Basal expression of the histone H5 gene is controlled by positive and negative cis-acting sequences

In Vitro DNase I Footprinting

The association of proteins with the DNA double helix can interfere with the accessibility of the latter to nucleases. This is particularly true when using bulky nucleases such as DNase I. The DNase I footprinting method was developed to take advantage of this fact in the study of DNA-protein interactions: it consists in comparing the pattern of fragments generated by the partial digestion of a DNA sequence in the absence of a protein to that produced by its partial digestion in the presence of said protein. Normally, when the two sets of fragments are separated side by side on a gel, the ladder of DNase I-generated fragments produced in the presence of the protein will feature blank regions (devoid of fragments, indicating protection) and/or enhanced cleavage sites (indicating increased availability to the nuclease). This technique can furthermore reveal if multiple sites for a DNA-binding protein are present on a same fragment and in such a case will also allow the comparison of their respective affinities.

DNase I footprinting

The association of proteins with the DNA double helix can interfere with the accessibility of the latter to nucleases. This is particularly true when using bulky nucleases such as DNAse I. The DNAse I footprinting method was developed to make use of this phenomenon in the study of DNA-protein interactions; it consists in comparing the pattern of fragments produced by the partial digestion of DNA in the absence of a protein to that produced by partial digestion of DNA in the presence of a protein. Normally, when the two sets of fragments are separated side by side on a gel, the fragments produced in the presence of the protein will feature blank regions (indicating protection) and/or enhanced cleavage sites (indicating increased availability). This technique can furthermore reveal if multiple sites for a DNA-binding protein are present on a same fragment, and allow the comparison of their respective affinities.

[Biochemical methods for the analysis of DNA-protein interactions]

Investigation of DNA-protein interactions is fundamental to understand the mechanism underlying a variety of life processes. In this article, various types of biochemical methods in DNA-protein interaction study in vivo and in vitro at the level of DNA, protein, and the complex, respectively were briefly reviewed. Traditional assays including Nitrocellulose filter-binding assay, Footprinting, EMSA, and Southwestern blotting were summarized. In addition, chromatin immunoprecipitation techniques including nChIP, xChIP, and ChIP-on-chip, which were widely used in epigenetics, were particularly introduced.

The transcription factor snail is a repressor of E-cadherin gene expression in epithelial tumour cells

The adhesion protein E-cadherin plays a central part in the process of epithelial morphogenesis. Expression of this protein is downregulated during the acquisition of metastatic potential at late stages of epithelial tumour progression. There is evidence for a transcriptional blockage of E-cadherin gene expression in this process. Here we show that the transcription factor Snail, which is expressed by fibroblasts and some E-cadherin-negative epithelial tumour cell lines, binds to three E-boxes present in the human E-cadherin promoter and represses transcription of E-cadherin. Inhibition of Snail function in epithelial cancer cell lines lacking E-cadherin protein restores the expression of the E-cadherin gene.

The cardiac-muscle specific enhancer-promoter of slow/cardiac troponin C binds HMG-2

The cardiac muscle-specific enhancer-promoter of the slow/cardiac troponin C (cTnC) gene contains five protein binding regions, four of which bind cardiac-myocyte specific proteins. We screened a stage 11 chick embryo expression library with a double-stranded oligonucleotide probe consisting of one of these regions, CEF-1. One of the clones obtained was the chicken high mobility group protein, HMG-2. An electrophoretic gel mobility shift assay (EMSA) showed a specific binding interaction between the HMG-2 protein and the dsDNA CEF-1 probe. The cardiac-specific enhancer region of cTnC contains at least one possible HMG binding region and it is in the CEF-1 sequence overlapping a known GATA-4 binding site. Mutation of the nucleotide sequence of this HMG binding region diminishes its protein binding ability and markedly decreases its cardiac specific transcriptional activity. HMG-2 is a DNA bending protein that is predominantly found in the nucleus in proliferating cells and in the cytoplasm of terminally differentiated cells. It is an integral and stabilizing factor in the transcription activation nucleoprotein complex and is often described as an 'architectural transcription factor'. It markedly stimulates the transcription of many genes, often in association with tissue-specific transcription factors. We believe that the presence of HMG-2 in the enhancer-promoter binding protein complex of cTnC augments DNA bending and facilitates the DNA binding and interaction of other tissue-specific factors (e.g. GATA-4, which also binds to this region). This would result in increased transcription of the cTnC gene during the proliferation phase of embryonic cardiac myocyte development.

