Far upstream regulatory elements enhance position-independent and uterus-specific expression of the murine alpha1(I) collagen promoter in transgenic mice.

The stage- and tissue-specific expression of many eukaryotic genes is regulated by cis-regulatory elements, some of which are located in proximity to the start site of transcription whereas others have been identified at considerable distances. In previous studies we have identified far upstream DNase I-hypersensitive sites in the murine alpha1(I) collagen (Col1a1) gene, which may play a role in the regulation of this abundantly expressed gene. Here we have cloned several of these sites into reporter gene constructs containing the Col1a1 promoter driving the green fluorescent protein (GFP) reporter gene and tested their possible functions in transfection experiments and transgenic mice. In transient and stable transfections none of the hypersensitive sites had a significant effect on Col1a1 promoter activity, indicating that they do not contain a classical transcriptional enhancer. In transgenic animals one element located at -18 to -19.5 kb enhanced the position-independent activity of the linked Col1a1 promoter and may be part of a locus control region. Another element located at -7 to -8 kb specifically enhanced reporter gene expression in the uteri of transgenic mice, suggesting that it contains a novel transcriptional enhancer that may be involved in the regulation of type I collagen expression in tissue remodeling in the uterus during the estrous cycle. Our studies also demonstrate the versatility of the GFP reporter gene for use in transgenic animals because it can be analyzed in live animals, whole mount embryos, histological thin sections, or primary cell cultures, and it can be quantified very sensitively in tissue or cell extracts using a fluorometer.

Molecular cloning and chromatin structure analysis of the murine alpha1(I) collagen gene domain.

We have isolated molecular clones of genomic mouse DNA spanning 55 kb, including the entire coding region of the murine alpha1(I) collagen (Col1a1) gene and 24 kb of 5' and 13 kb of 3'-flanking sequences, and have performed a detailed chromatin structure analysis of these sequences. Several new DNase-I-hypersensitive sites were identified. The distal 5'-flanking region contains two clusters of DNase-I-hypersensitive sites located between 7 and 8 kb and between 15 and 20 kb upstream of the start site of transcription, respectively. Several of these sites were shown to be present in collagen-producing, but not in non-producing cells, indicating that they are associated with transcription of the gene and may function in its regulation. One strong constitutive DNase-I-hypersensitive site at -18.5 kb was also cleaved by endogenous nucleases. The 3'-flanking region of the gene contains a DNase-I-hypersensitive site located 6 kb downstream of the end of the gene, as well as sequences that can induce a non-B DNA structure. Because these latter sequences coincide with DNase-I-hypersensitive sites in the homologous human gene, our results suggest that some regulatory elements may play a role in gene regulation, not by specific protein-DNA interactions but by virtue of their ability to induce a non-B DNA structure and/or an alternate chromatin conformation. A comparison of the murine and human Col1a1 domains shows a similar, although not identical, distribution of DNase-I-hypersensitive sites, indicating a conserved arrangement of regulatory elements. Our results strongly suggest that these new sites constitute regulatory elements which are involved in the transcriptional regulation and/or chromatin loop organization of the Col1a1 gene, and they are now amenable for functional analyses.

Binding of upstream stimulatory factor to an E-box in the 3'-flanking region stimulates alpha1(I) collagen gene transcription.

Since several lines of evidence implicate the 3'-flanking region in regulating alpha1(I) collagen gene transcription, we analyzed 12. 4-kilobase pairs of 3'-flanking sequence of the murine alpha1(I) collagen gene for transcriptional elements. A region of the 3'-flanking region stimulated expression of the heterologous beta-globin gene promoter in an enhancer trap plasmid and of the alpha1(I) collagen gene promoter in a collagen-luciferase reporter gene construct when located 3' to the luciferase reporter gene. DNase I footprinting analysis demonstrated the presence of three regions where DNA binding proteins specifically interact within this 3'-stimulatory region. Inspection of the DNA sequence revealed a consensus E-box, a binding site for basic helix-loop-helix proteins, in one of the protein binding sites. Mobility shift assays demonstrated that upstream stimulatory factors (USF) USF-1 and USF-2 bind to this E-box. Mutating the E-box in the context of the 3'-flanking region confirmed that it contributes to the enhancement of transcriptional activity of the alpha1(I) collagen gene promoter. Mutations in all three protein binding sites abolished transcriptional activation by the 3'-flanking region, suggesting a complex interaction among the trans-acting factors in enhancing transcriptional activity. Thus, a region of the 3'-flanking region of the alpha1(I) collagen gene stimulates transcription of the alpha1(I) collagen gene promoter, and USF-1 and USF-2 contribute to this transcriptional stimulation.

