Proteins binding to the liver-specific pyruvate kinase gene promoter. A unique combination of known factors

A 183 base-pair fragment of the liver-specific promoter of the L-type puruvate kinase (L-PK) gene has been shown by transfection assay to be sufficient to confer a tissue-specific expression to a reporter gene. The proteins binding in vitro to this fragment have been investigated by a combination of DNase I footprinting, gel retardation of synthetic oligonucleotides and ultraviolet cross-linking. Four proteins from liver nuclear extracts bind to the investigated fragment. They were called, from 3' to 5', L1 to L4 binding factors. The L1 site (nucleotides -95 to -66 with respect to the cap site) binds hepatocyte nuclear factor 1 (HNF1), a liver-specific protein. The L2 site (nucleotides -114 to -97) binds the ubiquitous nuclear factor 1 (NF1), or a related factor. The L3 site (nucleotides -144 to -126) binds liver factor A1 (LF-A1), another liver-specific protein. Finally, the L4 site (nucleotides -168 to -145) binds major late transcription factor (MLTF/USF/UEF), an ubiquitous protein. Each of these proteins has been detected in other liver-specific promoters, but their combination is unique to the liver-specific promoter of the L-PK gene.

[Specific interaction of a nuclear protein factor from the CTF/NF-I family with 2 different promoter regions of the rat tyrosine aminotransferase gene]

Using gel-retardation and DNase I footprinting assays, we have analysed sequence-specific DNA-protein interactions within proximal promoter fragment (from -2 to -210 bp relative to the transcription start) of the rat tyrosine aminotransferase (TAT) gene. Two distinct DNase I protection regions flanked at either boundary by sites of DNase I hypersensitivity were observed with the rat-liver nuclear extracts. The internal sequence of the region I non-coding strand, (-155)TGGGCCACCTTCCAAT(-170), is highly homologous to the NF-I consensus sequence TGG(N)6-7TGCCAA and also shares a CCAAT-box; the region II noncoding strand sequence includes asymmetrically positioned (-37)AGCCAAT(-43) recognition motif. Since there have been a number of reports about multiple DNA-binding factors that recognize CCAAT homologies, both regions were likely to interact with either a single or distinct factors. Here we show that both region I and II of the TAT gene promoter are binding to the same factor related to the human CTF/NF-I. The evidence for that is based on competition experiments using the DNA fragment containing a synthetic consensus sequence for the NF-I recognition site and on the indistinguishable chromatographic properties of the activity specifically binding to each of three DNA fragments containing NF-I consensus, region I and region II sequences.

Identification of HeLa cell nuclear factors that bind to and activate the early promoter of human polyomavirus BK in vitro

Human polyomavirus BK (BKV), an oncogenic DNA virus, differs from other papovaviruses in the organization of the regulatory region and in tissue tropism for kidney cells. The noncoding regulatory region of the viral genome in prototype strains includes three 68-base-pair (bp) repeats, each containing a number of potential regulatory elements. Some of these signals are unique to human papovaviruses, and others are homologous to those identified in many viral and cellular genes. We evaluated the contribution of individual 68-bp repeats to the initiation of transcription from the early promoter in a HeLa cell extract and identified cis-acting elements to which human cellular factors bind to activate transcription. The early promoter with only one copy of the 68-bp repeat could accurately initiate transcription in vitro, but additional copies were required for its stimulation. DNA-binding assays and DNase I protection experiments identified six domains in the regulatory region protected by human cellular factors. Two of these footprints were located within the proximal and distal 68-bp repeats, and one was located at the late side of the repeats. These footprints were centered over a TGGA(N)5-6GCCA core and were produced by a protein of the nuclear factor 1 (NF-1) family. This protein is either identical or similar to that which binds to the high-affinity site at the origin of adenovirus DNA replication. Three other domains, two at the junctions of the 68-bp repeats and one in the late side of the repeats, were partially protected by proteins with AP-1- and Sp-1-like activities. Transcription initiation from the early promoter was drastically reduced when a complete 68-bp repeat or the NF-1 binding site was used as a competitor in the in vitro assay. However, a point mutation within the NF-1 binding site, which reduced NF-1 binding in vitro to a level comparable to that of nonspecific DNA, also eliminated its ability to compete with early transcription. The murine homolog of the AP-1 binding site had a modest effect on in vitro transcription. Our results suggest that, among the multiple HeLa cell nuclear factors, NF-1 acts as a major activator of the early promoter in vitro.

Interaction of nuclear factors with multiple sites in the somatic cytochrome c promoter. Characterization of upstream NRF-1, ATF, and intron Sp1 recognition sequences

The rat somatic cytochrome c promoter is resolved into a mosaic of cis-acting upstream and intron elements required for maximal activity. Mutations in each diminished cytochrome c promoter activity and eliminated the specific binding of cognate nuclear factors. Among these is the recognition sequence for a nuclear factor designated NRF-1 (nuclear respiratory factor 1) also found in the upstream regions of several other nuclear genes whose products function in the mitochondria. The NRF-1 site was tightly coupled to a second functionally independent element (region I), and together these sites constitute a major determinant of cytochrome c expression. In addition to these novel sequence elements, the promoter also contained recognition sites for the common transcriptional activators ATF and Sp1. A potent promoter element within the first intron consisted of two adjacent Sp1 binding sites. Point mutations in the first site eliminated the promoter activity of the element as well as Sp1 binding to both sites. An ATF recognition sequence in the upstream promoter was identical to an authentic cyclic AMP (cAMP) responsive element in stimulating promoter activity and in conferring a cAMP response upon a heterologous promoter. These promoter elements and their cognate nuclear factors likely contribute to the housekeeping function of cytochrome c and to the coordinate modulation of respiratory gene expression according to cellular energy demands.

Homology of nuclear factor I with the protein kinase family

It is observed that a putative DNA binding domain in nuclear factor I (NF I) which is a eukaryotic sequence-specific DNA binding protein participating in both regulation of DNA replication and transcription displays sequence homology with catalytic domains in various protein kinases. In addition, hydropathy analysis reveals that the NF I polypeptide chain is likely to fold into similar secondary and tertiary structures to those of the protein kinases. Although it is not known whether NF I functions as a protein kinase in addition to recognizing a specific sequence on DNA, it is concluded that some of the eukaryotic DNA binding proteins and protein kinases may belong to a gene family, various members of which are evolutionarily related and responsible for the regulation of metabolism in diverse compartments of the cell. The present finding also suggests that a number of kinases may to varying extents be capable of direct interaction with DNA.

