Three regions upstream from the cap site are required for efficient and accurate transcription of the rabbit beta-globin gene in mouse 3T6 cells

Identification of two factors required for transcription of the ovalbumin gene

Two transcription factors, COUP and S300-II, were isolated and partially purified from HeLa cell nuclear extracts. Both factors are required for the efficient transcription in vitro of the ovalbumin gene but not the simian virus 40 early genes. COUP factor binds to the chicken ovalbumin upstream promoter (COUP) sequence which lies between -70 to -90 base pairs upstream from the cap site. A series of competition experiments with a band-shifting assay was carried out to determine the relative affinity of COUP box transcription factor for various promoters. We found that a promoter DNA fragment isolated from the ovalbumin gene competes better than those isolated from the ovomucoid, Y, and alpha-genes. In contrast, the the simian virus 40 early genes, the beta-globin gene, and the adenosine deaminase gene promoters do not compete well in this assay. The molecular weight of the COUP factor was estimated by S-300 column chromatography, glycerol gradient centrifugation to be 90,000. However, two bands were observed in sodium dodecyl sulfate gel electrophoresis of cross-linked COUP factor to a 32P-labeled oligonucleotide containing the COUP sequence. The protein moieties of the major and minor bands were estimated to be 85,000 to 90,000 and 40,000 to 45,000, respectively. The S300-II factor with an apparent molecular weight of 45,000 in an S-300 column is required for function in an in vitro reconstituted transcription system. In contrast to the COUP factor, the S300-II factor does not have apparent specificity for binding to the ovalbumin gene promoter. The S300-II factor may function by interacting with RNA polymerase or other DNA-binding transcription factors.

Characterisation of chicken erythroid nuclear proteins which bind to the nuclease hypersensitive regions upstream of the beta A- and beta H-globin genes

Chicken erythrocyte sequence-specific nuclear DNA-binding proteins, which bind to the 5'-flanking DNAseI hypersensitive sites of the erythrocyte chromosomal beta A- and beta H-globin genes, have been fractionated by HPLC gel filtration. Three beta A-globin gene DNA binding activities (to sites A, B and B' (10-12)) were separated. The erythroid precursor cell line HD3 has beta A-globin gene sites B and B' binding activities, but binding to site A is detected only after the HD3 cells are induced to differentiate. The fractionated protein binds to a redefined site B', which contains at its center the globin CACCC consensus sequence. The chromosomal beta H-globin gene has two 5'-flanking DNAseI hypersensitive sites which bracket two sequences (H and H') bound by erythrocyte and HD3 nuclear protein in vitro. The beta H- and beta A-globin gene binding sites (H and B) contain variants of the sequences bound by Nuclear Factor 1 and the TGGCA-binding protein, and their protein binding activity(ies) co-purify after HPLC gel filtration.

Delineation of transcriptional control signals within the Moloney murine sarcoma virus long terminal repeat

We identified three distinct elements within the Moloney murine sarcoma virus long terminal repeat that control transcription. The phenotypes of unidirectional deletion mutants of the long terminal repeat were assayed in microinjected frog oocytes and in transfected mouse fibroblasts. Steady-state levels of RNA bearing the same 5' terminus as the authentic Moloney murine sarcoma viral transcripts were measured by primer extension in assays that included a pseudo-wild-type internal reference. Mutant phenotypes define the boundaries of three functional elements. A region between 21 and 31 base pairs upstream from the mRNA cap site contains AT-rich sequences that function to establish the transcription start site. A second control element, termed the distal signal, lies between 31 and 84 base pairs upstream of the mRNA cap site. A CAT box consensus sequence is located at the 5' boundary of the distal signal. Additional components of the distal signal include a hexanucleotide sequence that is repeated four times. The distal signal augments transcription efficiency in oocytes but contributes only weakly to long terminal repeat-mediated expression in mouse fibroblasts. A third transcriptional control element lies between 156 and 364 base pairs upstream of the mRNA cap site. This element includes the 75-base-pair repeats previously identified as the Moloney murine sarcoma virus enhancer. In contrast to the distal signal, the Moloney murine sarcoma virus enhancer is crucial for significant expression in mouse fibroblasts but does not contribute to transcriptional expression in frog oocytes.

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon

Rats and mice have two, equally expressed, nonallelic genes encoding preproinsulin (genes I and II). Cytological hybridization with metaphase chromosomes indicated that both genes reside on rat chromosome I but are approximately 100,000 kilobases apart. In mice the two genes reside on two different chromosomes. DNA sequence comparisons of the gene-flanking regions in rats and mice indicated that the preproinsulin gene I has lost one of the two introns present in gene II, is flanked by a long (41-base) direct repeat, and has a remnant of a polydeoxyadenylate acid tract preceding the downstream direct repeat. These structural features indicated that gene I was generated by an RNA-mediated duplication-transposition event involving a transcript of gene II which was initiated upstream from the normal capping site. Sequence divergence analysis indicated that the pair of the original gene and its retroposed, but functional, counterpart (which appeared about 35 million years ago) is maintained by strong negative selection operating primarily on the segments encoding the chains of the mature hormone, whereas the segments encoding the parts of the polypeptide that are eliminated during processing and also the introns and the flanking regions are evolving neutrally.