Correct cell- and differentiation-specific expression of a murine alpha 1 (I) collagen minigene in vitro differentiating embryonal carcinoma cells.

An in vitro differentiation system utilizing retinoic acid (RA) treatment of pluripotent murine P19 embryonal carcinoma (EC) cells, which can be induced to differentiate into various cell types, was optimized for maximal induction of alpha 1 type I collagen (Col1a1) gene expression. Differentiation was associated with apoptotic death of the majority of cells, indicating that this in vitro system faithfully mimics the in vivo differentiation process. Col1a1 mRNA became detectable by RNase protection assay after 3 days of RA treatment and, after 6 days, reached a level comparable to that in NIH 3T3 fibroblasts. After induction of differentiation the Col1a1 gene remained transcriptionally active for extended periods of time even in the absence of RA. A minigene version of the murine Col1a1 gene was constructed that contains all of the so far known Col1a1 regulatory elements. This construct exhibited the correct expression pattern in stable transfection experiments: it was expressed in fibroblasts, but not in undifferentiated P19 EC cells, and it was transcriptionally activated after induction of differentiation. This experimental system should be a useful tool for dissecting the molecular mechanisms involved in the developmental activation and stage- and tissue-specific expression of the murine Col1a1 gene.

DNA methylation represses the murine alpha 1(I) collagen promoter by an indirect mechanism.

Several lines of evidence indicate that DNA methylation plays a role in the transcriptional regulation of the murine alpha 1(I) collagen gene. To study the molecular mechanisms involved, a reporter gene construct containing the alpha 1(I) promoter and part of the first exon linked to the luciferase gene (Col3luc) was methylated in vitro and transfected into murine fibroblasts and embryonal carcinoma cells. Methylation resulted in repression of the alpha 1(I) promoter in both cell types, although it was less pronounced in embryonal carcinoma cells than in fibroblasts. The extent of repression depended on the density of methylation. DNase footprint and mobility shift assays indicated that the trans-acting factors binding to the alpha 1(I) promoter and first exon are ubiquitous factors and that their DNA binding is not inhibited by methylation. Transfection of Col3luc into Drosophila SL2 cells together with expression vectors for the transcription factors Sp1 and NF-1 showed that DNA methylation also inhibits the alpha 1(I) promoter in nonvertebrate cells, although to a much lesser extent than in murine cells. However, Sp1 and NF-1 transactivated the unmethylated and methylated reporter gene in SL2 cells equally well, confirming that these factors can bind and transactivate methylated DNA and indicating that DNA methylation represses the alpha 1(I) promoter by an indirect mechanism. This was further confirmed by cotransfection experiments with unspecific methylated competitor DNA which partially restored the activity of the methylated alpha 1(I) promoter. Our results suggest that DNA methylation can inhibit promoter activity by an indirect mechanism independent of methyl-C-binding proteins and that in vertebrate cells, chromatin structure and methyl-C-binding proteins cooperatively mediate the transcriptional inhibitory effect of DNA methylation.

Type I collagen gene regulation and the molecular pathogenesis of cirrhosis.

Cirrhosis is characterized by an increased deposition of extracellular matrix proteins, including type I collagen. Type I collagen is a product of two genes, alpha 1(I) and alpha 2(I), which are generally coordinately regulated. Since expression of type I collagen genes is increased during cirrhosis, understanding the structure and function of the regulatory components of the type I collagen genes should provide insight into the molecular pathogenesis of cirrhosis. This review will analyze the collagen alpha 1(I) gene with respect to chromatin structure, DNA methylation, regulation by agonists, and DNA-protein interactions.

Developmental changes in the methylation status of regulatory elements in the murine alpha 1(I) collagen gene.

