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

Nuclear factor one transcription factors as epigenetic regulators in cancer

Tumour heterogeneity poses a distinct obstacle to therapeutic intervention. While the initiation of tumours across various physiological systems is frequently associated with signature mutations in genes that drive proliferation and bypass senescence, increasing evidence suggests that tumour progression and clonal diversity is driven at an epigenetic level. The tumour microenvironment plays a key role in driving diversity as cells adapt to demands imposed during tumour growth, and is thought to drive certain subpopulations back to a stem cell-like state. This stem cell-like phenotype primes tumour cells to react to external cues via the use of developmental pathways that facilitate changes in proliferation, migration and invasion. Because the dynamism of this stem cell-like state requires constant chromatin remodelling and rapid alterations at regulatory elements, it is of great therapeutic interest to identify the cell-intrinsic factors that confer these epigenetic changes that drive tumour progression. The nuclear factor one (NFI) family are transcription factors that play an important role in the development of many mammalian organ systems. While all four family members have been shown to act as either oncogenes or tumour suppressors across various cancer models, evidence has emerged implicating them as key epigenetic regulators during development and within tumours. Notably, NFIs have also been shown to regulate chromatin accessibility at distal regulatory elements that drive tumour cell dissemination and metastasis. Here we summarize the role of the NFIs in cancer, focusing largely on the potential mechanisms associated with chromatin remodelling and epigenetic modulation of gene expression.

nfi-I affects behavior and life-span in C. elegans but is not essential for DNA replication or survival

BACKGROUND

The Nuclear Factor I (one) (NFI) family of transcription/replication factors plays essential roles in mammalian gene expression and development and in adenovirus DNA replication. Because of its role in viral DNA replication NFI has long been suspected to function in host DNA synthesis. Determining the requirement for NFI proteins in mammalian DNA replication is complicated by the presence of 4 NFI genes in mice and humans. Loss of individual NFI genes in mice cause defects in brain, lung and tooth development, but the presence of 4 homologous NFI genes raises the issue of redundant roles for NFI genes in DNA replication. No NFI genes are present in bacteria, fungi or plants. However single NFI genes are present in several simple animals including Drosophila and C. elegans, making it possible to test for a requirement for NFI in multicellular eukaryotic DNA replication and development. Here we assess the functions of the single nfi-1 gene in C. elegans.

RESULTS

C. elegans NFI protein (CeNFI) binds specifically to the same NFI-binding site recognized by vertebrate NFIs. nfi-1 encodes alternatively-spliced, maternally-inherited transcripts that are expressed at the single cell stage, during embryogenesis, and in adult muscles, neurons and gut cells. Worms lacking nfi-1 survive but have defects in movement, pharyngeal pumping and egg-laying and have a reduced life-span. Expression of the muscle gene Ce titin is decreased in nfi-1 mutant worms.

CONCLUSION

NFI gene function is not needed for survival in C. elegans and thus NFI is likely not essential for DNA replication in multi-cellular eukaryotes. The multiple defects in motility, egg-laying, pharyngeal pumping, and reduced lifespan indicate that NFI is important for these processes. Reduction in Ce titin expression could affect muscle function in multiple tissues. The phenotype of nfi-1 null worms indicates that NFI functions in multiple developmental and behavioral systems in C. elegans, likely regulating genes that function in motility, egg-laying, pharyngeal pumping and lifespan maintenance.

NFI and Oct-1 bend the Ad5 origin in the same direction leading to optimal DNA replication

Two cellular transcription factors, nuclear factor I (NFI) and octamer binding protein (Oct-1), bind simultaneously to their recognition sequences in the Ad5 origin of replication thereby enhancing initiation. Using scanning force microscopy we have previously shown that NFI induces a 60 degrees bend in the origin DNA. Here we demonstrate that Oct-1 induces a 42 degrees bend in the origin DNA. Simultaneous binding of NFI and Oct-1 induces an 82 degrees collective bend suggesting that both bends are oriented towards each other. In functional replication assays we further demonstrate that this extensive DNA bending leads to a synergistic enhancement of DNA replication. We propose that collective DNA bending induced by NFI and Oct-1 facilitates the optimal assembly of the preinitiation complex and plays an important role in the stimulatory mechanism of NFI and Oct-1 in replication.