Novel DNase I hypersensitive sites in the 3'-flanking region of the human c-myc gene

DNase I hypersensitivity regions correlate with genetic regulatory loci and binding sites for sequence-specific DNA-binding proteins. We present data supporting the presence of novel DNase 1 hypersensitive sites (which we have designated sites VI-IX) in both the body of the human c-myc gene downstream from exon 2 and the 3'-flanking region of the c-myc gene in HL-60 cells. All of these novel DH sites are markedly decreased when HL-60 cells are treated with either dimethyl sulfoxide (DMSO) or retinoic acid. Moreover, a similar pattern of DNase I hypersensitive sites in this region of c-myc was present in MCF-7 human breast cancer cells growing in culture. Our results suggest a potential role for these sites in transcriptional regulation of the human c-myc gene.

Initiation binding repressor, a factor that binds to the transcription initiation site of the histone h5 gene, is a glycosylated member of a family of cell growth regulators [corrected]

Initiation binding repressor [corrected] (IBR) is a chicken erythrocyte factor (apparent molecular mass, 70 to 73 kDa) that binds to the sequences spanning the transcription initiation site of the histone h5 gene, repressing its transcription. A variety of other cells, including transformed erythroid precursors, do not have IBR but a factor referred to as IBF (68 to 70 kDa) that recognizes the same IBR sites. We have cloned the IBR cDNA and studied the relationship of IBR and IBF. IBR is a 503-amino-acid-long acidic protein which is 99.0% identical to the recently reported human NRF-1/alpha-Pal factor and highly related to the invertebrate transcription factors P3A2 and erected wing gene product (EWG). We present evidence that IBR and IBF are most likely identical proteins, differing in their degree of glycosylation. We have analyzed several molecular aspects of IBR/F and shown that the factor associates as stable homodimers and that the dimer is the relevant DNA-binding species. The evolutionarily conserved N-terminal half of IBR/F harbors the DNA-binding/dimerization domain (outer limits, 127 to 283), one or several casein kinase II sites (37 to 67), and a bipartite nuclear localization signal (89 to 106) which appears to be necessary for nuclear targeting. Binding site selection revealed that the alternating RCGCRYGCGY consensus constitutes high-affinity IBR/F binding sites and that the direct-repeat palindrome TGCGCATGCGCA is the optimal site. A survey of genes potentially regulated by this family of factors primarily revealed genes involved in growth-related metabolism.

Regulation of H1(0) gene expression by nuclear receptors through an unusual response element: implications for regulation of cell proliferation

Cloning and sequence analysis of the 5'-flanking region of the human H1(0) histone gene, a differentiation-specific member of the H1 family, has revealed several potential regulatory elements. In this study, we have characterized the interactions of nuclear receptors with an unusual response element consisting of two half-sites arranged as a direct repeat with an 8-bp spacer (DR-8). Thyroid hormone receptors (TR) bind this DR-8 as homodimers and heterodimers with RXR. Retinoic acid receptors (RARs) also bind as heterodimers with RXR to the DR-8, and this binding is enhanced in the presence of retinoic acid (RA) and/or 9-cis RA. Reporter constructs containing the DR-8 allowed a several-fold induction by T3 in the presence of TRs. RAR alpha and RAR beta allowed RA-dependent transcriptional activation whereas RAR gamma mostly increased basal activity. 9-cis RA inhibited the T3 response, indicating a hormonal cross-talk among the subfamily of nuclear receptors. Two orphan receptors, COUP-TF and v-erbA, also bind the DR-8 sequence in the human H1(0) promoter. COUP-TF, which usually represses RAREs, enhances transcriptional activation through the DR-8 whereas v-erbA completely represses TR-RXR induction of the H1(0) gene. Thus, a number of signaling pathways that play important roles during development and differentiation are able to influence the transcription rate of this special H1 subtype directly through a DR-8 response element in its promoter. Because H1(0) expression levels inversely correlate with cell proliferation, our data suggest that several nuclear receptors and the v-erbA oncogene can influence cell proliferation via the regulation of H1(0) expression.