Regulatory elements contributing to the tissue-specific regulation of the murine alpha 1(I) collagen (Colla1) gene have previously been identified in its promoter region and first intron. Because several lines of evidence indicate that DNA methylation may be involved in the tissue-specific regulation of Colla1 gene expression, we have analyzed the methylation status of the 5' region of the gene by restriction analysis and a methylation-dependent PCR assay. All sites tested were unmethylated in sperm DNA. The region surrounding the start site of transcription was partially or completely methylated in undifferentiated embryonal cell lines, suggesting that it may be marked by de novo methylation during early embryonic development. In differentiated cells and adult tissues, the Colla1 promoter was completely demethylated in collagen-producing and some nonproducing cells, and partially methylated in other nonproducing cells. The first intron was unmethylated in collagen-producing as well as nonproducing cells. Only sites in the first exon showed an inverse correlation with transcriptional activity, i.e., they were unmethylated in cells that express the gene, but predominantly methylated in cells that do not. Our results indicate that the methylation status of a small area (less than 1 kb) downstream of the Colla1 promoter, but not of the promoter itself or the first intron, may be critical for transcriptional activity of the promoter, presumably through an indirect mechanism.

Retrovirus-induced insertional mutagenesis: mechanism of collagen mutation in Mov13 mice.

The Mov13 mouse strain carries a mutation in the alpha 1(I) procollagen gene which is due to the insertion of a Moloney murine leukemia provirus into the first intron. This insertion results in the de novo methylation of the provirus and flanking DNA, the alteration of chromatin structure, and the transcriptional inactivity of the collagen promoter. To address the mechanism of mutagenesis, we reintroduced a cloned and therefore demethylated version of the Mov13 mutant allele into mouse fibroblasts. The transfected gene was not transcribed, indicating that the transcriptional defect was not due to the hypermethylation. Rather, this result strongly suggests that the mutation is due to the displacement or disruption of cis-acting regulatory DNA sequences within the first intron. We also constructed a Mov13 variant allele containing a single long terminal repeat instead of the whole provirus. This construct also failed to express mRNA, indicating that the Mov13 mutation does not revert by provirus excision as has been observed for other retrovirus-induced mutations.

Retrovirus-induced interference with collagen I gene expression in Mov13 fibroblasts is maintained in the absence of DNA methylation.

We have studied the role of DNA methylation in repression of the murine alpha 1 type I collagen (COL1A1) gene in Mov13 fibroblasts. In Mov13 mice, a retroviral provirus has inserted into the first intron of the COL1A1 gene and blocks its expression at the level of transcriptional initiation. We found that regulatory sequences in the COL1A1 promoter region that are involved in the tissue-specific regulation of the gene are unmethylated in collagen-expressing wild-type fibroblasts and methylated in Mov13 fibroblasts, confirming and extending earlier observations. To directly assess the role of DNA methylation in the repression of COL1A1 gene transcription, we treated Mov13 fibroblasts with the demethylating agent 5-azacytidine. This treatment resulted in a demethylation of the COL1A1 regulatory sequences but failed to activate transcription of the COL1A1 gene. Moreover, the 5-azacytidine treatment induced a transcription-competent chromatin structure in the retroviral sequences but not in the COL1A1 promoter. In DNA transfection and microinjection experiments, we found that the provirus interfered with transcriptional activity of the COL1A1 promoter in Mov13 fibroblasts but not in Xenopus laevis oocytes. In contrast, the wild-type COL1A1 promoter was transcriptionally active in Mov13 fibroblasts. These experiments showed that the COL1A1 promoter is potentially transcriptionally active in the presence of proviral sequences and that Mov13 fibroblasts contain the trans-acting factors required for efficient COL1A1 gene expression. Our results indicate that the provirus insertion in Mov13 can inactivate COL1A1 gene expression at several levels. It prevents the developmentally regulated establishment of a transcription-competent methylation pattern and chromatin structure of the COL1A1 domain and, in the absence of DNA methylation, appears to suppress the COL1A1 promoter in a cell-specific manner, presumably by assuming a dominant chromatin structure that may be incompatible with transcriptional activity of flanking cellular sequences.

Elevated expression of v-mos is correlated with altered differentiation of carcinoma cells.