Identification of the 5'-flanking regulatory region responsible for the difference in transcriptional control between mouse complement C4 and Slp genes

To elucidate the molecular basis underlying the difference in the mode of gene expression between mouse complement C4 (constitutive) and sex-limited protein (Slp) (testosterone-regulated), we compared nucleotide sequences and transcriptional regulatory activities of the 5'-flanking regions of these two genes. Although the two sequences showed a high degree of overall homology (95%) up to 1.9 kilobases (kb) upstream from the transcription initiation site, the Slp sequence lacked a 31-nucleotide segment containing ACACCC repeats and a 60-nucleotide segment containing ACAC repeats, which are present, respectively, 1.6 kb and 200 base pairs (bp) upstream from the transcription initiation site of the C4 gene. When assayed in human hepatoma-derived HepG2 cells, the 1.8-kb 5'-flanking DNA fragment of the C4 gene demonstrated strong transcriptional activity, whereas the corresponding DNA fragment of the Slp gene showed only negligible activity. By progressive deletion experiments, it was shown that the difference in the constitutive transcriptional activity of the C4 and Slp genes was accounted for by the presence or absence of the positive regulatory domain located between 1700 bp and 400 bp upstream of the transcription initiation site.

Characterization of the myosin light-chain-2 gene of Drosophila melanogaster

Recombinant DNA clones encoding the Drosophila melanogaster homolog of the vertebrate myosin light-chain-2 (MLC-2) gene have been isolated. This single-copy gene maps to the chromosomal locus 99E. The nucleotide sequence was determined for a 3.4-kilobase genomic fragment containing the gene and for two MLC-2 cDNA clones generated from late pupal mRNA. Comparison of these sequences shows that the gene contains two introns, the positions of which are conserved in the corresponding rat sequence. Extension of a primer homologous to the mRNA reveals two start sites for transcription 12 nucleotides apart. The sequence TATA is not present ahead of the mRNA cap site. There are two major sites of poly(A) addition separated by 356 nucleotides. The protein sequence derived from translation of the cDNA sequence shows a high degree of homology with that for the DTNB myosin light chain (MLC-2) of chicken. A lower degree of sequence homology was seen in comparisons with other evolutionarily related calcium-binding proteins. RNA blots show high levels of expression of several transcripts during the developmental time stages when muscle is being produced. In vitro translation of hybrid-selected RNA produces two polypeptides which comigrate on two-dimensional gels with proteins from Drosophila actomyosin, although the cDNA sequence reveals only one 26-kilodalton primary translation product.

A CCAAT box confers cell-type-specific regulation on the Xenopus hsp70 gene in oocytes

The Xenopus hsp70 gene is transiently heat-inducible in somatic cells; in injected oocytes, it is efficiently expressed without heat shock. I show here that this cell-type-specific and gene-specific activation is dependent on the presence of a heat shock regulatory element (HSE) and a CCAAT box in the hsp70 promoter; neither element by itself is sufficient for full activation. The same promoter elements are also required for heat inducibility in somatic cells. I propose that CAAT-binding transcription factor (CTF) interacts with heat shock transcription factor (HSTF), thereby enhancing the affinity of HSTF for the promoter; cell-type specificity could be explained by assuming either oocyte-specific forms or oocyte-specific high levels of CTF and/or HSTF.

Precise assignment of the light-strand promoter of mouse mitochondrial DNA: a functional promoter consists of multiple upstream domains

Using deletion mutagenesis we localized the promoter for the light strand of mouse mitochondrial DNA to a 97-base-pair region, from -88 to +9 nucleotides of the transcriptional initiation site. Within this region the light-strand promoter could be dissected into at least three different functional domains. The specificity region, a maximum of 19 base pairs between -10 and +9 of the transcriptional initiation site, was essential and sufficient for accurate transcriptional initiation. A second region, extending to -29 nucleotides from the initiation site, facilitated the formation of a preinitiation complex between the template DNA and factor(s) present in the mitochondrial RNA polymerase fraction and was required for efficient transcription. A third, ill-defined upstream region, which extended up to -88 nucleotides from the initiation site, appeared to influence template transcriptional efficiencies in competition assays. Without the specificity domain, the upstream regions were incapable of supporting any transcription. The presence of multiple upstream domains was confirmed by disrupting nucleotide sequences in the upstream region by using linker insertion and linker replacement techniques.

Precise assignment of the heavy-strand promoter of mouse mitochondrial DNA: cognate start sites are not required for transcriptional initiation

Transcription of the heavy strand of mouse mitochondrial DNA starts from two closely spaced, distinct sites located in the displacement loop region of the genome. We report here an analysis of regulatory sequences required for faithful transcription from these two sites. Data obtained from in vitro assays demonstrated that a 51-base-pair region, encompassing nucleotides -40 to +11 of the downstream start site, contains sufficient information for accurate transcription from both start sites. Deletion of the 3' flanking sequences, including one or both start sites to -17, resulted in the initiation of transcription by the mitochondrial RNA polymerase from alternative sites within vector DNA sequences. This feature places the mouse heavy-strand promoter uniquely among other known mitochondrial promoters, all of which absolutely require cognate start sites for transcription. Comparison of the heavy-strand promoter with those of other vertebrate mitochondrial DNAs revealed a remarkably high rate of sequence divergence among species.

