Eco RI restriction-site polymorphism of the albumin gene in different inbred strains of rat

Albumin and alpha-fetoprotein gene transcription in rat hepatoma cell lines is correlated with specific DNA hypomethylation and altered chromatin structure in the 5' region

We examined DNA methylation and DNase I hypersensitivity of the alpha-fetoprotein (AFP) and albumin gene region in hepatoma cell lines which showed drastic differences in the level of expression of these genes. We assayed for methylation of the CCGG sequences by using the restriction enzyme isoschizomers HpaII and MspI. We found two methylation sites located in the 5' region of the AFP gene and one in exon 1 of the albumin gene for which hypomethylation is correlated with gene expression. Another such site, located about 4,000 base pairs upstream from the AFP gene, seems to be correlated with the tissue specificity of the cells. DNase I-hypersensitive sites were mapped by using the indirect end-labeling technique with cloned genomic DNA probes. Three tissue-specific DNase I-hypersensitive sites were mapped in the 5' flanking region of the AFP gene when this gene was transcribed. Similarly, three tissue-specific DNase I-hypersensitive sites were detected upstream from the albumin gene in producing cell lines. In both cases, the most distal sites were maintained after cessation of gene activity and appear to be correlated with the potential expression of the gene. Interestingly, specific methylation sites are localized in the same DNA region as DNase I hypersensitive sites. This suggests that specific alterations of chromatin structure and changes in methylation pattern occur in specific critical regulatory regions upstream from the albumin and AFP genes in rat hepatoma cell lines.

Differential stability of the higher order structure of chromatin associated with genes having different transcriptional activity

We have investigated the stability of the higher order structure of chromatin associated to genes which display a different transcriptional activity in adult rat live. Nuclei were digested with micrococcal nuclease and chromatin was fractionated by sedimentation in sucrose gradients. Specific DNA sequences were revealed by dot-blotting. In conditions of physiological ionic strength the distribution of the inactive gamma-casein gene sequences is similar than the bulk of chromatin. In the same conditions the relative content of the albumin gene, highly expressed in adult rat liver, revealed an enhanced instability of the chromatin superstructure. The distribution of the potentially active but silent alpha-fetoprotein sequences in adult liver showed an intermediate unfolding of its chromatin superstructure. These distinct behavior was not observed in non-physiological ionic strength conditions. Our results suggest that distinct folding of the local higher order structure of chromatin actually occurs in the region of active, potentially active and inactive genes.

Albumin and alpha-fetoprotein gene transcription in rat hepatoma cell lines is correlated with specific DNA hypomethylation and altered chromatin structure in the 5' region

We examined DNA methylation and DNase I hypersensitivity of the alpha-fetoprotein (AFP) and albumin gene region in hepatoma cell lines which showed drastic differences in the level of expression of these genes. We assayed for methylation of the CCGG sequences by using the restriction enzyme isoschizomers HpaII and MspI. We found two methylation sites located in the 5' region of the AFP gene and one in exon 1 of the albumin gene for which hypomethylation is correlated with gene expression. Another such site, located about 4,000 base pairs upstream from the AFP gene, seems to be correlated with the tissue specificity of the cells. DNase I-hypersensitive sites were mapped by using the indirect end-labeling technique with cloned genomic DNA probes. Three tissue-specific DNase I-hypersensitive sites were mapped in the 5' flanking region of the AFP gene when this gene was transcribed. Similarly, three tissue-specific DNase I-hypersensitive sites were detected upstream from the albumin gene in producing cell lines. In both cases, the most distal sites were maintained after cessation of gene activity and appear to be correlated with the potential expression of the gene. Interestingly, specific methylation sites are localized in the same DNA region as DNase I hypersensitive sites. This suggests that specific alterations of chromatin structure and changes in methylation pattern occur in specific critical regulatory regions upstream from the albumin and AFP genes in rat hepatoma cell lines.