Mutant analysis of protein interactions with a nuclear factor I binding site in the SL3-3 virus enhancer

Nuclear factor I (NFI) is shown to be of importance for the activity of the enhancer element of a T-cell leukemogenic murine retrovirus, SL3-3, and for the regulation of this element by glucocorticoid. Each nucleotide of the binding site of the NFI proteins was mutated, and the effects of the mutations were quantitated with an electrophoretic mobility shift assay. Mutations in the inverted repeat of the binding site have symmetric effects which strongly support the notion that NFI proteins preferentially bind to dyad symmetry sites. Such binding sites were shown to be more than 100 fold stronger than the corresponding single binding sites. We find dyad symmetry sequences which are much stronger NFI binding sites than NFI sites identified in different genes and also stronger than previously proposed consensus binding sequences for NFI.

Co-operative interactions between NFI and the adenovirus DNA binding protein at the adenovirus origin of replication

The DNA-protein and protein-protein interactions proposed for the stability of nucleoprotein complexes at the origin of replication in prokaryotes are also thought to impart regulatory precision in eukaryotic DNA replication. This type of specificity can be observed, for example, during adenovirus DNA replication where efficient initiation requires that nuclear factor I (NFI) binds to the origin of DNA replication. Addition of purified NFI stimulates the initiation of adenovirus DNA replication in vitro in a reaction that is dependent on the concentration of the adenovirus DNA binding protein (DBP). However, the molecular basis for the synergistic action of NFI and DBP during replication is at present unknown. We report here that DBP increases the affinity of NFI for its binding site in the replication origin. DBP did not, however, increase the affinity of another eukaryotic sequence-specific DNA binding protein, EBP1, for its recognition site. Other single-stranded DNA binding proteins could not substitute for DBP in increasing NFI affinity for its binding site. In addition, DBP was found to alter the binding kinetics of NFI, both by increasing the rate of association and decreasing the rate of dissociation of NFI with the DNA template. The co-operativity between NFI and DBP was also demonstrated on another DNA template, a human NFI site (FIB2), suggesting that this interaction is of general occurrence and not restricted to the adenovirus origin of replication.

An enhancer in the c-mos locus binds a nuclear factor 1-like protein

We recently identified a DNA sequence element located in the rat c-mos protooncogene which fulfills operational criteria for enhancers, increasing transcription from a heterologous promoter in fibroblasts over large distances and in an orientation-independent manner. Here we report that three mouse nuclear proteins bind to the enhancer. Several lines of evidence indicate that one is a Nuclear Factor 1 like activity. Oligonucleotide-directed mutagenesis of the NF-1 binding site destroys binding of the protein, but leaves enhancer activity unaffected. Tumor growth factor-beta, which was shown to exert a stimulatory effect on the alpha 2(I) collagen promoter via its NF-1 binding site, has no effect on the activity of the enhancer. Thus, the NF-1 binding site of the c-mos enhancer is not essential for its activity in fibroblasts.

Clusters of nuclear factor I binding sites identify enhancers of several papillomaviruses but alone are not sufficient for enhancer function

The long control region (LCR) of human papillomaviruses (HPV) encompasses 5-12% of the viral genome and contains an intricate network of cis responsive elements. In the LCR of seven unrelated HPV-types, namely HPV-1, 6, 8, 11, 16, 18 and 33, we have identified clusters of 4 to 7 5-TTGGC-3 motifs suggesting nuclear factor I (NFI) binding sites. We randomly selected 20 (out of a total of 38) of these motifs and showed that pure NFI from porcine liver protects virtually the same nucleotides as a factor present in crude HeLa nuclear extracts. The footprints obtained with HeLa extracts in the LCR of HPV-16 are eliminated in competition experiments by an oligonucleotide representing the palindromic adenovirus NFI binding site. Restriction fragments from the genome of HPV-11, 16 and 18, which contain this cluster of NFI binding sites associated with binding sites of unrelated transcription factors, function as transcriptional enhancers. In contrast, a fragment from HPV-8 exhibiting exclusively NFI binding sites, or polymerized NFI sites from HPV-16, are functionally inactive. NFI seems to be necessary but not sufficient for HPV enhancer activation.

Interaction of a nuclear factor-1-like protein with the regulatory region of the human polyomavirus JC virus

We have initiated a study to identify host proteins which interact with the regulatory region of the human polyomavirus JC (JCV), which is associated with the demyelinating disease, progressive multifocal leukoencephalopathy. We examined the interaction of nuclear proteins prepared from different cell lines with the JCV regulatory region by DNA binding gel retardation assays. Binding was detected with nuclear extracts prepared from human fetal glial cells, glioma cells, and HeLa cells. Little or no binding was detected with nuclear extracts prepared from human embryonic kidney cells. Competitive binding assays suggest that the nuclear factor(s) which interacted with the JCV regulatory region was different from those which interacted with the regulatory region of the closely related polyomavirus SV40. We found three areas in the JCV regulatory region protected from DNase I digestion: site A, located just upstream from the TATA sequence in the first 98-base pair (bp) repeat; site B, located upstream from the TATA sequence in the second 98-bp repeat; and site C, located just following the second 98-bp repeat. There were some differences in the ability of the nuclear factor(s) from the two brain cell lines and HeLa cells to completely protect the nucleotides within the footprint region. The results from the DNase I protective studies and competitive DNA binding studies with specific oligonucleotides, suggest that nuclear factor-1 or a nuclear factor-1-like factor is interacting with all three sites in the JCV regulatory region. In addition, the results suggest that the nuclear factor which interacts with the JCV regulatory region from human brain cell lines is different from the factor found in HeLa cells.

Dual function of a nuclear factor I binding site in MMTV transcription regulation

Using linker-scanning mutagenesis we had previously identified four elements within the MMTV LTR which are necessary for transcriptional stimulation by glucocorticoid hormones. Two of them overlapped with regions to which the glucocorticoid receptor binds in vitro. The third element contained a NF-I binding site, and the fourth the TATA box. Here we show that mutations that abolish in vitro binding of NF-I had a negative effect also on the basal activity of the MMTV promoter of LTR-containing plasmids stably integrated in Ltk- fibroblasts. The analysis of double mutants altered in the NF-I plus either one of the receptor binding elements further demonstrated that the NF-I site functionally cooperated with the proximal (-120) element, which alone was extremely inefficient in stimulation. The stronger distal (-181/-172) element was independent of NF-I and showed functional cooperativity with the proximal hormone-binding element.