Genetic analysis of the human thymidine kinase gene promoter

The promoter of the human thymidine kinase gene was defined by DNA sequence and genetic analyses. Mutant plasmids with deletions extending into the promoter region from both the 5' and 3' directions were constructed. The mutants were tested in a gene transfer system for the ability to transform TK- cells to the TK+ phenotype. This analysis delimited the functional promoter to within an 83-base-pair region upstream of the mRNA cap site. This region contains sequences common to other eucaryotic promoters including G X C-rich hexanucleotides, a CAAT box, and an A X T-rich region. The CAAT box is in an inverted orientation and is part of a 9-base-pair sequence repeated twice in the promoter region. Comparison of the genomic sequence with the cDNA sequence defined the first exon of the thymidine kinase gene.

Features of the chicken c-myc gene that influence the structure of c-myc RNA in normal cells and bursal lymphomas

The chicken c-myc gene is the target for proviral insertion mutations in bursal lymphomas and has been transduced to generate several viral oncogenes, but the boundaries of its exons have not been securely established. To define the landmarks of the chicken c-myc gene necessary to produce its mRNA, we used an RNase protection assay and a cDNA clone to analyze the c-myc mRNAs from normal chicken embryos and from two bursal lymphomas: LL6, which contains an avian leukosis virus provirus downstream of the c-myc coding region, and LL7, which contains an avian leukosis virus provirus upstream of the c-myc coding region. Two initiation sites for normal c-myc mRNA are less than 7 bases apart, downstream of a GC-rich region lacking canonical TATA and CAAT sequences. The first exon has two open reading frames for the entire length but no initiator methionine codons. The splice donor and acceptor sites at the boundary of the first intron were assigned by comparing a sequence of an LL6 c-myc cDNA clone with a genomic DNA sequence and confirmed by RNase protection of labeled RNA probes by normal and LL6-derived mRNAs. Two potential polyadenylation signals are located approximately 250 and 400 bases downstream of the c-myc coding region in the third exon, but only the more distal signal is utilized in both normal cells and the LL7 tumor. The proviral integration in the LL6 tumor occurred upstream of the authentic c-myc polyadenylation signal accounting for polyadenylation of this transcript in the proviral long terminal repeat.

Control of transcription initiation in vitro requires binding of a transcription factor to the distal promoter of the ovalbumin gene

We used a cell-free HeLa cell transcription system to identify and characterize transcription factors and the promoter elements that they recognize in RNA polymerase II-transcribed genes. Deletion of the region (-71 to -83) containing the GTCAAA direct repeat resulted in a marked decrease of specific transcription of the ovalbumin gene; transcription could be competed with DNA fragments containing this sequence. Furthermore, DNase I footprinting identified a protein-binding site including this direct repeat with crude extracts and one of the partially purified protein fractions required for transcription. We propose that a soluble factor activates transcription through binding to the direct repeat of GTCAAA sequence upstream from the ovalbumin gene.

Preferential nucleosome placement on pBR322 restriction fragments

Two restriction fragments of DNA containing the regulatory feature GTG/CAC were experimentally associated with core histones. The reconstituted DNA-histone complexes consisted of different forms of mononucleosomes. Lambda exonuclease and Fnu4HI were used to probe the structure of each distinct nucleoprotein complex. For each of the DNA fragments, one form of particle was produced that showed preferred placement of the core octamer on the DNA. The GTG/CAC base triplets may play some role in determining the final histone core positions in these reconstitutes.

Regulated expression of human A gamma-, beta-, and hybrid gamma beta-globin genes in transgenic mice: manipulation of the developmental expression patterns

We have introduced the human fetal gamma- and adult beta-globin genes into the germ line of mice. Analysis of the resulting transgenic mice shows that the human gamma-globin gene is expressed like an embryonic mouse globin gene; the human beta-globin gene is expressed (as previously shown) like an adult mouse globin gene. These results imply that the regulatory signals for tissue- and developmental stage-specific expression of the globin genes have been conserved between man and mouse but that the timing of the signals has changed. Because the two genes are expressed differently, we introduced a hybrid gamma beta-globin gene construct. The combination of the regulatory sequences resulted in the expression of the hybrid gene at all stages in all the murine erythroid tissues.

Delimitation and characterization of cis-acting DNA sequences required for the regulated expression and transcriptional control of the chicken skeletal alpha-actin gene

We have previously observed that DNA sequences within the 5'-flanking region of the chicken skeletal alpha-actin gene harbor a cis-acting regulatory element that influences cell type and developmental stage-specific expression (J. M. Grichnik, D. J. Bergsma, and R. J. Schwartz, Nucleic Acids Res 14:1683-1701, 1986). In this report we have constructed unidirectional 5'-deletion and region-specific deletion-insertion mutations of the chicken skeletal alpha-actin upstream region and inserted these into the chloramphenicol acetyltransferase expression vector pSV0CAT. These constructions were used to locate DNA sequences that are required for developmental modulation of expression when transfected into differentiating myoblasts. With this assay we have delimited the 5' boundary of a cis-acting regulatory element to ca. 200 base pairs upstream of the mRNA cap site. In addition, we have preliminarily identified DNA sequences that may be important subcomponents within this element. A second major focus of this study was to identify those DNA signals within the regulatory element that control transcription. Toward this end, the expression phenotypes of progressive 5'-deletion and deletion-insertion mutants of the 5'-flanking region of the chicken skeletal alpha-actin gene were assayed in microinjected Xenopus laevis oocytes. These experiments defined a cis-acting transcriptional control region having a 5' border 107 base pairs preceding the alpha-actin RNA cap site. Proximal and distal functionally important regions of DNA were identified within this element. These DNA signals included within their DNA sequences the "CCAAT" and "TATA" box homologies.