Permanent alterations of the epithelial differentiation pattern were investigated after infection of HH-16 cl. 4 adenocarcinoma cells with Moloney murine sarcoma virus (MoMuSV). Transformed cell clones with fibroblastoid morphology were isolated and compared with clones of unchanged epithelioid phenotype. Southern blot analyses showed intact MoMuSV proviral genomes in copy numbers between 4 and 9 in the DNA of the morphologically transformed cell clones as well as in the clones with unaltered morphology. The fibroblastoid cells produced sarcomas after inoculation of newborn rats, whereas MoMuSV-infected cell clones with unaltered epithelioid morphology yielded adenocarcinomas. Immunocytochemical analyses revealed that morphological transformation into the fibroblastoid phenotype was accompanied by loss of cytokeratin expression and appearance of the mesenchymal marker protein vimentin. Proviral DNA was transcribed in the infected cell clones irrespective of their phenotype; however, transcription was significantly higher in cells with fibroblastoid morphology than in epithelioid cells.

Transcriptionally active genome regions are preferred targets for retrovirus integration.

We have analyzed the transcriptional activity of cellular target sequences for Moloney murine leukemia virus integration in mouse fibroblasts. At least five of the nine random, unselected integration target sequences studied showed direct evidence for transcriptional activity by hybridization to nuclear run-on transcripts prepared from uninfected cells. At least four of the sequences contained multiple recognition sites for several restriction enzymes that cut preferentially in CpG-rich islands, indicating integration into 5' or 3' ends or flanking regions of genes. Assuming that only a minor fraction (less than 20%) of the genome is transcribed in mammalian cells, we calculated the probability that this association of retroviral integration sites with transcribed sequences is due to chance to be very low (1.6 x 10(-2]. Thus, our results strongly suggest that transcriptionally active genome regions are preferred targets for retrovirus integration.

Regulatory elements in the 5'-flanking region and the first intron contribute to transcriptional control of the mouse alpha 1 type I collagen gene.

We have identified two blocks of regulatory sequences located in the 5'-flanking region and the first intron of the mouse alpha 1 type I collagen (COL1A1) gene. Both blocks were found to contain positive as well as negative regulatory elements. Sequences located within 222 base pairs upstream of the transcription start site showed a strong stimulatory effect on the COL1A1 promoter and were sufficient for tissue-specific regulation of the COL1A1 gene. The combined upstream and intron regulatory sequences showed a marked inhibition of COL1A1 promoter activity in fibroblasts. This finding suggests that additional, more remote regulatory sequences may be required for establishing the high level of activity of the endogenous COL1A1 gene in fibroblastoid cells.

Retrovirus integration and chromatin structure: Moloney murine leukemia proviral integration sites map near DNase I-hypersensitive sites.

The chromatin conformation of mouse genome regions containing Moloney murine leukemia proviral intergration sites in two Mov mouse strains and randomly selected integration sites in virus-infected mouse 3T3 fibroblasts was analyzed. All integrations have occurred into chromosomal regions containing several DNase-hypersensitive sites, and invariably the proviral integration sites map within a few hundred base pairs of a DNase-hypersensitive site. The probability that this close association between proviral integration sites and DNase-hypersensitive sites was due to chance was calculated to be extremely low (2 X 10(-4]. Because the proviral integrations analyzed were not selected for an altered phenotype, our results suggest that DNase-hypersensitive regions are preferred targets for retrovirus integration.

The soluble glycoprotein of vesicular stomatitis virus is formed during or shortly after the translation process.

Gs protein is a shorter, soluble form of the viral G protein of vesicular stomatitis virus (VSV) lacking the membrane-anchoring domain. Production of Gs protein appears to be a general property of VSV because infection of BHK-21 cells by five different isolates of the VSV serotype Indiana led in all cases to the synthesis of Gs protein. Moreover, it is formed in a variety of eucaryotic cell lines after VSV infection. In pulse-chase experiments, we observed a time-dependent change in the ratio of G to Gs protein released into the growth medium, suggesting that Gs is formed intracellularly rather than on the cell surface. Further experiments revealed that Gs protein can be synthesized in vitro in the reticulocyte lysate system after addition of a viral mRNA fraction and in a coupled transcription-translation system with VSV core particles. In the presence of microsomal membranes both G and Gs protein were glycosylated in the reticulocyte lysate, confirming that the authentic Gs protein is synthesized in vitro. The addition of various protease inhibitors to the cell-free system and variation of the incubation conditions did not alter the ratio of G to Gs formation. Taken together, these experiments suggest strongly that Gs protein is not a product of a membrane-associated proteolytic activity but is formed during or shortly after the translation process. Our attempts to detect a specific, shorter mRNA coding for the Gs protein by molecular hybridization procedures did not reveal the existence of such a mRNA species.