Bending of adenovirus origin DNA by nuclear factor I as shown by scanning force microscopy is required for optimal DNA replication

Nuclear factor I (NFI) is a transcription factor that binds to the adenovirus type 5 (Ad5) origin of replication and recruits the adenovirus DNA polymerase, thereby stimulating initiation of DNA replication in vitro. Using scanning force microscopy, we demonstrate that NFI induces a 60 degrees bend upon binding to the origin. The A/T-rich region preceding the core recognition sequence of NFI influences the DNA bend angle, since substitution of A/T base pairs by G/C base pairs severely decreases bending. Mutations in the A/T-rich region do not affect binding of NFI to DNA. However, mutations that reduce the protein-induced bend lead to a loss of NFI-stimulated replication, indicating that DNA bending is functionally important. In contrast, basal initiation or DNA binding of the polymerase is not impaired by these origin mutations. We conclude that binding of NFI to the Ad5 origin causes structural changes in DNA that are essential for the stimulatory function of NFI in replication. We propose that NFI-induced origin bending facilitates the assembly of a functional initiation complex.

Nuclear factor 1 family members mediate repression of the BK virus late promoter

BK virus (BKV) is a member of the polyoma virus family that is ubiquitous in humans. Its 5-kb DNA genome consists of a bidirectional promoter region situated between two temporally regulated coding regions. We mapped the transcription initiation site of the major late promoter (MLP) of the archetype strain BKV(WW) to nt 185. We found that it lies within the sequence TGGN6GCCA, a binding site for members of the nuclear factor 1 (NF1) family of transcription factors. Competition electrophoretic mobility shift and immunoshift assays confirmed that NF1 factors present in nuclear extracts of HeLa and CV-1 cells bind to the BKV-MLP. Because BKV(WW) grew poorly in tissue culture and failed to express detectable levels of RNA in vitro, SV40-BKV chimeric viruses were constructed to investigate the transcriptional function of this NF-1 binding site. These sequence-specific factors repressed transcription in a cell-free system when template copy number was low. This repression could be relieved by the addition in trans of oligonucleotides containing wild-type, but not mutated, NF1-binding site sequences. SV40-BKV chimeric viruses defective in this NF1-binding site overproduced late RNA at early, but not late, times after transfection of CV-1 cells. Finally, transient expression in 293 cells of cDNAs encoding the family members NF1-A4, NF1-C2, and NF1-X2 specifically repressed transcription from the BKV late promoter approximately 3-, 10-, and 10-fold, respectively, in a DNA binding-dependent manner. We conclude that some members of the NF1 family of transcription factors can act as sequence-specific cellular repressors of the BKV-MLP. We propose that titration of these and other cellular repressors by viral genome amplification may be responsible in part for the replication-dependent component of the early-to-late switch in BKV gene expression.

Polymorphisms in the human paraoxonase (PON1) promoter

Paraoxonase (PON1) is a protein component of high-density lipoprotein (HDL) particles that protects against oxidative damage to both low-density lipoprotein and HDL and detoxifies organophosphorus pesticides and nerve agents. A wide range of expression levels of PON1 among individuals has been observed. We examined the promoter region of PON1 for genetic factors that might affect PON1 activity levels. We conducted a deletion analysis of the PON1 promoter region in transient transfection assays and found that cell-type specific promoter elements for liver and kidney are present in the first 200bp upstream of the coding sequence. Sequence analysis of DNA from a BAC clone and a YAC clone identified five polymorphisms in the first 1000 bases upstream of the coding region at positions -108, -126, -162, -832 and -909. Additionally, the promoter sequences of two individuals expressing high levels of PON1 and two individuals expressing low levels of PON1 were analysed. The two polymorphisms at -126 and -832 had no apparent effect on expression level in the reporter gene assay. The polymorphisms at position -909, -162 (a potential NF-I transcription factor binding site) and -108 (a potential SP1 binding site) each have approximately a two-fold effect on expression level. The expression level effects of the three polymorphisms appear not to be strictly additive and may depend on context effects.