Heat shock regulatory elements function as an inducible enhancer in the Xenopus hsp70 gene and when linked to a heterologous promoter

The Xenopus hsp70 promoter contains three copies of the consensus heat shock element (HSE) between positions -260 and -100. When the gene is transfected into mammalian cells, maximal heat-induced expression requires two HSEs in addition to a CCAAT box located next to the TATA box. The HSE-containing region can be separated from the CCAAT/TATA region without affecting expression of the gene, and it can enhance transcription of a linked beta-globin gene upon heat shock. It thus has the properties of a heat-inducible enhancer. Such an enhancer can also be generated by duplication of HSE sequences from the Drosophila hsp70 promoter, which were previously identified as an upstream promoter element and are known to bind a purified heat shock transcription factor in vitro.

Upstream regions of the human cardiac actin gene that modulate its transcription in muscle cells: presence of an evolutionarily conserved repeated motif

Transfection into cultured cell lines was used to investigate the transcriptional regulation of the human cardiac actin gene. We first demonstrated that in both human heart and human skeletal muscle, cardiac actin mRNAs initiate at the identical site and contain the same first exon, which is separated from the first coding exon by an intron of 700 base pairs. A region of 485 base pairs upstream from the transcription initiation site of the human cardiac actin gene directs high-level transient expression of the bacterial chloramphenicol acetyltransferase gene in differentiated myotubes of the mouse C2C12 muscle cell line, but not in mouse L fibroblast or rat PC-G2 pheochromocytoma cells. Deletion analysis of this region showed that at least two physically separated sequence elements are involved, a distal one starting between -443 and -395 and a proximal one starting between -177 and -118, and suggested that these sequences interact with positively acting transcriptional factors in muscle cells. When these two sequence elements are inserted separately upstream of a heterologous (simian virus 40) promoter, they do not affect transcription but do give a small (four- to fivefold) stimulation when tested together. Overall, these regulatory regions upstream of the cap site of the human cardiac actin gene show remarkably high sequence conservation with the equivalent regions of the mouse and chick genes. Furthermore, there is an evolutionarily conserved repeated motif that may be important in the transcriptional regulation of actin and other contractile protein genes.

Sequence divergence and selection of cap sites in the rat gamma-crystallin gene family

The transcription initiation sites of the six rat gamma-crystallin genes were mapped by combining the results of primer extension and S1 nuclease mapping experiments. To obtain more accurate results from the S1 nuclease mapping experiments, intron-deleted clones were constructed by a novel and efficient modification of existing methods involving the use of primer extension products to seal the exons. Four of the six gamma-crystallin genes have multiple transcription start sites. The major and most of the minor transcripts start with an adenosine. Analysis of the 5' flanking sequences of the gamma-crystallin genes shows that the sequence determining the position of the cap site is merely -CA- and that its optimal distance from the first T of the TATA box is 32 base pairs. Our data further suggest that an A to G transition in the first two base pairs of the Goldberg/Hogness box of one the genes does not affect the position of its major cap site. This, together with the fact that most minor transcription start sites are located upstream from the major cap sites, suggests that in the long TATA boxes of the rat gamma-crystallin genes the major RNA polymerase 'trap site' is not directly at the beginning of the TATA sequence.

Fine structure genetic analysis of a beta-globin promoter

A novel procedure for saturation mutagenesis of cloned DNA was used to obtain more than 100 single base substitutions within the promoter of the mouse beta-major globin gene. The effects of these promoter substitutions on transcription were determined by transfecting the cloned mutant genes into HeLa cells on plasmids containing an SV40 transcription enhancer, and measuring the levels of correctly initiated beta-globin transcripts after 2 days. Mutations in three regions of the promoter resulted in a significant decrease in the level of transcription: (i) the CACCC box, located between -87 and -95, (ii) the CCAAT box, located between -72 and -77, and (iii) the TATA box, located between -26 and -30 relative to the start site of transcription. In contrast, two different mutations in nucleotides immediately upstream from the CCAAT box resulted in a 3- to 3.5-fold increase in transcription. With two minor exceptions, single base substitutions in all other regions of the promoter had no effect on transcription. These results precisely delineate the cis-acting sequences required for accurate and efficient initiation of beta-globin transcription, and they establish a general approach for the fine structure genetic analysis of eukaryotic regulatory sequences.