Retrovirus insertion inactivates mouse alpha 1(I) collagen gene by blocking initiation of transcription.

Mov13 mice carry a single Moloney murine leukaemia virus (M-MuLV) proviral copy in the first intron of the alpha 1(I) collagen gene. Virus insertion interferes with the synthesis of stable alpha 1(I) collagen messenger RNA and causes a recessive lethal mutation. The virus insertion has induced changes of the methylation pattern as well as the chromatin conformation in the mutated gene. Specifically, a DNase-hypersensitive site which is associated with active transcription of the wild-type collagen gene is not present in the mutant allele. The block of collagen expression could be caused by virus-induced instability of collagen mRNA or by impaired initiation of transcription. To distinguish between these possibilities, we have compared the activity of the alpha 1(I) collagen gene promoter in cell lines derived from wild-type and Mov13 embryos by nuclear run-on transcription experiments and S1 mapping of nuclear RNA. We show here that initiation of transcription of the mutant gene is reduced 20-100-fold. This indicates that the virus-induced change of chromatin structure in the promoter region of the mutant gene prevents RNA polymerase from binding to its DNA template. Our results are consistent with the notion that the promoter-associated DNase-hypersensitive site is a prerequisite for rather than a consequence of gene activity.

The mutant vasopressin gene from diabetes insipidus (Brattleboro) rats is transcribed but the message is not efficiently translated.

The vasopressin gene from normal and diabetes insipidus (Brattleboro) rats has been isolated and sequenced. Except for a single deletion of a G residue in region coding for the neurophysin carrier protein the approximately 2300 nucleotides of both genes are identical. Blot analysis of hypothalamic RNA as well as transfection and microinjection experiments indicate that the mutant gene is correctly transcribed and spliced, however the resulting mRNA is not efficiently translated.

Retrovirus-induced lethal mutation in collagen I gene of mice is associated with an altered chromatin structure.

The chromatin structure of the collagen alpha 1(I) gene, which has been mutated by retrovirus insertion in Mov13 mice, was compared with that of the wildtype allele. Limited digestions with DNAase I revealed the presence of two hypersensitive sites in all normal cells analyzed, while a third site at 100 to 200 bp 5' of the transcription start was detected only in cells synthesizing collagen alpha 1(I) mRNA. This transcription-associated site was not present in chromatin of the mutant allele, while the two other hypersensitive sites, one of which is located close to the provirus, were not changed by the virus integration. Our results suggest that the virus insertion in Mov13 mice may prevent the developmentally regulated appearance of a transcription-associated hypersensitive site, thereby interfering with proper activation of the gene during embryonic development.

Transcription of cloned Moloney murine leukemia proviral DNA injected into Xenopus laevis oocytes.

We have microinjected genomic DNA clones containing the Moloney murine leukemia virus (M-MuLV) proviral genome and flanking mouse sequences from Mov-3, Mov-7 and Mov-10 mice into Xenopus laevis oocytes and analyzed the virus-specific transcription and translation products. These mouse strains carry a proviral genome copy of M-MuLV in their germ line at different chromosomal positions and differ from each other with respect to expression of the proviral genome. We show here that the different M-MuLV proviral genome copies were transcribed into virus-specific RNA with similar efficiencies. Transcription of viral RNA initiated correctly at the viral promoter in the 5' LTR, whereas the promoter in the 3' LTR was used with a much lower frequency, if at all, for initiation of RNA synthesis. Most of the virus-specific transcripts were smaller than authentic M-MuLV mRNA and confined to the oocyte nucleus. Using immunoprecipitation, we were not able to detect virus-specific proteins after injection of proviral DNA, whereas after injection of a comparable amount of M-MuLV mRNA viral protein was readily detectable.