Specific sets of DNase I-hypersensitive sites are associated with the potential and overt expression of the rat albumin and alpha-fetoprotein genes

We have examined the chromatin structure of the 5'-flanking region of the albumin and alpha-fetoprotein (Afp) genes in different developing rat tissues and cloned cell lines that display various functional states of these genes. Nuclease-hypersensitive sites were probed with DNase I, using an indirect end-labeling technique. In albumin-producing rat cells two major DNase I-hypersensitive sites were found near the promoter region and one additional site was located approximately 3 kilobases (kb) upstream. Similarly, in Afp-producing rat tissues and cell lines we mapped one DNase I-hypersensitive region close to the promoter region and two cleavage sites further upstream at approximately 2.2 and approximately 3.8 kb from the cap site. The DNase I-hypersensitive sites of both genes were absent in nonhepatic rat cells and therefore appear to be tissue specific. Loss of specific sets of DNase I-hypersensitive sites accompanies the cessation of transcription for the Afp gene in adult rat liver and in a "dedifferentiated" hepatoma cell line. Likewise, specific sets of DNase I-hypersensitive sites disappear during the inactivation of the albumin gene in hepatoma cells. The distal upstream sites of the Afp and albumin genes display the same DNase I sensitivity in expressing and potentially expressible states. These findings suggest that reversible changes in short chromatin regions may be involved in the actual transcription of the albumin and Afp genes, while more permanent tissue-specific changes at other sites correlate with the capacity of these genes to be expressed during hepatic differentiation and neoplasia.

Isolation of a human liver ligandin cDNA clone and demonstration of sequence homology at ligandin loci in rats and humans

Using a monospecific antibody to the major cytosolic glutathione-S-transferase of human liver, we have isolated a cDNA clone from a human liver cDNA expression vector library in lambda gt11. The clone cross-hybridizes with a rat liver ligandin (glutathione-S-transferase 1-2) cDNA probe. The clone has an insert of 1.25 kb, a size sufficient to code for the 23 kilodalton subunit of human GST. Digestion of the insert with Hinf I produced three fragments (0.8 kb, 0.4 kb and 0.1 kb). A similar pattern of multiple bands was observed when rat liver GST1-2 cDNA probe was used for Southern blot analysis of Pst digests of rat and human genomic DNAs. These data suggest that these two functionally similar proteins exhibit sequence homology between their respective cDNAs and at ligandin loci, in spite of the lack of immuno-crossreactivity between them.

Methylation of the alphafetoprotein gene in cell populations isolated from rat livers during carcinogenesis

We examined the methylation pattern and organization of the AFP gene in whole livers and in isolated cell populations purified from livers of rats fed a carcinogenic diet which interferes with DNA methylation. Using restriction endonuclease digestion, we find no differences in methylation pattern and overall organization of the AFP gene in oval cells (AFP-producers) and hepatocytes (non-producers) isolated at the early stages of carcinogenesis. Our studies indicate that in cell populations which produce AFP as well as in cells which are not active in AFP synthesis, the majority of the CCGG sites of the AFP gene are extensively methylated. In addition, we describe the existence of polymorphism in the AFP and albumin genes of Sprague-Dawley rats.

Organization of the albumin and alpha-fetoprotein genes in fetal and adult rat tissues, and rat hepatomas

We compared the organization of the albumin and alpha-fetoprotein (AFP) genes in chromosomal DNA from different fetal and adult rat tissues as well as from two rat hepatomas. These two genes are expressed at widely different levels in the tissues and hepatomas analysed. Southern blots of DNAs digested with the restriction endonucleases EcoRI, HindIII or MspI were hybridized to albumin and AFP complementary DNA (cDNA) and genomic probes. No significant difference was observed in the hybridization patterns obtained for the DNAs from the different tissues, except for some interstrain variation between the chromosomal DNAs isolated from Sprague-Dawley and Buffalo rats, which was due to allelic polymorphism. We cannot rule out the possibility of changes in chromosomal gene organization which would result either in small alterations of restriction fragment size or in translocations of large blocks of DNA containing whole sets of restriction enzyme fragments within the chromosome; however, our results indicate that the gross organization of the albumin and AFP genes remains constant throughout the regulatory processes involved in the tissue- and time-specific transcription of these genes.

Structural basis for restriction-site polymorphism at the albumin locus in inbred strains of rats

Two types of variant EcoRI restriction enzyme patterns of albumin-gene DNA fragments are found in different inbred strains of rats and reflect allelic polymorphism. The structural basis of the two allelic forms has been analyzed by mapping the EcoRI fragments using cloned albumin cDNA probes corresponding to the 5' or 3' end of the rat albumin mRNA and different genomic subclones. Additional restriction fragment length polymorphism has been detected using the restriction endonucleases HindIII and MspI. The results suggest that the two allelic variants differ from each other by multiple cleavage-site variations (base-pair substitutions) and by an insertion or deletion of DNA sequences. An extensive DNA sequence variation appears to exist between the two forms of the albumin gene; we have estimated that as much as 4% of the nucleotides in this region varied between the two alleles. All of this genetic variation is found in the intervening sequences of the gene and has no phenotypic manifestation.