Nuclear factor E2F mediates basic transcription and trans-activation by E1a of the human MYC promoter

Transcription from one of the two initiation sites, P1 and P2, of the dual human MYC promoter seems to be essential in all proliferating cells. To identify proteins and target structures for MYC regulation, a DNA region was analyzed that is critical for P2 promoter activity. Here, we show that a nuclear factor binds to a DNA element within P2, which is conserved perfectly between mouse and man and displays a striking homology to the E1a-inducible E2 promoter of adenovirus type 5 (Ad5). We demonstrate that the same transcription factor, defined recently as E2F, which plays an essential role in the activation of adenovirus early promoters and enhancers, also interacts as a dominant nuclear factor with the MYC promoter. The presence of an intact E2F binding site is required for basic expression and for trans-activation of the P2 promoter by E1a proteins. The human MYC promoter is the first cellular target described for E2F. The results suggest that expression of MYC might be regulated via modulation of E2F by cellular 'E1a-like' factors.

Purification and analysis of RNA polymerase II transcription factors by using wheat germ agglutinin affinity chromatography

We recently found that many RNA polymerase II transcription factors are modified with N-acetylglucosamine residues. These sugar moieties confer upon transcription factors an ability to bind the lectin wheat germ agglutinin. We have taken advantage of this interaction to devise a purification procedure for the "GC-box" binding transcription factor Sp1. Crude nuclear extracts are first subjected to wheat germ agglutinin affinity chromatography and then subjected to sequence-specific DNA affinity chromatography. The Sp1 protein purified by this procedure is at least 95% pure, and the overall recovery is greater than 80%. In addition to yielding larger quantities of Sp1 than conventional schemes, the new purification procedure is also simpler and more rapid. We show that wheat germ agglutinin affinity chromatography can also be used to purify the glycosylated forms of the CCAAT-binding transcription factor. Thus, wheat germ agglutinin affinity chromatography may aid the purification of other transcription factors that bear N-acetylglucosamine residues. Furthermore, the ability to separate glycosylated forms of transcription factors from their unglycosylated counterparts by wheat germ agglutinin affinity chromatography should facilitate investigations into the role of N-acetylglucosamine residues in the functioning of transcription factor proteins.

Histone H1 binds to the putative nuclear factor I recognition sequence in the mouse alpha 2(I) collagen promoter

It has previously been demonstrated that nuclear factor I (NF I) or a related protein binds to a region between -315 and -295 from the start of transcription in the mouse alpha 2(I) collagen gene promoter. In the present work we have purified this factor to homogeneity from rat liver. DNA sequence-specific proteins were isolated from nuclear extracts using heparin-agarose affinity chromatography and two successive chromatographies on a recognition site affinity matrix. Approximately 160 micrograms of the DNA binding proteins was obtained from 100 g of rat liver. More than 1700-fold purification over the nuclear extract and 58% recovery of the DNA binding activity was achieved. The purified preparation contained five to six protein components ranging in molecular weight from 30,000 to 35,000, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. It was demonstrated using DNase I footprint analysis that the factor binds to the putative NF I binding site in the mouse alpha 2(I) collagen promoter. It has a dissociation constant of 7 nM for a short DNA fragment containing this binding site, while a constant of 0.45 nM was obtained for a similar-sized fragment containing the nuclear NF I consensus binding sequence. The purified factor is identical to histone H1 in several respects. They share similar amino acid compositions and they give similar V8-protease and N-bromosuccinimide peptides. In addition, antibodies raised to bovine histone H1 recognize the purified factor and interfere with its binding to DNA. Methylation interference and preparative gel shift assay show that histone H1 binds to the specific sequence from the preparation of the alpha 2(I) collagen promoter binding factor. It is thus evident from the present results, that histone H1 binds to the NF I recognition sequence in the mouse alpha 2(I) collagen promoter.

Site-specific mutagenesis of the class I regulatory element the Q10 gene allows expression in non-liver tissues

Classical transplantation Ag are found on nearly all cells, whereas Ag encoded by the genes of the Qa/Tla region have a restricted tissue distribution. To investigate the cause of these different patterns of expression, we have compared the regulatory regions of Q10, a Qa region gene that is expressed only in liver, with those of H-2Ld. Gel retardation analysis shows that the nuclear factor (rI) that binds to the inverted repeat (TGGGGATTCCCCA) of the class I regulatory element (CRE) present in H-2Ld and other classical class I genes does not bind to the equivalent region of the Q10 gene. However, the Q10 CRE binds another nuclear factor (rII) that binds to the H-2Ld CRE. The sequence of the Q10 CRE differs from the sequence present in classical class I genes by three nucleotides, two of these changes are within the inverted repeat sequence (TGaGGAcTCCCCA) and disrupt the region of dyad symmetry. We have used site-specific in vitro mutagenesis to individually change these two nucleotides and have investigated the ability of this region to promote transcription with and without these substitutions. A change of either base restores transcriptional activity in chloramphenicol acetyl transferase assays and allows for binding of the rI nuclear factor. These results suggest that the failure of the Q10 CRE to bind the rI nuclear factor may play a role in preventing Q10 expression in tissues other than the liver and fetal yolk sac. Thus, the dichotomy between the widespread tissue expression of classical class I genes and the restricted tissue expression of class I genes of the Qa/Tla region may be due in part to differences in the cis acting regulatory sequences that interact with trans-acting nuclear factors to direct transcription.

Nuclear factor I can functionally replace transcription factor Sp1 in a U2 small nuclear RNA gene enhancer

Polymerase II transcription of a human gene for the small nuclear RNA U2 is dependent on two different promoter elements: a TATA-equivalent proximal sequence element and a distal enhancer element, which has been shown to contain Sp1- and octamer-binding sites. We have investigated the functional interplay between these transcription factor-binding sites of the enhancer, following transfection of U2 maxigene constructions into HeLa cells. There is a functional non-additive co-operation between the octamer-binding factor and Sp1, which is not dependent on the evolutionally conserved steric arrangement of these binding sites. We demonstrate that the conserved Sp1-binding site of the U2 enhancer can be fully substituted by a nuclear factor I (NFI) binding site, and that the octamer-binding factor functions in stimulating transcription in conjunction with either Sp1 or NFI. Since the octamer-binding factor is most probably the same protein as nuclear factor III (NFIII), the results imply that the NFI/NFIII complex, involved in adenovirus DNA replication, also can function as an efficient activator of transcription.

