Lysozyme gene activity in chicken macrophages is controlled by positive and negative regulatory elements

A position-dependent silencer plays a major role in repressing alpha-fetoprotein expression in human hepatoma

A large percentage of human hepatomas produce alpha-fetoprotein (AFP), but the levels of AFP expression vary greatly among hepatomas. To understand the molecular basis for this variation, we analyzed transcriptional regulatory activities associated with the 5'-flanking region of the AFP gene in two human hepatoma cell lines, HuH-7 and huH-1/cl-2, which produce a high and a low level of AFP, respectively. We found that the low level of AFP production in huH-1/cl-2 is due to the action of at least two silencer regions located between the enhancer and the promoter of the AFP gene. In contrast, no silencer activity is expressed in HuH-7. We identified 5'-CTTCATAACTAATACTT-3' to be a core sequence responsible for the negative regulatory activity. This sequence is repeated four times in a strong, distal silencer region, Sd, whereas one copy is present in a weak, proximal silencer region, Sp. The silencer reduces transcriptional initiation by blocking enhancer activation of the AFP promoter in a position-dependent manner. The silencer functions in the presence of positive transcription factors and may play a key role in developmental repression as well as variable expression of the AFP gene in hepatomas.

A position-dependent silencer plays a major role in repressing alpha-fetoprotein expression in human hepatoma

A large percentage of human hepatomas produce alpha-fetoprotein (AFP), but the levels of AFP expression vary greatly among hepatomas. To understand the molecular basis for this variation, we analyzed transcriptional regulatory activities associated with the 5'-flanking region of the AFP gene in two human hepatoma cell lines, HuH-7 and huH-1/cl-2, which produce a high and a low level of AFP, respectively. We found that the low level of AFP production in huH-1/cl-2 is due to the action of at least two silencer regions located between the enhancer and the promoter of the AFP gene. In contrast, no silencer activity is expressed in HuH-7. We identified 5'-CTTCATAACTAATACTT-3' to be a core sequence responsible for the negative regulatory activity. This sequence is repeated four times in a strong, distal silencer region, Sd, whereas one copy is present in a weak, proximal silencer region, Sp. The silencer reduces transcriptional initiation by blocking enhancer activation of the AFP promoter in a position-dependent manner. The silencer functions in the presence of positive transcription factors and may play a key role in developmental repression as well as variable expression of the AFP gene in hepatomas.

Goose-type lysozyme gene of the chicken: sequence, genomic organization and expression reveals major differences to chicken-type lysozyme gene

This report describes the cloning, sequencing and expression pattern of the chicken goose-type lysozyme gene. The cDNA sequence was found to have no homology to that of the chicken-type lysozyme gene and exhibits a completely different exon-intron organization. In addition, goose-type lysozyme displays an overlapping but different tissue expression pattern in chickens than chicken-type lysozyme.

Every enhancer works with every promoter for all the combinations tested: could new regulatory pathways evolve by enhancer shuffling?

The promoters and enhancers of cell type-specific genes are often conserved in evolution, and hence one might expect that a given enhancer has evolved to work best with its own promoter. While this expectation may be realized in some cases, we have not found evidence for it. A total of 27 combinations of different promoters and enhancers were tested by transfection into cultured cells. We found that the relative efficiency of the enhancers is approximately the same, irrespective of the type of promoter used, i.e., there was no strong preference for any given enhancer/promoter combination. Notably, we do not see particularly strong transcription when the immunoglobulin kappa enhancer (or the immunoglobulin heavy chain enhancer) is used to activate a kappa gene promoter. We propose that a generally permissive enhancer/promoter interaction is of evolutionary benefit for higher eukaryotes: by enhancer shuffling, genes could be easily brought under a new type of inducibility/cell type specificity.

Lack of correlation between DNA methylation and transcriptional inactivation: the chicken lysozyme gene

We have analyzed the methylation state of all nine CpG sites in the transcription start region (-420 to +250 base pairs) of the chicken lysozyme gene by genomic sequencing. One of these sites, at -81, lies within the promoter, seven are clustered within the first exon, and the last is in the first intron. Five cell types and tissues have been investigated to study the relationship between methylation level and gene expression. For each cell type used, the majority of CpG sites showed a similar level of methylation. Of two gene-nonexpressing tissues, erythrocytes are hypomethylated, whereas liver is methylated at most of its CpG sites. For gene-expressing tissues, oviduct is completely unmethylated, whereas HD-11 culture cells are methylated. Thus no correlation is observed between degree of CpG methylation and level of expression of the lysozyme gene. The observed methylation patterns are discussed in terms of possible features of the local chromatin structure.