The chicken delta 1-crystallin gene promoter: binding of transcription factor(s) to the upstream G+C-rich region is necessary for promoter function in vitro

There are two linked delta-crystallin genes in the chicken (5' delta 1-delta 2 3'). Only the delta 1 gene has been shown definitively to be active in the lens. Transcription of deletion mutants, reported here, shows that the sequences necessary for the functioning of the delta 1 promoter in a HeLa cell extract are located upstream from the RNA initiation site, between nucleotide positions -121 and -38. This region includes a number of G+C-rich motifs, including one hexanucleotide sequence, CCGCCC, that is repeated six times in the simian virus 40 (SV40) promoter. Competition experiments with purified fragments from the delta 1-crystallin gene promoter showed that binding of transcription factor(s) from the HeLa cell extract to this G+C-rich region is required for promoter activity in vitro. Further, competition experiments using three different fragments from the SV40 promoter suggest that the transcription factor(s) is similar to Sp1, which stimulates transcription by binding to the G+C-rich 21-base-pair repeats of the SV40 promoter, and differs from that which interacts with the SV40 enhancer region.

Genomic cloning, characterization, and multilineage growth-promoting activity of human granulocyte-macrophage colony-stimulating factor

Through the use of long single-sequence oligonucleotide probes, the complete gene for human granulocyte-macrophage colony-stimulating factor (hGM-CSF) has been cloned from a human genomic library. The gene is 2.5 kilobases in length, contains three introns, and is present as a single copy in the human genome. When subcloned into the mammalian expression vector pD3, the gene directs the synthesis of authentic hGM-CSF. In addition to its stimulation of in vitro granulopoiesis and monopoiesis, recombinant hGM-CSF stimulates in vitro erythropoiesis and megakaryopoiesis.

The polyomavirus early promoter: role of proximal promoter elements in the formation of 5' termini in vivo

Analysis of polyomaviruses with altered early promoter sequences indicates that in vivo (1) the polyomavirus early ATA motif and nearby upstream sequences dictate homogeneity of 5' termini, in contrast to what has been observed in vitro, where the cap site was reported to affect homogeneity of 5' termini (P. Jat, V. Novak, A. Cowie, C. Tyndall, and R. Kamen, 1982, Mol. Cell. Biol. 2, 737-751). (2) Substitution of the polyomavirus ATA motif by the adenovirus 2 major later promoter suppresses minor early 5' termini between the origin and the early cap sites, indicating that these termini are not the result of DNA replication.

Sequence signals which may be required for efficient formation of mRNA 3' termini

It has been known for sometime that AATAAA (Proudfoot and Brownlee, 1976) is often required for 3' mRNA processing. More recently, McLauchlan et al. (1985) have shown the high incidence of YGTGTTYY (Y is a pyrimidine) downstream from the poly (A) addition site. Our results fully support their findings. There have been indications that additional sequences are required either for transcription termination of mRNA or for its cleavage/processing. Here I present the results of detailed analysis of mammalian DNA sequences around the 3' ends of mRNAs. The distributions of 256 quartets and some pentamers have been studied. Except for the AATAAA several additional signals emerge, namely, the homooligomers A4-5, T4-5 and C4-5, C3-4 interspersed with a single T, alternations of T and G, TTCTT and GGAGG. These are highly regular sequences which may exhibit unique conformations. The results also show a clear-cut asymmetry in the distribution of complementary oligomers on the same DNA strand. The possibility that at least some of these signals are recognized on the DNA and thus play a role in the termination process is discussed.

The presence of nucleosomes on a DNA template prevents initiation by RNA polymerase II in vitro

RNA was synthesized in vitro using HeLa cell nuclear extracts and circular DNA templates onto which varying numbers of nucleosomes had been reconstituted with Xenopus oocyte extracts. We found that fully reconstituted templates supported no specific initiation by RNA polymerase II; however, DNA exposed to the reconstitution extracts under conditions which did not allow nucleosome deposition was transcribed normally. A set of successively less reconstituted templates was also transcribed. No initiation occurred on reconstitutes with more than two-thirds of the physiological nucleosome density; reconstitutes with less than one-third of the physiological nucleosome density were transcribed as efficiently as naked DNA.

Some guidelines for identification of recognition sequences: regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A)

Inspection of many proposed recognition signal sequences shows that TGTG/CACA, GAGA/TCTC or their triplet subsets, and TGA/TCA occur frequently. These repeated elements, conserved in recognition sequences from evolutionarily distant organisms, are likely to possess unique structural characteristics. Recurrence of these oligomers may aid in identification of further regulatory sequences in upstream or other regions. Another class of recognition sequences is GC-rich. At present there are only a few examples of this class. It is likely that these sequences function via a different mechanism.

The legumin gene family: structure of a B type gene of Vicia faba and a possible legumin gene specific regulatory element

The field bean, Vicia faba L. var. minor, possesses two sub-families of 11 S legumin genes named A and B. We isolated from a genomic library a B-type gene (LeB4) and determined its primary DNA sequence. Gene LeB4 codes for a 484 amino acid residue prepropolypeptide, encompassing a signal peptide of 22 amino acid residues, an acidic, very hydrophilic alpha-chain of 281 residues and a basic, somewhat hydrophobic beta-chain of 181 residues. The latter two coding regions are immediately contiguous, but each is interrupted by a short intron. Type A legumin genes from soybean and pea are known to have introns in the same two positions, in addition to an extra intron (within the alpha-coding sequence). Sequence comparisons of legumin genes from these three plants revealed a highly conserved sequence element of at least 28 bp, centered at approximately 100 bp upstream of each cap site. The element is absent from the equivalent position of all non-legumin and other plant and fungal genes examined. We tentatively name this element "legumin box" and suggest that it may have a function in the regulation of legumin gene expression.