Purification methods for the sequence-specific DNA-binding protein nuclear factor I (NFI)--generation of protein sequence information

The paper describes a potent purification method, preparative gel retention, for the purification of sequence-specific DNA-binding proteins. This procedure exploits the sequence-specific DNA-binding affinity of such proteins for their enrichment, comparable to recognition site DNA affinity chromatography. The method was employed to obtain a pure preparation of nuclear factor I (NFI) from porcine liver from which sequences of partial peptides could be obtained. Oligonucleotide probes derived from these amino-acid sequences were used to identify genomic and cDNA clones of NFI.

Enhancer of human polyoma JC virus contains nuclear factor I-binding sequences; analysis using mouse brain nuclear extracts

Neurotrophic human JC virus carries a 98 bp duplicate enhancer responsible for tissue-specific gene expression. DNase I footprinting studies using mouse brain nuclear extracts revealed weak (pseudo NFI motif) and strong (NFI motif) nuclear factor I-binding sequences just upstream (at 229) and in the middle (at 156 and 58) of the enhancer, respectively. In vitro transcription driven in brain extracts demonstrated that the NFI motif is a possible transcription control element. Together with previous observations (Khalili, K., Rappaport, J. and Khoury, G. (1988) EMBO J. 7, 1205-1210 (20], the NFI motif is suggested to play an important role in early gene expression of JCV.

Multiple genes encode nuclear factor 1-like proteins that bind to the promoter for 3-hydroxy-3-methylglutaryl-coenzyme A reductase

DNA-binding proteins of the nuclear factor 1 (NF1) family recognize sequences containing TGG. Two of these proteins, termed reductase promoter factor (RPF) proteins A and B, bind to the promoter for hamster 3-hydroxy-3-methylglutaryl-coenzyme A reductase, a negatively regulated enzyme in cholesterol biosynthesis. In the current study, we determined the sequences of peptides derived from hamster RPF proteins A and B and used this information to isolate a cDNA, designated pNF1/Red1, that encodes RPF protein B. The peptide sequence of RPF protein A, the other reductase-related protein, suggests that it is the hamster equivalent of NF1/L, which was previously cloned from rat liver. We also isolated a hamster cDNA for an additional member of the NF1 family, designated NF1/X. Thus, the hamster genome contains at least three genes for NF1-like proteins. It is likely to contain a fourth gene, corresponding to NF1/CTF, which was previously cloned from the human. The NH2-terminal sequences of all four NF1-like proteins (NF1/Red1, NF1/L, NF1/X, and NF1/CTF), which are virtually identical, contain the DNA-binding domain that recognizes TGG. Functional diversity may arise from differences in the COOH-terminal sequences. We hypothesize that the COOH-terminal domain interacts with adjacent DNA-binding proteins, thereby stabilizing the binding of a particular NF1-like protein to a particular promoter. This protein-protein interaction confers specificity to a class of proteins whose DNA-recognition sequence is widespread in the genome. Sterols may repress transcription of the reductase gene by disrupting this protein-protein interaction.

The Xenopus laevis ribosomal gene promoter contains a binding site for nuclear factor-1

Nuclear Factor I (NF1) is a DNA binding protein that is known to function in the replication of Adeno virus and also binds to many promoters recognized by RNA polymerase II. We have found that there is also an NF1 binding site within the ribosomal gene promoter from Xenopus laevis as well as in several other promoters recognized by RNA polymerase I. The function of a binding site for a polymerase II transcription factor within a promoter recognized by polymerase I is not known. However, its presence suggests interesting regulatory possibilities.

TGGCA protein is present in erythroid nuclei and binds within the nuclease-hypersensitive sites 5' of the chicken beta H- and beta A-globin genes

The developmentally regulated 5'-flanking DNase-I-hypersensitive site of the chicken beta H-globin gene in nuclei contains a subregion which is resistant to DNase I and which disappears when nuclei are extracted with 0.3 M NaCl, suggesting that there are salt-extractable proteins bound to sequences within this region. The 0.3 M NaCl extract contains two proteins which bind in vitro to these sequences. One of the binding sequences has an inverted repeat very similar to that bound by TGGCA protein. Partially purified TGGCA protein from chicken liver binds to this sequence in vitro giving exactly the same footprint as that obtained with erythroid nuclear proteins. Similarly TGGCA protein binds to an inverted repeat with the beta A-globin 5'-hypersensitive site giving a footprint identical to that obtained with erythroid nuclear protein extracts. From competition footprinting experiments and the electrophoretic mobility of the protein-DNA complex, it is concluded that the erythroid proteins previously described as binding to the beta H- and beta A-globin inverted repeats within the 5'-flanking hypersensitive sites both belong to the TGGCA protein family.

Purified hepatocyte nuclear factor 1 interacts with a family of hepatocyte-specific promoters

During development cell types arise through the activation or repression of classes of specific genes. One hypothesis is that this phenomenon is realized by tissue-specific factors playing a role at the transcription level. Recently we have described a liver-specific nuclear protein, hepatocyte nuclear factor 1, that appears to be involved in the transcription of the fibrinogen and alpha 1-antitrypsin genes. In this report we describe the purification of hepatocyte nuclear factor 1 and demonstrate that it interacts with essential promoter regions of many liver-specific genes, including albumin, alpha-fetoprotein, and transthyretin. This finding suggests that hepatocyte nuclear factor 1 could be one factor necessary for establishing the liver phenotype. We also show that this protein binds to the promoter of the surface-antigen gene of the hepatitis B virus, a virus characterized by a high degree of hepatotropism.

Purification of a NF1-like DNA-binding protein from rat liver and cloning of the corresponding cDNA

NF1-like proteins play a role in transcription of liver-specific genes. A DNA-binding protein, recognizing half of the canonical NF1 binding site (TGGCA) present on the human albumin and retinol-binding protein genes, has been purified from rat liver. Several peptides deriving from a tryptic digest of the purified protein were sequenced and the sequence was used to synthesize specific oligonucleotides. Two overlapping cDNA clones were obtained from a rat-liver cDNA library; their sequence reveals an open reading frame coding for 505 amino acids, including all the peptides sequenced from the purified protein. The DNA-binding domain, most likely located within the first 250 amino acids, is highly homologous to the sequence of CTF/NF1 purified from HeLa cells. Northern analysis reveals several mRNA species present in different combinations in various rat tissues.

Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box

The expression of HLA class II genes is regulated by a series of cis-acting elements and trans-acting factors. Several cis-acting elements have been identified and have been termed the Z box, X box, Y box, octamer, and "TATA" box. The Y box contains an inverted CCAAT box. By probing a phage lambda gt11 library with double-stranded oligonucleotides, we have directly isolated a cDNA encoding a Y box-binding protein designated YB-1. YB-1 binding has an absolute requirement for the CCAAT box and relative specificity for the Y box. It has a Mr of 35,414, contains 18% basic residues, and contains putative nuclear localization signals. An inverse correlation of YB-1 and HLA-DR beta chain mRNA levels suggests that YB-1 is a negative regulatory factor.

Point mutations and small substitution mutations in three different upstream elements inhibit the activity of the mouse alpha 2(I) collagen promoter

Point mutations and small substitution mutations were introduced in three different promoter segments of the mouse alpha 2(I) collagen gene that are binding sites for specific DNA-binding proteins. The first of these promoter elements contains a CCAAT motif between -80 and -84 and binds a novel factor consisting of two different components which are both needed for DNA binding (Hatamochi, A., Golumbek, P.T., Van Schaftingen, E., and de Crombrugghe, B. (1988) J. Biol. Chem. 263, 5940-5947). Four different point mutations in the CCAAT motif, which strongly inhibit binding of this heterodimeric CCAAT-binding factor, decrease the activity of the promoter at least 8-fold when assayed by DNA transfection of NIH 3T3 fibroblasts. The second cis-acting element is located around -250. Two mutations in this element, one a 3-base pair (bp), another a 4-bp substitution mutation, decrease the activity of the promoter in DNA transfection experiments by about 8- and 12-fold, respectively. The third element is located between -315 and -295 and binds nuclear factor 1 (NF1). Both 1- and 2-bp mutations which strongly inhibit binding of NF1 to this site decrease the activity of the promoter 8-10-fold in DNA transfection assays whereas another mutation in this site shows less inhibition in the activity of the promoter. Transfer of this NF1-binding site 5' to the SV40 early promoter increases the activity of this promoter more than 10-fold. These results indicate that the integrity of each of these three cis-acting elements is required for optimal activity of the alpha 2(I) collagen promoter and suggest a model whereby the factors which bind to these sequences cooperate in the formation of a transcription initiation complex.

Binding of cellular proteins to the regulatory region of BK virus DNA

The human papovavirus BK has a noncoding regulatory region located between the divergently transcribed early and late coding regions. Many strains of BK virus (BKV) have direct DNA sequence repeats in the regulatory region, although the number and extent of these repeats varies widely between independent isolates. Until recently, little was known about the individual functional elements within the BKV regulatory region, and the biological significance of the variable repeat structure has been unclear. To characterize the interaction between sequences in the BKV regulatory region and host cell transcription factors, we have carried out DNase I footprinting and competitive binding experiments on three strains of BKV, including one strain that does not contain direct sequence repeats. We have used relatively crude fractions from HeLa cell nuclear extracts, as well as DNA affinity-purified preparations of proteins. Our results demonstrate that BK(Dunlop), BK(WW), and BK(MM) each contain multiple binding sites for a factor, NF-BK, that is a member of the nuclear factor 1 family of transcription factors. We predict the presence of three to eight binding sites for NF-BK in the other strains of BKV for which a DNA sequence is available. This suggests that the binding of this protein is likely to be required for biological activity of the virus. In addition to NF-BK sites, BK(WW) and BK(MM) each contain a single binding site for transcription factor Sp1, and BK(Dunlop) contains two binding sites for transcription factor AP-1. The AP-1 sites in BK(Dunlop) span the junction of adjacent direct repeats, suggesting that repeat formation may be an important mechanism for de novo formation of binding sites not present in a parental strain.

Isolation and characterization of the porcine nuclear factor I (NFI) gene

This study describes the isolation of a major portion of the gene for nuclear factor I (NFI) including its 5'-flanking region with transcriptional start sites. We screened a porcine liver, genomic DNA library in phage EMBL3A with synthetic oligonucleotides derived from tryptic and cyanogen-bromide peptide sequences obtained from purified NFI protein. The NFI gene is present as a single copy in porcine DNA.

A liver-specific factor and nuclear factor I bind to the rat alpha-fetoprotein promoter

Proteins putatively involved in the transcriptional control of rat (alpha-fetoprotein (AFP) gene expression in the liver were identified by analyzing the in vitro binding of proteins from nuclear extracts of fetal and adult rat livers to the cloned rat AFP promoter region (-197 to +48) using a combination of gel shift and DNase I footprinting assays. Three stable and specific high affinity complexes (I, II, and III) were detected by gel shift analysis of fetal rat liver extracts. Complex II was specific to extracts from fetal liver while the two others (I and III) were also formed with extracts from adult liver. Complex I was highly liver-specific since it was not detected with extracts of kidney, spleen, and brain. DNase I and gel shift competition experiments using a synthetic oligonucleotide indicated that it is formed upon binding of a liver-specific factor to region -65 to -46 of the rat AFP promoter. This region, perfectly conserved in the rat, mouse, and man, had been previously shown to be crucial for liver-specific expression of the mouse AFP gene. The binding of this liver-specific factor to this DNA region may thus represent a key step in the specificity of expression of AFP gene in liver. Gel shift and DNase I footprinting competition experiments showed that complex III was formed by binding of the widely distributed nuclear factor I to the rat AFP promoter in the region -125 to -100. It is potentially significant that, in extracts from fetal liver, nuclear factor is also involved with another binding factor in the formation of the stage-specific complex II.