Tissue-specific regulation of the rabbit 15-lipoxygenase gene in erythroid cells by a transcriptional silencer

The 15-lipoxygenase (lox) gene is expressed in a tissue-specific manner, predominantly in erythroid cells but also in airway epithelial cells and eosinophils. We demonstrate in this report that the 5' flanking DNA of the 15-lox gene contains sequences which down-regulate its activity in a variety of non-erythroid cell lines but not in two erythroid cell lines. The element has characteristics of a transcriptional 'silencer' since it functions in both orientations. The main activity of the silencer has been mapped to the first 900 bp of 5' flanking DNA, which contains nine binding sites for a nuclear factor present in non-erythroid cells but not in erythroid cells. These binding sites have similar sequences and multiple copies of the binding sites confer tissue-specific down-regulation when attached to a minimal lox promoter fragment. The 5' flanking DNA also contains a cluster of three binding sites for the GATA family of transcription factors.

Two copper-responsive elements associated with the Chlamydomonas Cyc6 gene function as targets for transcriptional activators

In Chlamydomonas reinhardtii, cytochrome c6 (cyt c6) is synthesized only under conditions of copper deficiency when plastocyanin cannot be synthesized. In previous work, the copper-responsive regulation of cyt c6 synthesis was demonstrated to occur by control of transcription, with no contribution from post-transcriptional processes. To understand the mechanism underlying its regulation, the genomic DNA encoding cyt c6 (Cyc6) was analyzed for the presence of copper-responsive elements. Sequences lying between positions -127 and -7 with respect to the start site of transcription were found to be sufficient to confer copper-responsive expression on either a promoterless or a minimal beta-tubulin promoter-driven (arylsulfatase-encoding) reporter gene. Analysis of this 120-bp fragment indicated that copper-responsive elements lie in two distinct regions (between -110 to -56 and -127 to -109). ATG fusions between copper-insensitive promoters and the coding plus 3' untranslated region of the Cyc6 gene resulted in the accumulation of cyt c6 in copper-supplemented medium; this confirms earlier studies indicating a lack of post-transcriptional control in this copper-responsive pathway. In the context of a constitutive promoter (derived from the beta-tubulin gene), each region was found to function as an activator of transcription in copper-deficient cells, and the metal specificity of the response of reporter genes containing either one or both regions was identical to that of the endogenous Cyc6 gene. The copper-responsive synthesis of cyt c6 is thus attributed to these two 5' upstream sequences.

Two copper-responsive elements associated with the Chlamydomonas Cyc6 gene function as targets for transcriptional activators

In Chlamydomonas reinhardtii, cytochrome c6 (cyt c6) is synthesized only under conditions of copper deficiency when plastocyanin cannot be synthesized. In previous work, the copper-responsive regulation of cyt c6 synthesis was demonstrated to occur by control of transcription, with no contribution from post-transcriptional processes. To understand the mechanism underlying its regulation, the genomic DNA encoding cyt c6 (Cyc6) was analyzed for the presence of copper-responsive elements. Sequences lying between positions -127 and -7 with respect to the start site of transcription were found to be sufficient to confer copper-responsive expression on either a promoterless or a minimal beta-tubulin promoter-driven (arylsulfatase-encoding) reporter gene. Analysis of this 120-bp fragment indicated that copper-responsive elements lie in two distinct regions (between -110 to -56 and -127 to -109). ATG fusions between copper-insensitive promoters and the coding plus 3' untranslated region of the Cyc6 gene resulted in the accumulation of cyt c6 in copper-supplemented medium; this confirms earlier studies indicating a lack of post-transcriptional control in this copper-responsive pathway. In the context of a constitutive promoter (derived from the beta-tubulin gene), each region was found to function as an activator of transcription in copper-deficient cells, and the metal specificity of the response of reporter genes containing either one or both regions was identical to that of the endogenous Cyc6 gene. The copper-responsive synthesis of cyt c6 is thus attributed to these two 5' upstream sequences.