Negative regulatory sequences in the EIa-inducible enhancer of the adenovirus-2 early EIIa promoter

The adenovirus type 2 early EIIa (EIIaE) transcriptional control region exhibits an EIa-dependent enhancer activity (Imperiale et al., 1985, Proc. Natl. Acad. Sci. USA 82, 381-385). We have determined the sequence requirements for this enhancer activity by analysing the enhancing capacity of the entire EIIa promoter region, or portions of it, when inserted approximately 400 bp upstream of the rabbit beta-globin gene. Globin-specific transcription efficiency from the resulting recombinants was measured after transfection into HeLa cells, both in the presence and absence of the EIa products. It was found that the minimal EIIa element with bidirectional, EIa-dependent enhancer activity extends between -111 and -27 relative to the EIIaE major startsite (+1). Furthermore an extensive deletion analysis revealed, within this element, three functionally distinct regions: a central region between about -90 and -70, corresponding to an essential EIIaE upstream promoter element, and two flanking control elements (about 20 bp each) which, in the absence of the EIa products, exert a negative effect on the enhancer activity. Deletion of either one of these control elements renders the EIIaE enhancer activity constitutive, suggesting that the EIa products stimulate the EIIaE enhancer by relieving the negative control mediated by these sequences.

The effect of changing the distance between the TATA-box and cap site by up to three base pairs on the selection of the transcriptional start site of a cloned eukaryotic gene in vitro and in vivo

We have studied how small changes in the distance between the TATA-box and cap site affect transcription of a eukaryotic gene in vitro and in vivo. The trout protamine gene TPG-3 [Gregory et al. (1982) Nucl. Acids Res. 10, 7581-7592] is a good model for such a study as it has (i) a consensus TATA-box 32 base pairs (bp) upstream from an A-residue which is the natural cap site (designated +1) (ii) two further A-residues at -5 and +5, providing alternative transcriptional start sites which are in significantly different sequence environments and (iii) a unique AvaII restriction site immediately downstream from the TATA-box which is ideal for the insertion or deletion of up to 3bp. Transcripts of the wild type and mutant genes were generated in vitro using a HeLa whole cell extract or 'in vivo' by transient expression following their transfection into HeLa cells. These 'spacer' mutations did not affect the efficiency of transcription of the gene in vitro but they did affect the selection of transcriptional start site both in vitro and 'in vivo'. Analysis of 5'-ends by S1-mapping and primer extension showed that the A-residue(s) selected are those which, by insertion or deletion, come to lie on the same face of the DNA double helix as the TATA-box, although the DNA sequence in the immediate vicinity of the potential start sites influences their utilisation. Comparison of the TPG-3 wild type transcripts in these experimental systems with natural mRNA suggests that cap site selection is more stringent in the developing trout testis.

Nucleosomes are phased along the mouse beta-major globin gene in erythroid and nonerythroid cells

We have used the chemical cleavage reagent methidiumpropyl-EDTA-Fe(II) to determine the location of the nucleosomes along the mouse beta-major globin gene in erythroid and nonerythroid cells. In mouse L cells, in which the globin gene is inactive, the nucleosomes are precisely positioned with respect to the underlying DNA sequence from positions -3000 to +1500 relative to the cap site. In uninduced and induced murine erythroleukemia cells, the same phasing persists but is interrupted from positions -200 to +500. This gap in the phased distribution of nucleosomes appears to be protected from MPE-Fe(II) digestion, and is bounded on both sides by hypersensitive sites. These results define at least two structural states for the globin gene: an inactive state in which the gene is covered with a continuous array of phased nucleosomes and an active state in which this array is disrupted over the 5' half of the structural gene.

Cloning, sequencing, and evolutionary analysis of the mouse erythropoietin gene

The gene for mouse erythropoietin was cloned and sequenced. We present here a preliminary analysis of the overall genomic organization of the coding portions and the two flanking regions of the gene. This is the third mammalian erythropoietin for which the sequence is available, but it represents the first from a nonprimate species. We investigated the evolutionary divergence of sequence and structure of the three erythropoietins and identified specific regions of the molecules that are apparently under various degrees, and perhaps different types, of functional constraint.

Partial purification of a nuclear protein that binds to the CCAAT box of the mouse alpha 1-globin gene

We enriched a fraction from nuclear extracts of murine erythroleukemia cells which contains a protein able to form stable complexes with the promoter region of the alpha 1-globin gene. Binding activity, which is present in mouse brain and a variety of cultured mouse and human cell lines, is not erythroid cell specific. Binding studies with alpha-globin gene promoter deletion mutants as well as DNase I footprinting and dimethyl sulfate protection studies showed that the factor bound specifically to the CCAAT box of the alpha 1 promoter. Enriched factor preparations exhibited weak binding to the promoter region of the beta maj-globin gene. This suggests that this protein could bind differentially to these two promoters in vivo. The enriched factor may be a ubiquitous nuclear protein involved in the differential regulation of the alpha 1- and beta maj-globin genes.