Initiation of adenovirus DNA replication. II. Structural requirements using synthetic oligonucleotide adenovirus templates

Adenovirus (Ad) virions contain a 55-kDa terminal protein covalently linked to both 5'-ends of the linear duplex DNA genome. The origin of DNA replication is contained within the terminal 50 base pair of the inverted terminal repeats. In the accompanying paper (Kenny, M. K., Balogh, L. A., and Hurwitz, J. (1988) J. Biol. Chem. 263, 9801-9808), it was demonstrated that synthetic oligonucleotide templates which contain the Ad origin, but lack the 55-kDa terminal protein, can serve as templates for the initiation of Ad DNA replication. Partially duplex oligonucleotides that lacked up to 14 nucleotides from the 5'-end of the nontemplate (displaced) strand supported initiation as much as 20-fold more efficiently than fully duplex oligonucleotides. The removal of 18 nucleotides or more from the 5'-end of the displaced strand resulted in a sharp decrease in the ability of the DNA templates to support initiation. The poor template efficiency of certain DNAs could be explained by their inability to bind nuclear factor I. The initiation efficiency observed with other DNAs correlated with their ability to bind the preterminal protein-Ad DNA polymerase complex. At low concentrations of the Ad DNA-binding protein, protein-primed initiation was also observed on single-stranded DNAs. The single-stranded template strand of the Ad origin was at least 5-20-fold better at supporting initiation than other single-stranded DNAs. These findings suggest a model in which the 3'-end of the template strand is rendered single-stranded as a prerequisite for initiation of Ad DNA replication.

Initiation of adenovirus DNA replication. I. Mechanism of action of a host protein required for replication of adenovirus DNA templates devoid of the terminal protein

The in vitro replication of adenovirus (Ad) DNA covalently attached to the 55-kDa terminal protein requires at least five proteins including the 80-kDa preterminal protein, the Ad DNA polymerase, the Ad DNA binding protein, nuclear factor I, and topoisomerase I. The replication of Ad DNA templates devoid of the terminal protein requires an additional protein, designated factor pL, which has been purified from uninfected HeLa cell nuclei (Guggenheimer, R. A., Nagata, K., Kenny, M., and Hurwitz, J. (1984) J. Biol. Chem. 259, 7815-7825). Factor pL has been found to contain an intrinsic 5'----3' exonuclease activity. When Ad DNA templates lacking the terminal protein were pretreated with factor pL, the requirement for factor pL in the replication reaction was abolished. Synthetic partially duplex oligonucleotide templates containing Ad origin sequences were constructed in order to determine the structure of the DNA molecules that are active in the absence of factor pL. These experiments indicated that factor pL degrades the 5'-end of the nontemplate (displaced) strand of the Ad origin thereby creating a single-stranded region at the 3'-end of the template strand. Such DNAs are competent for initiation of Ad DNA replication in the absence of factor pL but remain dependent on nuclear factor 1.

Upstream region of hepatitis B virus S gene responsible for transcriptional stimulation by dexamethasone

Transcriptional regulation of hepatitis B virus (HBV) surface antigen (HBs Ag) gene was studied in human hepatoma-derived cell lines. Treatment with dexamethasone (Dex; 1 microM) induced an increase in the smaller HBs-mRNA initiated within Pre-S region encoding S and Pre-S2 proteins, but not the larger HBs-mRNA initiated in the further upstream encoding Pre-S1 protein. The Bg1II-MstII fragment (map position 2425-3201) in the upstream of the S gene was used as a transcriptional promoter of chloramphenicol acetyltransferase (CAT) gene. The CAT activity brought about by this construct in the transient assay was elevated by 5-fold in the presence of Dex. Deletion analysis localized the sequence required for the full response to Dex within a 590-base pair fragment in the upstream of the transcriptional initiation site of the smaller HBs-mRNA. And this fragment contained the binding site for the nuclear factor I (NF-I), which might have some role in Dex-dependent transcriptional stimulation.

[Chromatin proteins specifically interacting with certain DNA sequences. Nuclear factor I]

A comprehensive survey of the data on the nuclear factor I (NF-I) published by the end of 1987 is given. Among all the known DNA-binding chromosomal protein factors which are capable of specific interaction with certain nucleotide sequences, NF-I compels a particular attention as the first example of a conservative multifunctional factor being involved in the assembly of nuclease-hypersensitive chromatin structure within regulatory regions of active genes, in the trans-activation of RNA polymerase II transcription, and also in the replication of the adenoviral genome and presumably in the replication of some other DNAs including the cellular one.

A far upstream ovalbumin enhancer binds nuclear factor-1-like factor

Band-shifting and DNase I footprinting analyses detected a specific DNA binding protein extracted from oviduct nuclei that binds to the ovalbumin gene 5' sequence between -1094 and -1125. This "-1100" fragment, when inserted upstream of the SV40 or ovalbumin promoters fused to a chloramphenicol acetyltransferase reporter gene, enhances chloramphenicol acetyltransferase activity 5-10-fold following transfection into CV1 cells. The sequence to which the oviduct factor binds contains a nuclear factor-1 (NF-1) half-site (GCCAA). An oligonucleotide matching the sequence of the adenovirus NF-1 binding site competed for binding to the -1100 footprinted region with a higher affinity than an oligonucleotide for the -1100 region itself. Similarly, the -1100 region oligonucleotide also competes for binding of the factor to the NF-1 oligonucleotide. These data suggest that the oviduct factor which binds to the -1100 region is an NF-1-like protein that serves as a steroid hormone-independent enhancer of the ovalbumin gene transcription.

A quantitative analysis of nuclear factor I/DNA interactions

Nuclear factor I (NFI) was purified to homogeneity from porcine liver by DNA-affinity chromatography and displays a single band with a molecular weight of 36 kDa in SDS-polyacrylamide gels. The purified protein was used to determine absolute equilibrium binding constants by gel retardation techniques for a variety of DNA fragments with genuine or mutated NFI binding sites and a number of DNA fragments derived from various eukaryotic promoters carrying the CCAAT-box as a half-site for NFI binding. We present a model which allows prediction of the functional significance of mutated NFI binding-sites from sequence data. The data suggest that the single molecular species of NFI from porcine liver may not be able to recognize and activate the -CCAAT- promoter element in vivo without additional interactions, e.g. with other proteins.

Initial characterization of a potential transcriptional enhancer for the human c-K-ras gene

The nucleotide sequence of the 5' end distal region of the human c-K-ras gene promoter was determined. This region, coincident with a variable DNAse I hypersensitive site in native chromatin, contains sequence similarities with known enhancers. A 400 bp MstII DNA fragment of this region stimulated in cis the correctly initiated transcription of the human beta-globin gene in transfected Hela cells. The stimulation of beta-globin transcription (5-6 fold) was dependent on the distance and orientation of the c-K-ras sequences and on the presence of the CCAAT and CACCC elements in the beta-globin promoter. Interaction of nuclear factors with these c-K-ras sequences was analysed by DNAase I footprinting assays using Hela nuclear extracts. A protein binding to these sequences was identified as nuclear factor 1 (NF-1) by DNAase I competition footprinting experiments. However, disruption of the c-K-ras NF-1 binding site by insertion mutagenesis had no effect on the transcriptional activity of the c-K-ras element.