An upstream control region required for inducible transcription of the mouse H1(zero) histone gene during terminal differentiation

The replacement linker histone H1 (zero) is associated with terminal differentiation in many mammalian cell types, and its accumulation in chromatin may contribute to transcriptional repression occurring during terminal differentiation. H1 (zero) also accumulates in a variety of cell culture lines undergoing terminal differentiation. During in vitro mouse erythroleukemia cell differentiation, H1 (zero) gene expression is induced very rapidly, prior to the time when the cells actually commit to terminal differentiation. We have used a combination of transfection assays and in vitro DNA-protein interaction studies to identify nuclear protein binding sites in the H1 (zero) promoter that control expression and induction of the H1(zero) gene in mouse erythroleukemia cells. The results indicate that transcription of the H1 (zero) gene is controlled by three elements present in the upstream region of the promoter between positions -305 and -470. Site-directed mutagenesis of each of these elements showed that one of them controls inducibility of the gene in differentiating cells. The other two elements in the upstream control region affect primarily the level of transcription of the gene in undifferentiated and differentiating cells. These two elements share a DNA sequence motif consisting of a (dG)6 tract contained in an eight-base consensus, (A/C)GGGGGG(A/C). Additional copies of this motif are present elsewhere in the H1 (zero) promoter.

Developmentally regulated expression of linker-histone variants in vertebrates

The identification of histone H1 variants in vertebrates suggests that these proteins may have specialized functions. During embryonic development, a correspondence between the expression of each of the linker-histone variants and the proliferative and transcriptional activity of embryonic cells can be observed. Analysis of the developmentally regulated expression of these variants leads to the subdivision of these variants into distinct classes. This subdivision may also provide insight into the significance of the differential expression of variants and the roles individual linker histones have in chromatin structure and function.

Molecular basis of the activation of basal histone H1(0) gene expression

Histone H1(0) is encoded by a gene that is expressed only in cells committed to differentiation. We have previously cloned the Xenopus laevis H1(0) gene and studied elements involved in the regulation of its expression in transfected Xenopus laevis A6 cells, and in microinjected embryos. In this work, in order to understand the basis of the action of these elements, we used an A6 cell nuclear extract and showed that the H1(0) promoter is able to direct efficient in vitro transcription, which is highly dependent on a functional TATA box. However, in contrast to what we observed in vivo, in transfected A6 cells, the in vitro transcription was independent of major regulatory elements, defined in vivo. We then used this in vitro system to reconstitute H1(0) gene regulation. The creation of a repressive environment by the addition of purified histone H1 to the in vitro transcription system allowed us to obtain transcription dependent on the integrity of the regulatory elements. Investigating the basis of this regulation we found that protein-DNA interaction on the proximal promoter region was dependent on the integrity of proximal elements, and moreover the distal regulatory element, the UCE, was able to modulate this interaction. We conclude that the role of these regulatory elements is to maintain the basal TATA-dependent transcription of H1(0) under repressive condition: i.e., H1-mediated repression of transcription, or chromatin assembly in general.

Transcription factor GATA-1-multiprotein complexes and chicken erythroid development

The chicken erythrocyte transcription factor, GATA-1, is associated with several non-DNA binding proteins. We show that GATA-1 multiprotein complexes exist in primitive and definitive erythrocytes. These complexes bind to GATA motifs of the rho-globin promoter and histone H5 enhancer with high affinity, and to the chicken beta-globin promoter specialized TATA element and enhancer GATA with low affinity. The low affinity beta-globin TATA element would allow basal transcription factors to displace the GATA-1 multiprotein complex. Further, our results suggest that rho-globin promoter's low affinity Sp1 binding site and reduced levels of Sp1 in definitive cells prevent its expression in these cells.