Identification of pirin, a novel highly conserved nuclear protein

In this article we describe the molecular cloning of Pirin, a novel highly conserved 32-kDa protein consisting of 290 amino acids. Pirin was isolated by a yeast two-hybrid screen as an interactor of nuclear factor I/CCAAT box transcription factor (NFI/CTF1), which is known to stimulate adenovirus DNA replication and RNA polymerase II-driven transcription. Pirin mRNA is expressed weakly in all human tissues tested. About 15% of all Pirin cDNAs contain a short 34-base pair insertion in their 5'-untranslated regions, indicative of alternative splicing processes. Multiple Pirin transcripts are expressed in skeletal muscle and heart. Western blots and immunoprecipitations employing monoclonal anti-Pirin antibodies reveal that Pirin is a nuclear protein. Moreover, confocal immunofluorescence experiments demonstrate a predominant localization of Pirin within dot-like subnuclear structures. Homology searches using the BLAST algorithm indicate the existence of Pirin homologues in mouse and rat. The N-terminal half of Pirin is significantly conserved between mammals, plants, fungi, and even prokaryotic organisms. Genomic Southern and Western blots demonstrate the presence of Pirin genes and their expression, respectively, in all mammalian cell lines tested. The expression pattern, the concentrated localization in subnuclear structures, and its interaction with NFI/CTF1 in the two-hybrid system classify Pirin as a putative NFI/CTF1 cofactor, which might help to gain new insights in NFI/CTF1 functions.

Nuclear factor I as a potential regulator during postembryonic organ development

Nuclear factor I (NFI) family members are transcription factors that are believed to also participate in DNA replication. We have cloned two Xenopus laevis NFIs that are up-regulated by thyroid hormone. They are 84-95% identical to their counterparts in birds and mammals. In contrast, the two Xenopus NFIs are much less homologous to each other, sharing only 58% homology, which largely resides in the DNA binding domain at the amino terminus. However, both NFIs can bind to a consensus NFI binding site and activate the transcription of a promoter bearing the site. Northern blot reveals that both NFI genes are regulated in tissue- and developmental stage-dependent manners. They are first activated, independently of thyroid hormone, to low levels at stages 23/24, around the onset of larval organogenesis. After stage 54, their mRNA levels are dramatically upregulated by endogenous thyroid hormone, and high levels of their expression correlate with organ-specific metamorphosis. Furthermore, gel mobility shift assay indicates that the NFI proteins are present in different organs and that their levels are regulated similarly to the mRNA levels. These results strongly suggest that NFIs play important roles during postembryonic organ development, in contrast to the general belief that NFIs are ubiquitous factors.

Does histone H1 bind specifically to the nuclear factor I recognition sequence?

The issue of whether histone H1 possesses specificity of binding to certain nucleotide sequences in DNA is of fundamental importance to the suggested role of the linker histone in the regulation of gene transcription. The purpose of the present study was to reinvestigate the specificity of binding of histone H1 to the putative nuclear factor I (NFI) recognition sequence suggested by a previous report in the literature. The interaction of purified mouse liver histone H1 with a synthetic oligonucleotide representing the natural NFI binding site from the adenovirus 2 origin of replication cloned in pBR322 has been studied by filter binding and a solid-phase procedure performed on nitrocellulose filter-immobilized protein dots. No indication of specific interactions of the lysine-rich histone H1 with the NFI recognition sequence was obtained.