The immunoglobulin heavy-chain B-lymphocyte enhancer efficiently stimulates transcription in non-lymphoid cells

The mouse immunoglobulin heavy-chain (IgH) B-lymphocyte enhancer stimulates transcription from heterologous promoters 20- to 40-fold when transfected into several non-lymphoid cell lines. Stimulation in B-lymphocyte melanoma cell-lines is only about 5--10 times better. A central sequence is equally active in both cell types, whilst flanking sequences, on either side of the common enhancer sequences, specifically stimulate transcription in myeloma cells. These results suggest that there are factors in non-lymphoid cells that can interact with the IgH enhancer to stimulate transcription.

Homologous recognition of a promoter domain common to the MSV LTR and the HSV tk gene

We have partially purified, from rat liver, a nuclear protein fraction with sequence-specific affinity to a promoter domain shared by the herpesvirus tk gene and the Moloney murine sarcoma virus LTR. For both promoters, the protein-binding domain occurs roughly 80 bp upstream of the mRNA cap site and harbors the pentanucleotide sequence 5'-CCAAT-3'. The MSV LTR pentanucleotide occurs on the coding strand in an orientation pointing toward the retroviral transcription unit. The HSV tk pentanucleotide occurs on the noncoding strand in an orientation pointing away from the gene. Assays in microinjected frog oocytes and transfected mouse L cells indicate that equivalent point mutations, introduced at each residue of the CAT pentanucleotide of each promoter, lead to similar changes in promoter activity. Furthermore, they similarly alter binding of the nuclear protein fraction. Surprisingly, a C to G transversion at the first residue of the CAT pentanucleotide, which severely impairs the activity of both promoters, appears to increase affinity of the CAT binding protein.

Tissue restricted and stage specific transcription is maintained within 411 nucleotides flanking the 5' end of the chicken alpha-skeletal actin gene

alpha-skeletal actin message levels have been shown to be tightly regulated in chicken primary myoblast cultures. To test for gene elements required for muscle cell specific expression, DNA sequences containing the 5'-flanking regions of the chicken alpha-skeletal actin, beta-cytoplasmic actin, and the histone H2b genes were linked to the coding sequences of the chloramphenicol acetyltransferase gene and transfected into myogenic and non-myogenic cells. In contrast to beta-actin CAT hybrids, the alpha-skeletal actin CAT constructions displayed restricted CAT expression in transfected non-myogenic cells. We showed that a 411 nucleotide fragment flanking the 5' end of of the alpha-skeletal actin gene was responsible for a 9-15 fold increase in CAT enzymatic activity during myoblast fusion, versus only a transient 2 fold rise for the beta-actin and histone flanking sequences. These results indicate that DNA sequences within 411 bp of the 5' terminus of the alpha-skeletal actin gene influenced its cell type and stage specific expression.

Regulatory DNA elements localized remotely upstream from the drug-metabolizing cytochrome P-450c gene

We have investigated regulatory DNA elements in the expression of the drug metabolizing P-450c gene of rats. After combining the 5' flanking and upstream untranslated regions of the isolated P-450c gene with structural gene for chloramphenicol acetyltransferase (CAT), the fusion genes were transfected into cultured cells (Hepa-1 and L cells) for the assay of transient expression of CAT activity. CAT activity was expressed inducibly in response to 3-methylcholanthrene only in Hepa-1 cells. At least three regions containing regulatory DNA elements were indentified; one, which is present in the sequence from -44b to -0.2kb immediately upstream of the TATA box, functions in the basal level of transcription, and the other two which were located in the sequence from -0.8kb to -1.0kb and from -1.0kb to -6.3kb, enhance in combination, transcription in response to inducers in a manner independent of their orientation.

Multiple regulatory elements in the intergenic region between the alpha-fetoprotein and albumin genes

Three enhancer elements spanning a distance of 7 kilobases have been found at the 5' end of the alpha-fetoprotein (AFP) gene. These elements were identified by transient expression assay after the introduction of a modified mouse AFP gene with variable amounts of 5' flanking sequence into a human hepatoma cell line, Hep G2. These regulatory elements function in a position-independent and orientation-independent manner that is typical of enhancers. All three elements will stimulate transcription from the promoter of the herpes simplex virus thymidine kinase gene. In Hep G2 cells, transcriptional activation from the heterologous promoter was approximately 25- to 50-fold higher than the basal levels obtained in the absence of AFP enhancer elements. In HeLa cells, the increase in thymidine kinase gene transcription varied from 6- to 14-fold, indicating that the enhancer elements exhibit some cell type specificity. Deletion analysis of the region proximal to the AFP transcription initiation site identified an essential region between 85 and 52 bases upstream of the site of initiation of transcription whose removal resulted in almost complete extinction of transcriptional activity. This region, which has been shown to be dispensable for transcription in HeLa cells, defines a second tissue-specific regulatory region in the gene.