Stimulation of transcription in vitro by binding sites for nuclear factor I

Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus DNA in vitro and in vivo. We have examined the effect of natural and synthetic binding sites for NFI (FIB sites) on RNA synthesis in HeLa whole cell extracts. The natural binding site used is the 26bp FIB-2 site previously isolated from the human genome. When present upstream of the TATA box of the adenovirus major late promoter, the FIB-2 site stimulates RNA synthesis 3 to 5-fold. This stimulation occurs with either orientation of the FIB-2 site. A point mutation in FIB-2 that decreases NFI binding at least 100-fold reduces, but does not completely abolish, the stimulation of transcription. A number of synthetic binding sites for NFI were tested for the ability to increase RNA synthesis. The strongest binding sites stimulated transcription the most, while the weakest sites had the least effect. These studies strongly suggest a role for NFI and cellular FIB sites in the control of RNA synthesis.

A nuclear factor 1 binding site mediates the transcriptional activation of a type I collagen promoter by transforming growth factor-beta

Transforming growth factor-beta (TGF-beta) increases the steady-state RNA levels of several fibroblast extracellular matrix proteins. Using DNA transfection, we show that TGF-beta stimulates the activity of the mouse alpha 2(l) collagen promoter 5- to 10-fold in mouse NIH 3T3 and rat osteosarcoma cells. Deletion analysis indicates that a segment of this promoter between -350 and -300, overlapping a nuclear factor 1 (NF1) binding site, is needed for TGF-beta stimulation. A 3 bp substitution mutation abolishing NF1 binding to this site inhibits TGF-beta activation. Insertion of this NF1 binding site 5' to the SV40 early promoter makes the promoter TGF-beta inducible, but the 3 bp substitution does not. Similarly, when the NF1 binding site at the replication origin of adenovirus 2 and 5 is inserted 5' to the SV40 promoter, the promoter responds to TGF-beta. Therefore an NF1 binding site mediates the transcriptional activation of the mouse alpha 2(l) collagen promoter by TGF-beta.

Nuclear factor 1 (NF-1) binding sites in the genomes of human oncoviruses: a hypothetic role for reintegrated cellular origins of replication in malignant transformation

We have found that genomes of human T cell leukemia-lymphoma virus type I (HTLV-I), BK virus (BKV), and a hepatitis B virus (HBV) DNA sequence integrated into DNA of a hepatoma-derived cell line contain binding sites for nuclear factor 1 (NF-1), a cellular protein which binds to adenoviral and putative cellular origins of DNA replication. We suggest that cellular origins of DNA replication acquired by oncoviruses may play a role in malignant transformation after reintegration into the cellular genome by providing new targets for cellular factors initiating DNA replication and by perturbing the temporal order of replication.

The interplay of DNA-binding proteins on the promoter of the mouse albumin gene

The promoter of the mouse albumin gene contains at least six binding sites for specific DNA-binding proteins (A to F). Four of these sites (A, D, E, and F) can be occupied by transcription factors that are considerably enriched in liver nuclei, as compared to spleen or brain nuclei. These factors consist of a heat-stable protein that fills sites A, D, and F, and a member of a family of nuclear factor I (NF-I) related proteins that occupies site E. Site C binds a protein that is equally abundant in liver, brain, and spleen nuclei. Occupancy of this site and the binding of the heat-stable factor to the immediately adjacent site D appear to be mutually exclusive. However, both of these competing binding sites are required for maximal in vitro transcription.

Chicken liver TGGCA protein purified by preparative mobility shift electrophoresis (PMSE) shows a 36.8 to 29.8 kd microheterogeneity

The TGGCA protein, the chicken homologue of HeLa cell NF-I, was purified to homogeneity from liver tissue by a procedure which includes preparative mobility shift electrophoresis (PMSE) as the final step. PMSE was here adjusted for the isolation of the TGGCA protein, but can be used as a general method to characterize the protein moiety of specific DNA-binding proteins. The TGGCA protein is a family of 6 protein species, which show minor differences in molecular weight from 36.8kd to 29.8kd. This microheterogeneity differs from the size distribution reported for HeLa cell NF-I polypeptides. All species of the TGGCA protein bind identically to a synthetic DNA-binding site and appear to be highly related in primary structure. We discuss the possible functional importance of this microheterogeneity.

Incorporation of 5-bromodeoxycytidine in the adenovirus 2 replication origin interferes with nuclear factor 1 binding

We have studied the binding of nuclear factor 1 (NFI), a human sequence-specific DNA-binding protein, to a DNA fragment substituted in vitro with 5-bromodeoxycytidine (5-BrdC). Even at low substitution grades binding of NFI to its recognition sequence was considerably lower than with the unsubstituted control fragment. We developed a procedure to cleave substituted DNA specifically at a BrdC residue and searched for contacts between NFI and 5-BrdC residues by an interference assay. Surprisingly, no specific contacts were found in or near the recognition sequence. It appeared instead that interference was inversely related to the distance of a 5-BrdC residue from the NFI binding site. Models to explain these results, including a possible sliding mechanism, are discussed.

Separate binding sites for nuclear factor 1 and a CCAAT DNA binding factor in the mouse alpha 2(I) collagen promoter

A factor present in nuclear extracts of NIH-3T3 fibroblasts was identified which binds to a region between -315 and -295 with respect to the start of transcription in the mouse alpha 2(I) collagen promoter. This factor was assayed using three different DNA binding assays. Evidence that this factor is nuclear factor 1 or a related protein is based on competition experiments using fragments of another promoter that contains a nuclear factor 1 binding site as well as a fragment containing a consensus sequence for nuclear factor 1 binding sites. The nucleotide sequence of the binding site in the alpha 2(I) promoter. TCGN5GCCAA, presents similarities to the sequence published previously as a consensus recognition sequence for nuclear factor 1. Methylation interference experiments indicate that the factor interacts at least with two successive G residues in the major groove complementary to the two successive C residues in the GCCAA motif. This factor is different from a factor that binds to a CCAAT element between -84 and -80 in the mouse alpha 2(I) collagen promoter. This was shown by competition experiments using both crude NIH-3T3 fibroblast nuclear extracts and a partially purified CCAAT binding factor. These results suggest that in the alpha 2(I) collagen promoter nuclear factor 1 and a CCAAT binding factor bind to separate sites, despite analogies in their recognition sequences.