Transcription factor binding and spacing constraints in the human beta-actin proximal promoter

The human beta-actin promoter, including its 5' flanking region and 5' untranslated region, is ubiquitously active in mammalian cells in culture. In this report we investigated the transcriptional activity of, and the protein-DNA interactions that occur within, the proximal region of the human beta-actin promoter. Efficient beta-actin promoter activity in transfected human HeLa cells requires only 114bp of 5' flanking sequences. Two of the cis-actin regulatory elements within this region of the beta-actin promoter, the CCAAT box and proximal CCArGG box, are specific in vitro binding sites for the transcription factors, nuclear factor Y (NF-Y) and serum response factor (p67SRF), respectively. These two elements are required together to stimulate in vivo transcription from the homologous as well as a heterologous promoter. Finally, a particular spatial alignment between the CCAAT box and proximal CCArGG box is required for trans-activation in vivo. The above provides strong evidence for a functional interaction between NF-Y and p67SRF when bound to their respective binding sites in the beta-actin promoter.

Identification of a protein that interacts with the nuclear factor-1 (NF-1) binding site in cells that do not express NF-1: comparison to NF-1, cellular distribution, and effect on transcription

We examined expression of nuclear factor-1 (NF-1) in different cell lines. Expression was low or undetectable in T and B lymphocyte cell lines, whereas fibroblasts and other adherent cell lines generally had a relatively high level of NF-1 mRNA. In cell lines that did not express NF-1, gel retardation assays, nevertheless, indicated complexes between a protein or proteins and the NF-1 site. These complexes were less abundant than those formed with NF-1, they migrated more slowly, and they appeared as single species instead of the multiple species observed with NF-1. NF-1 site-binding proteins were compared in the fibrosarcoma cell line HT-1080 (expressed the highest level of NF-1 in our study) and the B cell line Raji (does not express NF-1). UV-crosslinking studies indicated that the NF-1 site-binding proteins in both cell lines were similar in size. Proteolytic clipping band shift assays suggested that the Raji protein and NF-1 share structural similarity in their DNA binding domains, but are distinct proteins. The NF-1 site mediated transcriptional stimulation in cell lines where NF-1 is expressed; however, this element did not affect transcription in cell lines that do not express NF-1, suggesting that the NF-1 site-binding protein in these cells is functionally distinct from NF-1.

In vivo stimulation of a chimeric promoter by binding sites for nuclear factor I

Nuclear factor I (NFI) is composed of a family of site-specific DNA-binding proteins which recognize a DNA-binding site with the consensus sequence TGGC/A(N)5GCCAA. Binding sites for NFI have previously been shown to stimulate mRNA synthesis in vitro when present upstream of the TATA box of the adenovirus major late promoter (AdMLP). We have examined the effect of NFI-binding sites on transcription in vivo in transiently transfected HeLa and COS cells. An NFI-binding site isolated from the human genome activated expression from the minimal AdMLP in vivo in both the absence and presence of the simian virus 40 enhancer. A point mutation that decreased NFI binding affinity for the site in vitro reduced expression to near the basal level of the AdMLP. Several NFI-binding sites which differed in their spacer and flanking sequences were tested for their ability to activate expression in vivo. The ability of these sites to activate expression correlated with the strength of NFI binding in vitro. An NFI-binding site stimulated expression equally well when placed from 33 to 65 bp upstream of the TATA box. However, expression dropped to basal levels when the site was located from 71 to 77 bp upstream of the TATA box. These studies indicate that an NFI-binding site in this chimeric promoter activates expression in vivo only if located within a critical distance of the TATA box.