Expression of the mouse HPRT gene: deletional analysis of the promoter region of an X-chromosome linked housekeeping gene

The mouse hypoxanthine phosphoribosyltransferase gene, like several other housekeeping genes, lacks many of the features associated with promoters of RNA polymerase II-transcribed genes. HPRT transcripts have multiple initiation sites and an HPRT minigene was used to show that only 49 bases of 5' flanking sequence was necessary for normal expression in cultured cells. The essential region, which occurs within a complex series of direct repeats, is homologous to sequences upstream of other housekeeping genes. When this sequence was deleted, cryptic upstream initiation sites were revealed. Similar aberrant patterns of initiation were seen with all minigenes assayed in Xenopus oocytes. We speculate that this region of the HPRT promoter is involved in a different interaction with the transcriptional machinery to that occurring at more conventional promoters.

Detailed analysis of the mouse H-2Kb promoter: enhancer-like sequences and their role in the regulation of class I gene expression

Sequencing and deletion analyses of the H-2Kb promoter have suggested that several regions may be important for expression and regulation of this gene. Two of these regions are conserved inside the promoter of several genes coding for classical transplantation antigens, but not in the promoter of class I genes located in the Qa region. They display enhancer-like activity in cells that express H-2 genes, but show some tissue specificity in that they function very poorly in undifferentiated embryonal carcinoma cells in which H-2 genes are not expressed. They also have been shown not to be the target of the adenovirus-12 induced repression of class I gene expression recently demonstrated by Schrier et al. The promoter of the beta 2-microglobulin gene also contains a sequence with enhancer-like activity, but shares no homology with the H-2Kb promoter region.

Structural and functional analysis of the goat epsilon-globin genes

Since none of the vertebrate beta-globin loci studied to date has more than two functional embryonic beta-like globin genes, it would be unique if all six goat embryonic beta-globin genes were required for its survival. In this study we have asked whether all six embryonic genes in the goat are functional. This question has been addressed by examining the transient expression of these genes in HeLa cells and correlating these results with the sequence information obtained to date. Our studies show that only epsilon I and epsilon II are functional while the remaining four epsilon-globin genes are nonfunctional, i.e., pseudogenes. Interestingly, the two active epsilon-globin genes are located at the 5' end of the locus. While this unusual inactivation pattern may be the result of chance, it could also have resulted because the two duplication events, of the ancestral gene set epsilon-epsilon-psi beta-beta, did not include distally located regulatory region(s) essential for epsilon-globin gene expression. Once separated from the 5'-regulatory sequences the remaining four embryonic genes (epsilon III, epsilon IV, epsilon V and epsilon VI) accumulated mutations and became pseudogenes.

Sequences from sea urchin TU transposons are conserved among multiple eucaryotic species, including humans

Sequences homologous to various structural domains of the Strongylocentrotus purpuratus TU family of transposons are present in sea urchin species closely related to S. purpuratus and were found in close proximity to each other in linkage patterns that differed for different species. Sequence homologs of the inverted repeat outer domain (IVR-OD) segment were, in addition, present in a sea urchin related only distantly to S. purpuratus and in all other eucaryotic organisms surveyed. In humans, a polymorphic hybridization pattern was seen for genomic DNA obtained from different individuals. Sequence comparisons revealed that repeated sequence motifs similar to those making up the 15-base-pair direct repeat unit of the IVR-OD domain of the TU elements exist in the IVRs of transposons identified in Drosophila melanogaster and maize and in the transcription control regions of certain eucaryotic viral and cellular genes. The remarkable evolutionary conservation of IVR-OD homologs may reflect a biological role for these sequences in DNA transposition, the regulation of gene expression, or both.

Sequence analysis of the larval beta II-globin gene of Xenopus laevis

The 1822 bp sequence of the larval Xenopus laevis beta II-globin gene is reported together with 240 bp upstream of the gene and 190 bp beyond the site of polyadenylation. The mRNA start point was determined by primer extension as well as nuclease S1 mapping and the polyadenylation site by comparison of the gene sequence to the mRNA sequence derived from a corresponding cDNA clone. Like other vertebrate globin genes, this gene comprises three exons interrupted by two intervening sequences (IVS). IVS I spans over 582 nucleotides and interrupts the exon sequences within codon 30. IVS II is located between the codons 104/105 and spans over 617 nucleotides. The 5' region of the gene contains the canonical TATAA homology at position -31. Comparison of the upstream sequence to that of Xenopus laevis larval beta I-globin gene revealed a conserved sequence, located between nucleotide positions -60 and -87, which might function as regulatory element of transcription. Whereas the upstream region of the larval beta II-globin gene does not contain a CAAT box, we notice a reiterated AAATGA motif and discuss its possible significance.

Segmental homology between the promoter region of the human renin gene and the mouse ren1 and ren2 promoter regions

We have isolated and determined the nucleotide (nt) sequence of the 5' region of the human renin gene (h-ren). Two TATA boxes and a CAAT box were found. Start point determination has shown that only the proximal TATA box was used as the transcription initiation signal, both in the kidney and in a renin-secreting tumor. Comparison of the sequence of the 500-bp region upstream from the transcription start point with the corresponding regions of the ren1 and ren2 genes of the Swiss mouse revealed no overall homology between the human and mouse renin sequences. Only very short sequences of high homology ranging in size from 10 to 18 nt were found in the sequenced regions. By hybridization experiments, we have detected a region upstream from each mouse renin gene related to the h-ren; analysis of the nt sequence of this region reveals that they belong to the Alu family of repetitive DNA.

Structure of transcriptionally active chromatin

Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.