Organization and expression of H1 histone and H1 replacement histone genes

The H1 family is the most divergent subgroup of the highly conserved class of histone proteins [Cole: Int J Pept Protein Res 30:433-449, 1987]. In several vertebrate species, the H1 complement comprises five or more subtypes, and tissue specific patterns of H1 histones have been described. The diversity of the H1 histone family raises questions about the functions of different H1 subtypes and about the differential control of expression of their genes. The expression of main type H1 genes is coordinated with DNA replication, whereas the regulation of synthesis of replacement H1 subtypes, such as H1 zero and H5, and the testis specific H1t appears to be more complex. The differential control of H1 gene expression is reflected in the chromosomal organization of the genes and in different promoter structures. This review concentrates on a comparison of the chromosomal organization of main type and replacement H1 histone genes and on the differential regulation of their expression. General structural and functional data, which apply to both H1 and core histone genes and which are covered by recent reviews, will not be discussed in detail.

Differential regulation of the human H1 zero-histone-gene transcription in human tumor-cell lines

Cloning and sequence analysis of about 2 kb of the 5' flanking region of the human H1 zero histone gene reveals several potential regulatory elements upstream of the transcribed portion of this gene. Transfection studies using the chloramphenicol acetyl transferase (CAT) gene as a reporter gene with a series of promoter deletions revealed that the expression of the H1 zero gene may depend on a complex interplay of several transcription factors, including members of the retinoic acid and/or thyroid-hormone-receptor superfamily, at the 5' flanking region of the H1 zero gene. CAT assays demonstrate varied patterns of expression and regulation in different human tumor-cell lines. The leukemia cell line HL60 does not express H1 zero mRNA and shows no CAT activity. HeLa cells strongly express the CAT gene under the control of the H1 zero promoter. Under the same conditions, HepG2 cells also transcribe the CAT gene, although at a lower rate than HeLa cells. Using different promoter-deletion clones, the CAT activity differs in HepG2 and HeLa cells in the very distal promoter region. In both cell lines, the CAT activity decreases several fold when the region between nucleotides -450 and -600 upstream of the mRNA start site is deleted. It also decreases when just the proximal portion but not the distal promoter region is deleted. In summary, the regulatory patterns of these three cell lines differ, indicating a cell-type-specific regulation of the human H1 zero-histone-gene expression.

Transcription of the histone H5 gene is regulated by three differentiation-specific enhancers

Histone H5, an early marker of the avian erythroid lineage, is expressed at low levels in early erythroid precursors and at higher levels in more mature cells. We show that the increase in H5 expression is due to transcriptional activation of the H5 gene following differentiation of precursor CFU(E). We have found and characterized two upstream enhancers, E1 (between -2233 and -1878 from the site of transcription initiation, +1) and E3 (between -1321 and -1163), and confirmed the presence of a downstream enhancer (C. D. Trainor, S. J. Stamler, and J. D. Engel, Nature [London] 328:827-830, 1987) E7 (between +846 and +1181) which are responsible for the increase in H5 gene transcription. The enhancers had a weak effect in nondifferentiated CFU(E) but a strong effect when the cells were induced to differentiate. Cooperation among the three enhancers, however, was not required for H5 gene activity in the differentiated cells. The enhancers contain binding sites for several ubiquitous and erythroid cell-specific nuclear proteins, including GATA-1, as demonstrated with GATA-1-specific antibodies. Although the GATA sites were required for enhancer function, the concentration of GATA-1, GATA-2, and GATA-3 decreased during cell differentiation, and overexpression of these factors had little effect on H5 transcription. Hence, the differentiation-specific effect of the enhancers is not mediated by changes in relative levels of the GATA factors. Functional analysis of the H5 promoter indicated that the requirement of several elements, including a GC box necessary for transcription enhancement, did not change during the early stages of CFU(E) differentiation. However, the UPE, a positive element in proliferating CFU(E) recognized by the transcription factor H4TF2, was dispensable in the differentiated cells. These results suggest that as the cells enter the final stages of differentiation, there is a reprogramming of the regulatory factors that control H5 transcription and that the enhancers rescue and increase the activity of the promoter.