Differential DNase I sensitivity of the albumin and alpha-fetoprotein genes in chromatin from rat tissues and cell lines

We have examined the DNase I sensitivity of the albumin and alpha-fetoprotein (AFP) genes in different rat tissues (adult liver and kidney) and cloned cell lines (hepatoma 7777-C8, JF1 fibroblasts), which show drastic differences in the level of expression of these two genes. This was done by studying the disappearance of defined restriction endonuclease fragments of these genes as a function of limited DNase I digestion. The sensitivity of these genes was compared to that of a gene not expressed in the hepatic cells and to that of a ubiquitously expressed gene. In nuclei from adult rat liver the albumin and AFP genes were preferentially degraded by the nucleolytic action of DNase I, whereas they were not in rat kidney nuclei. In the hepatoma cells the AFP gene was much more sensitive to DNase I digestion than the albumin gene; both genes were very resistant to DNase I action in fibroblastic nuclei. When analyzed in relation to the level of gene expression our results indicate that alterations in the chromatin structure of the albumin and AFP genes might be involved in the early establishment of the tissue-specific potential of overt gene expression; such alterations reflected in an altered DNase I sensitivity do not appear to be responsible for the changes in gene activity occurring during the terminal differentiation of the hepatocyte; and modifications in the chromatin structure of these genes might occur during oncogenic events; these structural modifications could be related to the changes in gene expression observed in hepatocarcinogenic processes.

Polymorphisms of human albumin gene after DNA restriction by HaeIII endonuclease

Hybridization of albumin clones cDNA with human DNAs digested by several restriction endonucleases reveals two HaeIII polymorphisms. The first polymorphism, H1, is of low frequency (f1 = 0.05); the second, which is validated by family analysis, occurs frequently (f2 = 0.21) and is an intronic polymorphism, probably of substitution--base type.

Structural variants of the alpha-fetoprotein gene in different inbred strains of rat

Two structural variants of the rat alpha-fetoprotein (AFP) gene have been detected in different inbred strains of rats by EcoRI or HindIII restriction enzyme cleavage of cellular DNA, agarose gel electrophoresis and Southern blot hybridization using 32P-labeled cloned rat AFP cDNA probes. The type I AFP gene variant is characteristic of the Sprague-Dawley strain, and type II is found in Buffalo rats. These variants appear to represent two different allelic forms of the rat AFP gene since they are inherited in a normal Mendelian fashion when Sprague-Dawley and Buffalo rats are crossed. The mapping results suggest that the two allelic variants differ from each other by multiple cleavage site variations (base pair substitutions) and by an insertion or deletion of DNA sequences. An extensive sequence variation appears to exist between the two forms of the rat AFP gene; we have estimated that as much as 2.7% of the nucleotides in this region vary between the two alleles.

Changes in methylation pattern of albumin and alpha-fetoprotein genes in developing rat liver and neoplasia

To determine whether methylation changes in specific DNA sequences of the albumin and AFP genes are implicated in the modulation of transcriptional activity during rat liver development and neoplasia we have analysed the methylation pattern of C-C-G-G sequences within these genes in DNA isolated from fetal and adult hepatocytes, from adult kidney and from a clonal hepatoma cell line which produces AFP but no albumin. We have assayed for methylation of the internal cytosine of this sequence by using the restriction enzyme isoschizomers HpaII and MspI. 32P-labelled cloned cDNA probes were used to reveal the albumin and AFP gene containing fragments. Genomic subclones of the albumin gene were also utilized as molecular probes to measure quantitatively the level of methylation of 6 specific sites within the albumin gene in the different DNA samples. The results indicate that methylation changes at the sites analysed are not responsible for the changes in gene activity during rat liver development. Further they demonstrate that: 1) extensively methylated genes can be actively transcribed; 2) prominent changes in methylation of specific genes during normal development are not necessarily related to alterations in gene activity.