Genomic footprinting of proteins interacting with the chicken lysozyme promoter

The functions of the promoter of the chicken-lysozyme-encoding gene (Lsz) are complex, since, on the one hand, the promoter serves to mediate the effects of five upstream regulatory elements and, on the other, it contains itself important regulatory sequences. To analyze this interplay we first monitored protein-DNA interactions at the Lsz promoter in hormonally regulated oviducts and in constitutively expressing HD11 cells by in vivo genomic footprinting. Two regions of strong protein-DNA interactions shared by both HD11 and oviduct cells were localized between nucleotides (nt) -105 and -119 and between nt -61 and -74, respectively. A third region of protein-DNA contacts was found selectively in HD11 cells from nt -199 to -204; this region corresponds in position with a previously identified HD11 cell-specific enhancer element. Furthermore, we determined the sites hypersensitive to an endogenous endonuclease in isolated nuclei using the genomic sequencing protocol. These sites fall into two regions: one encompasses the in vivo localized protein-DNA contacts between nt -105 and -119 and between nt -61 and -74; the other was found in a sequence largely devoid of in vivo protein-DNA interactions. We hypothesize that hypersensitive cleavage sites are generated by protein-induced changes in the DNA conformation.

Modular structure of a chicken lysozyme silencer: involvement of an unusual thyroid hormone receptor binding site

Silencer elements, by analogy to enhancer elements, function independently of their position and orientation. We show that the chicken lysozyme silencer S-2.4 kb has many other characteristics in common with enhancer elements. The silencer is comprised of modules that independently repress gene activity--repression being increased synergistically when different or identical modules are combined. Repression is effective both on a complete and on a minimal promoter consisting of a TATA box only. One silencer module is bound in vitro by a 75-93 kd protein, termed NeP1; the other can be bound either by the product of the oncogene v-erbA or by the thyroid hormone receptor. This erbA binding site is unusual in that the palindromic sequence is inverted.

Cell-type specificity of regulatory elements identified by linker scanning mutagenesis in the promoter of the chicken lysozyme gene

The chicken lysozyme gene is constitutively expressed in macrophages, in oviduct cells its expression is controlled by steroid hormones, and in fibroblasts the gene is not expressed. A fusion gene consisting of promoter sequences of the lysozyme gene from -208 to +15 in front of the chloramphenicol acetyltransferase (CAT) coding region was more than 50 times less active in non-expressing cells as compared to expressing cells. In order to identify the element(s) responsible for this cell-type specificity 31 different linker scanning mutations were generated within this promoter fragment and analyzed by transient transfections in the three types of chicken cells mentioned above. Three mutation sensitive regions located around position -25, -100 and between -158 and -208 were detected in each cell type, however, several LS mutations displayed clear cell-type specific differences in their phenotypic effects. Interestingly, a few LS mutations led to an increase in promoter activity in fibroblasts suggesting that the corresponding wildtype sequences represent binding sites for negatively acting transcription factors.

A nuclear DNA attachment element mediates elevated and position-independent gene activity

The transcriptional activity of genes that have randomly integrated into the genomes of transfected cells and transgenic organisms is in general unpredictable, varying with the chromosomal site of the insertion. This effect of chromosomal position on gene expression may reflect the organization of chromosomes into topologically constrained loops and functional domains. To assess the biological significance of these loop domains, the anchorage of DNA to the nuclear scaffold has been studied at specific gene loci. We have previously defined cis-acting regions flanking the chicken lysozyme-gene domain that mediate the attachment of the chromatin to the nuclear scaffold. These 'A-elements' map to the 5' and 3' boundaries of the region of general DNase sensitivity in the active chromatin, which contains the lysozyme gene and its cis-regulatory elements. Here we report that when a reporter gene is flanked by 5' A-elements from the lysozyme gene, its expression in stably transfected cells is significantly elevated and is independent of chromosomal position.