Transcription of the histone H5 gene is regulated by three differentiation-specific enhancers

Histone H5, an early marker of the avian erythroid lineage, is expressed at low levels in early erythroid precursors and at higher levels in more mature cells. We show that the increase in H5 expression is due to transcriptional activation of the H5 gene following differentiation of precursor CFU(E). We have found and characterized two upstream enhancers, E1 (between -2233 and -1878 from the site of transcription initiation, +1) and E3 (between -1321 and -1163), and confirmed the presence of a downstream enhancer (C. D. Trainor, S. J. Stamler, and J. D. Engel, Nature [London] 328:827-830, 1987) E7 (between +846 and +1181) which are responsible for the increase in H5 gene transcription. The enhancers had a weak effect in nondifferentiated CFU(E) but a strong effect when the cells were induced to differentiate. Cooperation among the three enhancers, however, was not required for H5 gene activity in the differentiated cells. The enhancers contain binding sites for several ubiquitous and erythroid cell-specific nuclear proteins, including GATA-1, as demonstrated with GATA-1-specific antibodies. Although the GATA sites were required for enhancer function, the concentration of GATA-1, GATA-2, and GATA-3 decreased during cell differentiation, and overexpression of these factors had little effect on H5 transcription. Hence, the differentiation-specific effect of the enhancers is not mediated by changes in relative levels of the GATA factors. Functional analysis of the H5 promoter indicated that the requirement of several elements, including a GC box necessary for transcription enhancement, did not change during the early stages of CFU(E) differentiation. However, the UPE, a positive element in proliferating CFU(E) recognized by the transcription factor H4TF2, was dispensable in the differentiated cells. These results suggest that as the cells enter the final stages of differentiation, there is a reprogramming of the regulatory factors that control H5 transcription and that the enhancers rescue and increase the activity of the promoter.

The role of the 5'-flanking region in the cell-specific transcription of the human von Willebrand factor gene

Transcriptional regulation of the human von Willebrand factor (vWF) gene was investigated in calf pulmonary artery endothelial (CPAE), HeLa, COS 7 and Hep G2 cells. Various lengths of flanking sequences extending up to 2123 bp 5' of the transcription initiation site and containing 19 bp of the first exon, were linked to the bacterial chloramphenicol acetyltransferase (CAT) gene and these constructs were assayed in transient transfection assays. Sequences up to 89 bp upstream of the cap site showed transcriptional activity in all cell types. Sequences between -147 and -419 bp markedly reduced CAT activity in CPAE cells and abolished it in other cell lines. A domain from -592 to -810 bp generated low levels of expression only in CPAE cells. This transcriptional activity was repressed with constructs containing 1041 to 1240 bp upstream of the cap site. Endothelial cell-specific transcription was restored by a construct that contained 1286 bp upstream of the cap site. The additional 46 bp upstream of the negative regulatory domain were within the 5' end of an inverse human Alu-family DNA repeat. RNAase-protection assays confirmed the correct transcriptional initiation. The sequence between -89 and -420 contained at least one negative regulatory element able to repress the CAT gene expression controlled by the heterologous thymidine kinase promoter in all cell types. A construct that included the sequence from -89 to -1286 bp increased the transcriptional activity directed by the thymidine kinase promoter only in CPAE cells. These results indicate that negative and positive elements in the 5'-flanking region interact to regulate vWF gene expression.