In vivo stimulation of a chimeric promoter by binding sites for nuclear factor I

Nuclear factor I (NFI) is composed of a family of site-specific DNA-binding proteins which recognize a DNA-binding site with the consensus sequence TGGC/A(N)5GCCAA. Binding sites for NFI have previously been shown to stimulate mRNA synthesis in vitro when present upstream of the TATA box of the adenovirus major late promoter (AdMLP). We have examined the effect of NFI-binding sites on transcription in vivo in transiently transfected HeLa and COS cells. An NFI-binding site isolated from the human genome activated expression from the minimal AdMLP in vivo in both the absence and presence of the simian virus 40 enhancer. A point mutation that decreased NFI binding affinity for the site in vitro reduced expression to near the basal level of the AdMLP. Several NFI-binding sites which differed in their spacer and flanking sequences were tested for their ability to activate expression in vivo. The ability of these sites to activate expression correlated with the strength of NFI binding in vitro. An NFI-binding site stimulated expression equally well when placed from 33 to 65 bp upstream of the TATA box. However, expression dropped to basal levels when the site was located from 71 to 77 bp upstream of the TATA box. These studies indicate that an NFI-binding site in this chimeric promoter activates expression in vivo only if located within a critical distance of the TATA box.

Analysis of multiple forms of nuclear factor I in human and murine cell lines

Nuclear factor I (NFI) is a group of related site-specific DNA-binding proteins that function in adenovirus DNA replication and cellular RNA metabolism. We have measured both the levels and forms of NFI that interact with a well-characterized 26-base-pair NFI-binding site. Five different NFI-DNA complexes were seen in HeLa nuclear extracts by using a gel mobility shift (GMS) assay. In addition, at least six forms of NFI were shown to cross-link directly to DNA by using a UV cross-linking assay. The distinct GMS complexes detected were composed of different subspecies of NFI polypeptides as assayed by UV cross-linking. Different murine cell lines possessed varying levels and forms of NFI binding activity, as judged by nitrocellulose filter binding and GMS assays. The growth state of NIH 3T3 cells affected both the types of NFI-DNA complexes seen in a GMS assay and the forms of the protein detected by UV cross-linking.

Analysis of multiple forms of nuclear factor I in human and murine cell lines

Nuclear factor I (NFI) is a group of related site-specific DNA-binding proteins that function in adenovirus DNA replication and cellular RNA metabolism. We have measured both the levels and forms of NFI that interact with a well-characterized 26-base-pair NFI-binding site. Five different NFI-DNA complexes were seen in HeLa nuclear extracts by using a gel mobility shift (GMS) assay. In addition, at least six forms of NFI were shown to cross-link directly to DNA by using a UV cross-linking assay. The distinct GMS complexes detected were composed of different subspecies of NFI polypeptides as assayed by UV cross-linking. Different murine cell lines possessed varying levels and forms of NFI binding activity, as judged by nitrocellulose filter binding and GMS assays. The growth state of NIH 3T3 cells affected both the types of NFI-DNA complexes seen in a GMS assay and the forms of the protein detected by UV cross-linking.

RNA polymerase II-directed gene transcription by rat skeletal muscle nuclear extracts

A cell-free transcription system was developed using nuclear extracts of rat skeletal muscle to examine the transcription of specific genes involved in ribosome biogenesis and histone synthesis. Isolation and purification of muscle tissue nuclei were required prior to obtaining a transcriptionally active extract. The transcriptional abilities of myoblast, myotube, and muscle tissue nuclear extracts were then compared using the adenovirus major late promoter as a reporter gene. Transcription of r-protein L32 and histone H4 gene templates remained high in all extracts while histone H3 gene transcription was reduced in both myotube and muscle tissue extracts. These data indicate that transcription of these genes in myotubes and muscle tissue nuclear extracts is similar. Therefore, the L6 myoblast system accurately reflects the ability of intact muscle tissue to transcribe the genes concerned with histone production and ribosome biogenesis.

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.

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.

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.