Calcitriol enhances transcriptional activity of lysozyme and cathepsin D genes in U937 promonocytes

Calcitriol (1,25-dihydroxyvitamin D3) has been reported to enhance the rate of synthesis of lysozyme [Rouis, Thomopoulos, Louache, Testa, Heroy & Titeux, (1985) Exp. Cell Res. 157, 539-543] and of cathepsin D [Stein, Braulke, von Figura & Hasilik (1987) Biol. Chem. Hoppe-Seyler 368, 413-418] in human promonocytes U937. In this study we show hat the hormone enhances the steady-state levels of cathepsin D and lysozyme mRNAs. The enhancement of the latter but not of the former is strongly inhibited by cycloheximide. The degradation rates of cathepsin D and lysozyme mRNAs as revealed in the presence of actinomycin D are not significantly affected by the treatment of the cells with calcitriol. In nuclei prepared from calcitriol-treated cells, an enhanced rate of synthesis of cathepsin D and lysozyme mRNA precursors is observed. These results suggest that in human promonocytes the rate of the transcription of cathepsin D and lysozyme genes is enhanced in the presence of calcitriol and that the regulation by the hormone of the transcription of lysozyme gene involves a short-lived or an induced protein.

Role of molecular biology in hypertension research. State of the Art lecture

In this article we will examine the potential impact of molecular biology on hypertension research. We will review the available molecular techniques, which include gene cloning, transient and stable expressions, as well as the use of transgenic animals. To facilitate our discussion, we will focus primarily on research of the renin gene. Renin provides a useful model that illustrates the power of biotechnology in providing detailed structural and biochemical information on a complex protein that exists in low quantities in vivo. Studies of its messenger RNA and gene expression have resulted in an improved understanding of the biology of the renin system and in generating new hypotheses. These approaches can be generalized to studies of other vasoactive hormones, contractile protein, and other gene products related to cardiovascular regulation. To elucidate the role of a specific gene in genetic hypertension, we will discuss the use of genetic markers in cosegregation or linkage analysis. Finally, we will examine the potential of transgenic animals in the study of regulation of gene expression in the whole animal and the contribution of selective genes to hypertension. We believe that molecular biology complements the biochemical and physiological approaches and provides new opportunities for furthering our concept of hypertension mechanisms.

Specific interactions of histone H1 and a 45 kilodalton nuclear protein with a putative matrix attachment site in the distal promoter region of a cell cycle-regulated human histone gene

Protein-DNA interactions within the promoter of a cell cycle-regulated human H4 histone gene were examined by binding of 5'-end-labeled DNA segments to Western blots of nuclear protein fractions. Specific protein interactions were observed with DNA segments located between -500 bp and -1,070 bp upstream of the ATG initiation codon and included a histone H1 binding segment flanked on both sides by binding sites for a 45 kD nuclear protein. This region of the gene contains a DNase I-sensitive site in the center (-720 to -820 bp), and sequence analysis revealed the presence of scaffold attachment sequences in the two flanking segments. Topoisomerase II consensus sequences and in vitro topoisomerase II cleavage sites were also detected in the two flanking segments. Our results suggest that the 45 kd nuclear protein may preferentially interact with these two segments of the H4 histone gene to mediate association with the nuclear matrix. The presence of negative regulatory elements in this putative matrix attachment region provides a basis for the speculation that such nuclear proteins are associated with alterations in gene-matrix interaction that are functionally related to gene expression.

Negative control elements and cAMP responsive sequences in the tissue-specific expression of mouse renin genes

The 5' flanking regions of the mouse renin genes (Ren1d and Ren2d) contain putative negative control and cAMP responsive elements. Sequence analysis shows additionally that these putative control elements in the Ren2d gene are interrupted by a 160-base-pair insertion. To document the functions of these elements, we isolated these regions and fused them to the reporter gene chloramphenicol acetyltransferase (CAT), which was linked upstream to a thymidine kinase (TK) promoter (pUTKAT1). The chimeric constructs were transfected into mouse pituitary tumor AtT-20 and human choriocarcinoma JEG-3 cells. At the basal unstimulated condition, Ren1d 5' flanking sequence in the sense orientation inhibited basal CAT expression from the TK promoter of pUTKAT1, whereas the same sequence in the antisense orientation did not. The 5' flanking region of Ren2d had no inhibitory effect on basal CAT expression. These data demonstrate that the negative control element is functional in Ren1d but is nonfunctional in Ren2d, suggesting that the 160-base-pair insertion in Ren2d interferes with the function of the negative control elements. In response to 8-bromo-cAMP, both renin genes increased transcription 3-fold, suggesting a functional cis action of the cAMP responsive element in both genes. These data may be important in the understanding of the regulation of the tissue-specific expression of mouse renin genes.