A small single-"finger" peptide from the erythroid transcription factor GATA-1 binds specifically to DNA as a zinc or iron complex

Sequence-specific DNA binding has been demonstrated for a synthetic peptide comprising only one of the two "finger"-like domains of the erythroid transcription factor GATA-1 (also termed Eryf-1, NF-E1, or GF-1). Quantitative analysis of gel-retardation assays yields a specific association constant of 1.2 x 10(8) M, compared with values of about 10(9) M for the full-length natural GATA-1 protein. By the use of peptides of various lengths, it was possible to delineate the smallest region necessary for specific binding. A single C-terminal finger of the double-finger motif is necessary but not sufficient for sequence-specific interaction. Basic amino acids located C-terminal to the finger (some more than 20 amino acids away) are also essential for tight binding. In addition to demonstrating that zinc is important for the formation of an active binding complex, we show that other ions, notably Fe2+, can fulfill this role. Our results make it clear that the GATA-1 metal binding motif is quite distinct from that found in the steroid hormone family and that GATA-1 is a member of a separate class of DNA binding proteins.

Basal level transcription of the histone H1(0) gene is mediated by a 80 bp promoter fragment

The replacement histone H1(0) of the H1 group, known to interact with general transcription factors, has been found associated with transcriptionally repressed chromatin. Transcription of the gene in F9 stem cells is low but can be stimulated by treating the cells with retinoic acid. Using mutant deletions, we now demonstrate that basal level transcription in F9 cells is mediated by an 80 bp DNA fragment, located 430 bp upstream of the TATA box, which does not include the retinoic acid responsive element (RARE) known to bind retinoic acid receptors and stimulate transcription from an heterologous promoter after retinoic acid treatment. By footprinting, DMS interference, site-directed mutagenesis and UV-cross linking techniques we demonstrate that at least two nuclear factors, with MW of 90,000 and 30,000, bind to the 80 bp fragment and that this binding is necessary for transcription. Furthermore, positioning of this fragment upstream of the HSV-tk gene promoter stimulates transcription 2-3 times over control values, far less than the activity observed for this fragment in the homologous promoter, indicating that full activity of this fragment requires sequences located in the proximal part of the promoter.

Analysis of erythroid nuclear proteins binding to the promoter and enhancer elements of the chicken histone H5 gene

The chicken erythroid proteins binding to the histone H5 5' promoter and 3' erythroid-specific enhancer regions were identified. In DNase I footprinting and gel mobility shift experiments with immature adult erythrocyte nuclear extracts, we have demonstrated the binding of proteins to the GC-box, a high affinity Sp1 binding site, and to the upstream promoter element. We have previously demonstrated that a multisubunit complex containing the transcription factor GATA-1 was associated with the enhancer. Here, we show that the enhancer region also has four Sp1 binding sites (one medium and three weak affinity, one of which may also bind the CACCC factor), a potential NF-E4 binding site, and a binding site for a NF1-like factor. The results of gel mobility-shift and competition experiments provide evidence that the Sp1 binding sites are associated with a high molecular mass (greater than 450 kDa), Sp1 containing protein complex. We propose that Sp1 multimers bound at the promoter and enhancer interact to mediate the juxta-positioning of the enhancer and promoter elements, bringing the GATA-1 multisubunit complex next to the initiation site. The GATA-1 complex may contribute to the protein-protein interactions between the enhancer and promoter.

Multiple cis-acting elements of the proximal promoter region are required for basal level transcription of the H1(0) histone gene

Basal level transcription of the mouse histone H1(0) gene is mediated by 531 base pairs of the promoter region. Deletion of the most distal upstream 80 bp of this fragment reduces transcription to very low values. By in vitro footprinting we demonstrate now that multiple factors bind to the DNA fragment localized between the 80 bp and the cap nucleotide. In addition to the presence of motifs for the binding of SP1, H1-box, H4TF-2 and TATA-box-factors, other not yet described protein-binding elements were identified. Internal deletions in the wild type promoter enclosing these motifs strongly restrict transcription. Furthermore, when one of these motifs was modified by site-directed mutagenesis a strong impairment of transcription followed. Thus for basal level transcription, in addition to the 80 bp distal fragment, cis-acting elements localized in the 450 bp proximal promoter region are required.