Cis- and trans-acting factors for transcription of the adenovirus 12 E1A gene

Cis- and trans-acting factors were analyzed for transcription of the adenovirus 12 E1A gene possessing two sites for transcription initiation. These sites are located at nucleotide positions 306 and 445 with respect to the left end of the viral genome as position 1. The template activity of DNAs with various deletions at the 5'-upstream region of the E1A gene was examined in a cell-free system using a nuclear extract of Ehrlich ascites tumor cells. A DNA region specifically stimulating transcription initiated at the site distal to the E1A coding sequence was found located between positions 1 and 166. No DNA sequence affecting transcription from a proximal start-site appeared to be present in the region between positions 1 and 378. DNaseI-footprinting indicated that factors present in the extract bind to two distinct DNA segments, both of which are located within a region stimulating distal transcription. Two footprints were observed, one between positions 19 and 55 and the other between 77 and 94. The former footprint was inhibited by synthetic oligonucleotides containing a sequence recognized by nuclear factor I and the latter contained a sequence similar to one present in the B-enhancer of polyoma virus. Competition of in vitro transcription with synthetic oligonucleotides indicated (a) nuclear factor(s) bound to the region between positions 19 and 55 to be responsible for stimulating distal transcription of the adenovirus 12 E1A gene.

Point mutational analysis of the human c-fos serum response factor binding site

A series of point mutants were generated in the human c-fos dyad symmetry element (DSE), found within the c-fos serum response element, to study the sequence requirements for its interaction with the human HeLa cell serum response factor (SRF). Plasmids that contain base substitutions within a core CC(A/T)6GG motif in the center of the DSE did not compete, or competed very poorly, with the wild-type c-fos DSE for formation of a specific SRF-DSE complex in vitro. The CC(A/T)6GG motif is not sufficient for maximal binding of SRF, as several plasmids that contain base substitutions in the sequences flanking this core motif competed either poorer or better than the wild-type c-fos DSE for SRF binding. Evidence is presented that supports the idea that SRF binds in a symmetrical fashion. Results of in vivo transient expression assays in HeLa cells suggest that negative regulation of c-fos transcription observed in serum-deprived cells is mediated through SRF binding to the DSE.

5' flanking and first intron sequences of the human beta-actin gene required for efficient promoter activity

We have identified a CCAAT box element that is required for the efficient transcription of the human beta-actin gene. Both in vivo transient transfection assays in cultured HeLa cells and in vitro run-off transcription assays in HeLa whole cell extracts demonstrated the requirement of this element for efficient promoter activity. A gel mobility shift assay revealed a Hela nuclear factor that specifically interacted with the beta-actin CCAAT element in vitro; mutation of the first three base pairs of the CCAAT pentanucleotide abolished binding of this factor. Competition gel shift experiments revealed that three sequence elements located within the beta-actin promoter, each containing a CC(A/T)6GG motif similar to that contained within the c-fos serum response element, were able to bind a different nuclear factor, serum response factor (SRF). One of these CC(A/T)6GG motifs is contained within a first intron fragment that enhanced transcription from a heterologous promoter in vivo.

Analysis of transcription control elements of the mouse myelin basic protein gene in HeLa cell extracts: demonstration of a strong NFI-binding motif in the upstream region

Promoter elements of the mouse myelin basic protein (MBP) gene were analyzed by in vitro transcription using HeLa cell extracts. We demonstrated the MBTE (MBP transcription element), GC-box core and TATA-box elements, at -130, -93 and -34, respectively. The TATA-box was indispensable for the promoter function. The GC-box was suggested to function co-operatively with far upstream sequences including the MBTE. The MBTE was crucial to direct maximal transcription, and also functioned with a heterologous promoter irrespective of its orientation. We identified a ubiquitous binding factor which interacted specifically with the MBTE and activated transcription. Intensive foot-printing studies demonstrated that the MBTE had a NFI-binding sequence. The MBTE was considered to be one of the strongest NFI-binding motif among known cellular genes. Interestingly, similar strong NFI-binding motifs were suggested to be present in the enhancer of JC virus whose gene is expressed like the MBP gene, in the nervous system.