Many transcription factors interact synergistically with steroid receptors

Progesterone (PRE) or glucocorticoid receptor (GRE) DNA binding sites are often found clustered with binding sites for other transcription factors. Individual protein binding sites were tested without the influence of adjacent factors by analyzing isolated combinations of several transcription factor binding sites with PREs or GREs. All show strong synergistic effects on steroid induction. The degree of synergism is inversely related to the strength of the GRE. Thus, a steroid responsive unit can be composed of several modules that, if positioned correctly, act synergistically.

A complex androgen-responsive enhancer resides 2 kilobases upstream of the mouse Slp gene

Neighboring genes encoding the mouse sex-limited protein (Slp) and fourth component of complement (C4) show extensive homology. In contrast to C4, however, Slp is regulated by androgen. One region of the Slp gene capable of hormonal response following transfection was located about 2 kilobases upstream of the transcription start site, where the C4 and Slp sequences diverge. This region, delimited here to a 0.75-kilobase fragment, showed cryptic promoter activity as well as androgen responsiveness in either orientation in front of the bacterial chloramphenicol acetyltransferase coding region. When this fragment was placed upstream of a viral long terminal repeat, increased chloramphenicol acetyltransferase expression derived from the viral promoter. Proteins from nuclear extracts specifically bound to four sequences within the region, near sites that are DNase I hypersensitive in vivo and reflect the hormonal and developmental regulation of Slp. Like several other cellular enhancers, this androgen-responsive element seems to be modular in nature and complex in its function.

Mouse lysozyme M gene: isolation, characterization, and expression studies

We have isolated and characterized both cDNA and genomic DNA of the mouse lysozyme M gene. Derivation of the amino acid sequence from the nucleotide sequences revealed six positions in the carboxyl terminus that differ from partial sequences previously published. The differential detection of specific mRNAs from the closely related lysozyme M and P genes has revealed different but overlapping tissue specificities of expression. The M gene is expressed weakly in myeloblasts, moderately in immature macrophages, and strongly in both mature macrophages and macrophage-rich tissues, while high levels of P transcripts are present only in small intestine. Sites of protein accumulation, rather than gene expression, have been identified by comparative quantitation of mRNA and enzyme levels.

A complex androgen-responsive enhancer resides 2 kilobases upstream of the mouse Slp gene

Neighboring genes encoding the mouse sex-limited protein (Slp) and fourth component of complement (C4) show extensive homology. In contrast to C4, however, Slp is regulated by androgen. One region of the Slp gene capable of hormonal response following transfection was located about 2 kilobases upstream of the transcription start site, where the C4 and Slp sequences diverge. This region, delimited here to a 0.75-kilobase fragment, showed cryptic promoter activity as well as androgen responsiveness in either orientation in front of the bacterial chloramphenicol acetyltransferase coding region. When this fragment was placed upstream of a viral long terminal repeat, increased chloramphenicol acetyltransferase expression derived from the viral promoter. Proteins from nuclear extracts specifically bound to four sequences within the region, near sites that are DNase I hypersensitive in vivo and reflect the hormonal and developmental regulation of Slp. Like several other cellular enhancers, this androgen-responsive element seems to be modular in nature and complex in its function.

Cooperativity of the glucocorticoid receptor and the CACCC-box binding factor

Glucocorticoid receptor binding sites (GRE) are often tightly clustered with other transcription factor binding sequences. Examples of this occur upstream of the genes for chicken lysozyme and human metallothionein IIA (ref. 3), in several retroviral LTRs and upstream of the rat tryptophan oxygenase (TO) gene. In the TO gene, sequences immediately upstream of a glucocorticoid receptor binding site are required for steroid induction and contain a CACCC-box identical to that found in the beta globin gene. Here we demonstrate specific binding to this TO-CACCC element and show that it will also act cooperatively with a MMTV glucocorticoid receptor binding site. The response to dexamethasone is independent of the order and relative orientation of these elements but does depend on their precise spacing. Optimal induction occurs at a periodicity of approximately 10 base pairs (bp) indicating a requirement for stereospecific alignment. Binding to the CACCC box, however, is not affected by its distance from the glucocorticoid receptor site. We conclude that the observed cooperativity is mediated by protein:protein interactions and does not depend on cooperative DNA binding.