find that Rep68 is
capable of binding to a linear DNA sequence that is contained within a 25-bp
sequence of the A stem of the adeno-associated virus (AAV) terminal repeat
proximal to the B and C palindromes. This has been shown conclusively by
demonstrating that Rep68 could specifically bind to a synthetic oligonucleotide
containing the 25-bp region in the absence of the other sequences within the
terminal repeat. Rep78 was also capable of binding the A stem recognition
element, as demonstrated by the fact that a DNA affinity column containing the
25-bp sequence can be used to purify Rep78. The ability to recognize the linear
DNA sequence within the A stem provides a mechanism by which the Rep protein can
be oriented on the terminal repeat so that only the correct strand is cut at the
terminal resolution site (trs site) during terminal resolution. In addition,
computer analysis suggests that sequences similar to the A stem element are
present within the three AAV promoter regions. Electrophoretic mobility shift
experiments clearly demonstrate that the p5 promoter contains a Rep binding
sequence. DNase protection experiments indicate that the Rep binding sequence
within the p5 promoter is located between the YY1 initiator sequence and the
TATA binding site. This position immediately suggests a mechanism by which the
Rep protein could act as a repressor or a transactivator of p5 transcription by
interacting with either YY1 or TBP. In addition, gel shift experiments suggest
that the p19 promoter also contains a Rep binding site. The presence of Rep
binding sites upstream of both promoters suggests that these sites may be
involved in coordinate regulation of AAV transcription. In addition, we have
identified a heterologous Rep binding sequence within pBR322 DNA. A comparison
of the sequences within the A stem, p5, and pBR322 binding sites suggests that a
repeating GAGC motif is at least part of the Rep recognition sequence. In the
accompanying report (D. M. McCarty, J. H. Ryan, S. Zolutukhin, X. Zhou, and N.
Muzyczka, J. Virol. 68:4998-5006, 1994), we examine the relative affinity of Rep
to the A stem site and the complete terminal repeat. Finally, we also have
reexamined the ability of Rep68 and Rep78 to cut at the trs site in substrates
that do not contain the B and C palindromes or any apparent secondary
structure.(ABSTRACT TRUNCATED AT 400 WORDS)

PMID: 8035498 [PubMed - indexed for MEDLINE]


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16: Cell. 1994 Mar 25;76(6):1115-21. 

TATA-binding protein-independent initiation: YY1, TFIIB, and RNA polymerase II
direct basal transcription on supercoiled template DNA.

Usheva A, Shenk T.

Howard Hughes Medical Institute, Department of Molecular Biology, Princeton
University, New Jersey 08544-1014.

YY1 is a zinc finger transcription factor whose DNA-binding motif exhibits the
properties of an initiator element. Only three factors were required to direct
specific basal transcription on a supercoiled template DNA carrying the YY1
initiator: YY1, general transcription factor IIB, and RNA polymerase II. This
minimal in vitro reaction did not require the TATA-binding protein (TBP). We
propose that, under appropriate conditions, YY1 can function like TBP, as a
factor that binds to the core promoter and recruits the polymerase to the
initiation complex.

PMID: 8137426 [PubMed - indexed for MEDLINE]


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