Multisubunit erythroid complexes binding to the enhancer element of the chicken histone H5 gene

We identified the factor(s) that bind to the chicken erythroid-cell-specific histone H5 enhancer region which is located on the 3' end of the gene. In DNAase I footprinting and u.v. cross-linking experiments with nuclear extracts from adult chicken immature erythrocytes, we determined that the trans-acting factor GATA-1 was the predominating protein interacting with the histone H5 enhancer. GATA-2 and GATA-3 were not detected. In contrast, gel-mobility-shift assays and competition experiments demonstrated that several specific complexes formed with the histone H5 enhancer region. Gel-mobility-shift assays with 23 bp oligonucleotides containing the GATA-binding site (AGATAA) of the histone H5 enhancer or of the beta-globin enhancer showed that the GATA sequence was sufficient for the formation of at least five complexes. Diagonal mobility-shift assays demonstrated that multisubunit complexes were forming with the GATA-1 protein. Our interpretation of the results is that GATA-1 interacts with a protein of approx. 105 kDa which, in turn, can associate with protein or protein complexes of approx. 26 kDa, 146 kDa and a protein(s) of molecular mass greater than 450 kDa. The different multisubunit complexes formed via the trans-acting factor GATA-1 may impart different transcriptional responses to the promoter and enhancer elements of the histone H5 and globin genes.

Protein/DNA interactions involving ATF/AP1-, CCAAT-, and HiNF-D-related factors in the human H3-ST519 histone promoter: cross-competition with transcription regulatory sites in cell cycle controlled H4 and H1 histone genes

Protein/DNA interactions of the H3-ST519 histone gene promoter were analyzed in vitro. Using several assays for sequence specificity, we established binding sites for ATF/AP1-, CCAAT-, and HiNF-D related DNA binding proteins. These binding sites correlate with two genomic protein/DNA interaction domains previously established for this gene. We show that each of these protein/DNA interactions has a counterpart in other histone genes: H3-ST519 and H4-F0108 histone genes interact with ATF- and HiNF-D related binding activities, whereas H3-ST519 and H1-FNC16 histone genes interact with the same CCAAT-box binding activity. These factors may function in regulatory coupling of the expression of different histone gene classes. We discuss these results within the context of established and putative protein/DNA interaction sites in mammalian histone genes. This model suggests that heterogeneous permutations of protein/DNA interaction elements, which involve both general and cell cycle regulated DNA binding proteins, may govern the cellular competency to express and coordinately control multiple distinct histone genes.

trans-Activation of a globin promoter in nonerythroid cells

We show that expression in fibroblasts of a single cDNA, encoding the erythroid DNA-binding protein Eryf1 (GF-1, NF-E1), very efficiently activates transcription of a chicken alpha-globin promoter, trans-Activation in these cells occurred when Eryf1 bound to a single site within a minimal globin promoter. In contrast, efficient activation in erythroid cells required multiple Eryf1 binding sites. Our results indicate that mechanisms exist that are capable of modulating the trans-acting capabilities of Eryf1 in a cell-specific manner, without affecting DNA binding. The response of the minimal globin promoter to Eryf1 in fibroblasts was at least as great as for optimal constructions in erythroid cells. Therefore, the assay provides a very simple and sensitive system with which to study gene activation by a tissue-specific factor.

trans-Activation of a globin promoter in nonerythroid cells

We show that expression in fibroblasts of a single cDNA, encoding the erythroid DNA-binding protein Eryf1 (GF-1, NF-E1), very efficiently activates transcription of a chicken alpha-globin promoter, trans-Activation in these cells occurred when Eryf1 bound to a single site within a minimal globin promoter. In contrast, efficient activation in erythroid cells required multiple Eryf1 binding sites. Our results indicate that mechanisms exist that are capable of modulating the trans-acting capabilities of Eryf1 in a cell-specific manner, without affecting DNA binding. The response of the minimal globin promoter to Eryf1 in fibroblasts was at least as great as for optimal constructions in erythroid cells. Therefore, the assay provides a very simple and sensitive system with which to study gene activation by a tissue-specific factor.