Site-specific DNA binding of nuclear factor I: effect of the spacer region

Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus type 2 DNA in vitro and in vivo. To study sequence requirements for the interaction of NFI with DNA, we have measured the binding of the protein to a variety of synthetic sites. Binding sites for NFI (FIB sites) were previously shown to contain a consensus sequence composed of 2 motifs, TGG (Motif 1), and GCCAA (Motif 2), separated by a 6 or 7bp spacer region. To assess conserved sequences in the spacer region and flanking sequences which affect NFI binding, we have isolated clones from oligonucleotide libraries that contain the two motifs flanked by 3 degenerate nucleotides and separated by degenerate spacer regions of 6 or 7 nucleotides. With a 6bp spacer region, a strong bias exists for a C or A residue in the first position of the spacer. Sites with a 7bp spacer region contain a G and C or A residue at the first and second positions, respectively, of the spacer, but also possess conserved residues at other positions of the site.

Interaction of the TGGCA-binding protein with upstream sequences is required for efficient transcription of mouse mammary tumor virus

A high-affinity binding site for the TGGCA-binding protein, also known as nuclear factor I, has previously been shown to reside within the mouse mammary tumor virus (MMTV) long terminal repeat. We have introduced mutations into this binding site to test the importance of this ubiquitous nuclear protein in MMTV transcription. Mutations which abolish the binding of the TGGCA protein in vitro are shown to impair strongly glucocorticoid-induced transcription from this promoter in vivo. These data demonstrate that the TGGCA-binding protein is a multifunctional DNA-binding protein, capable of serving a transcriptional role in the case of MMTV, in addition to its known involvement in the replication of adenovirus.

Contactpoint analysis of the HeLa nuclear factor I recognition site reveals symmetrical binding at one side of the DNA helix

Nuclear factor I (NFI) is a HeLa sequence-specific DNA-binding protein that is required for initiation of adenovirus (Ad) DNA replication and may be involved in the expression of several cellular genes. The interaction between NFI and its binding site on the Ad2 origin has been studied. Methylation interference and protection, u.v. irradiation of 5-BrdU substituted DNA and ethylation interference revealed major groove contacts with G and T, and phosphate backbone contacts. Computer stereographics show that the contacts are located in two blocks showing dyad symmetry to each other and 22 out of 23 contacts are accessible from one side of the helix. Inversion of the NFI binding site did not change the NFI dependent stimulation of Ad2 DNA replication in a reconstituted system. All data are compatible with NFI binding as a dimer at one side of the DNA helix.

Analysis of nuclear factor I binding to DNA using degenerate oligonucleotides

Nuclear factor I (NFI) binds tightly to DNA containing the consensus sequence TGG(N)6-7GCCAA. To study the role of the spacing between the TGG and GCCAA motifs, oligonucleotides homologous to the NFI binding site FIB-2 were synthesized and used for binding assays in vitro. The wild-type site (FIB-2.6) has a 6bp spacer region and binds tightly to NFI. When the size of this spacer was altered by +/- 1 or 2bp the binding to NFI was abolished. To further assess the role of the spacer and bases flanking the motifs, two oligonucleotide libraries were synthesized. Each member of these libraries had intact TGG and GCCAA motifs, but the sequence of the spacer and the 3bp next to each motif was degenerate. The library with a 6bp spacer bound to NFI to 40-50% the level of FIB-2.6. The library with a 7bp spacer bound to NFI to only 4% the level of FIB-2.6 and some of this binding was weaker than that of FIB-2.6 DNA. This novel use of degenerate DNA libraries has shown that: 1) the structural requirements for FIB sites with a 7bp spacer are more stringent than for sites with a 6bp spacer and 2) a limited number of DNA structural features can prevent the binding of NFI to sites with intact motifs and a 6bp spacer region.

High affinity binding site for nuclear factor I next to the hepatitis B virus S gene promoter

The hepatitis B virus (HBV) surface antigen (HBsAG) is encoded by the S gene under the regulation of a promoter in the pre-S1 region. The S gene promoter does not contain a 'TATA' box-like sequence, but there is a sequence resembling, in part, the late promoter of Simian virus 40 (SV40). In an attempt to study the regulation of the S gene promoter we looked for cellular proteins which bind to this region. We report here that a nuclear protein is tightly bound to the HBV genome at a position approximately 190 bases upstream from the S gene promoter. Evidence is provided to show that (a) this nuclear protein is the nuclear factor I (NF-I) that was previously found to be bound to the inverted terminal repeat of the adenovirus (Ad) DNA and to enhance Ad DNA replication in vitro and (b) this NF-I binding site is required for optimal activity of the S gene promoter.

Nuclear factor 1 interacts with five DNA elements in the promoter region of the human cytomegalovirus major immediate early gene

The human cytomegalovirus (HCMV), a ubiquitous pathogen of the herpesvirus group, has a linear double-stranded DNA genome of 235 kb. The expression of its major immediate early gene (IE1) is entirely dependent on host factors, presumably proteins binding to DNA elements in the regulatory regions of the gene. We have identified four high-affinity binding sites for nuclear factor 1 (NF1) in the promoter upstream region of IE1 gene between nucleotides -780 and -610, and an additional, even stronger, binding site in the first intron near nucleotide +350. NF1 activity is found in a wide range of species and binds to the sequence 5' TGGC/ANNNNNGCCAA3' on double-stranded DNA, protecting approximately 25 bp from DNase I digestion; its functional importance has been found first in the necessity for adenovirus DNA replication, where it may be important in mediating the binding of other proteins. The regulatory significance of NF1 recognition elements within other genes is unknown. The NF1 binding sites in the HCMV IE1 gene coincide with regions that had been shown to be sensitive to DNase I in the active gene but not sensitive in the silent gene; there was, however, no NF1 binding in the strong and constitutively DNase I-hypersensitive transcription enhancer of the IE1 gene. This suggests that the specific protein--DNA interaction described is important in the regulated control of the IE1 gene.