Unusual methylation pattern of the alpha 2 (l) collagen gene

Mechanisms of DNA methylation and histone modifications

The field of genetics has expanded a lot in the past few decades due to the accessibility of human genome sequences, but still, the regulation of transcription cannot be explicated exclusively by the sequence of DNA of an individual. The coordination and crosstalk between chromatin factors which are conserved is indispensable for all living creatures. The regulation of gene expression has been dependent on the methylation of DNA, post-translational modifications of histones, effector proteins, chromatin remodeler enzymes that affect the chromatin structure and function, and other cellular activities such as DNA replication, DNA repair, proliferation and growth. The mutation and deletion of these factors can lead to human diseases. Various studies are being performed to identify and understand the gene regulatory mechanisms in the diseased state. The information from these high throughput screening studies is able to aid the treatment developments based on the epigenetics regulatory mechanisms. This book chapter will discourse on various modifications and their mechanisms that take place on histones and DNA that regulate the transcription of genes.

Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs

External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 °C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.

DNA Methylation of Mouse Testes, Cardiac and Lung Tissue During Long-Term Microgravity Simulation

Under microgravity, the gene expression levels vary in different types of cells; however, the reasons for this have not been sufficiently studied. The aim of this work was to evaluate the methylation of CpG islands in the promoter regions of the genes encoding some cytoskeletal proteins, the total methylation and 5 hmC levels, and the levels of enzymes that regulate these processes in the testes, heart, and lungs in mice after a 30-day microgravity modeling by antiorthostatic suspension and after a subsequent 12-hour recovery as well as in the corresponding control group and identical groups treated with essential phospholipids. The obtained results indicate that under modeling microgravity in the examined tissues a decrease of cytoskeletal gene expression (mainly in the heart and lungs tissues) correlated with an increase in the CpG islands methylation and an increase of the expression (mainly in the testes tissue) - with a decrease of the CpG-methylation, despite of the fact that in the examined tissues took place a decrease of the content methylases and demethylases. But the deacetylase HDAC1 content increased in the heart and lungs tissues and decreased in the testes, letting us suggest its participation in the regulation of the methylation level under microgravity conditions.

Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens

The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region -2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [-357 (G > A), -447 (C > G), and -663 (A > G)] in the 5' regulatory region and one in the 3' non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5' regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens.

Genetics and epigenetics of pediatric leukemia in the era of precision medicine

Pediatric leukemia represents a heterogeneous group of diseases characterized by germline and somatic mutations that manifest within the context of disturbances in the epigenetic machinery and genetic regulation. Advances in genomic medicine have allowed finer resolution of genetic and epigenetic strategies that can be effectively used to risk-stratify patients and identify novel targets for therapy. This review discusses the genetic and epigenetic mechanisms of leukemogenesis, particularly as it relates to acute lymphocytic leukemias, the mechanisms of epigenetic control of leukemogenesis, namely DNA methylation, histone modifications, microRNAs, and LINE-1 retroelements, and highlights opportunities for precision medicine therapeutics in further guiding disease management. Future efforts to broaden the integration of advances in genomic and epigenomic science into the practice of pediatric oncology will not only identify novel therapeutic strategies to improve clinical outcomes but also improve the quality of life for this unique patient population. Recent findings in precision therapeutics of acute lymphocytic leukemias over the past three years, along with some provocative areas of epigenetics research, are reviewed here.

Cytoskeleton structure and total methylation of mouse cardiac and lung tissue during space flight

The purpose of this work was to evaluate the protein and mRNA expression levels of multiple cytoskeletal proteins in the cardiac and lung tissue of mice that were euthanized onboard the United States Orbital Segment of the International Space Station 37 days after the start of the SpaceX-4 mission (September 2014, USA). The results showed no changes in the cytoskeletal protein content in the cardiac and lung tissue of the mice, but there were significant changes in the mRNA expression levels of the associated genes, which may be due to an increase in total genome methylation. The mRNA expression levels of DNA methylases, the cytosine demethylases Tet1 and Tet3, histone acetylase and histone deacetylase did not change, and the mRNA expression level of cytosine demethylase Tet2 was significantly decreased.

CpG Islands: A Historical Perspective

The discovery of CpG islands (CGIs) and the study of their structure and properties run parallel to the development of molecular biology in the last two decades of the twentieth century and to the development of high-throughput genomic technologies at the turn of the millennium. First identified as discrete G + C-rich regions of unmethylated DNA in several vertebrates, CGIs were soon found to display additional distinctive chromatin features from the rest of the genome in terms of accessibility and of the epigenetic modifications of their histones. These features, together with their colocalization with promoters and with origins of DNA replication in mammals, highlighted their relevance in the regulation of genomic processes. Recent approaches have shown with unprecedented detail the dynamics and diversity of the epigenetic landscape of CGIs during normal development and under pathological conditions. Also, comparative analyses across species have started revealing how CGIs evolve and contribute to the evolution of the vertebrate genome.

DNA methylation in mammals

DNA methylation is one of the best characterized epigenetic modifications. In mammals it is involved in various biological processes including the silencing of transposable elements, regulation of gene expression, genomic imprinting, and X-chromosome inactivation. This article describes how DNA methylation serves as a cellular memory system and how it is dynamically regulated through the action of the DNA methyltransferase (DNMT) and ten eleven translocation (TET) enzymes. Its role in the regulation of gene expression, through its interplay with histone modifications, is also described, and its implication in human diseases discussed. The exciting areas of investigation that will likely become the focus of research in the coming years are outlined in the summary.

Tissue-specific variation in DNA methylation levels along human chromosome 1

BACKGROUND

DNA methylation is a major epigenetic modification important for regulating gene expression and suppressing spurious transcription. Most methods to scan the genome in different tissues for differentially methylated sites have focused on the methylation of CpGs in CpG islands, which are concentrations of CpGs often associated with gene promoters.

RESULTS

Here, we use a methylation profiling strategy that is predominantly responsive to methylation differences outside of CpG islands. The method compares the yield from two samples of size-selected fragments generated by a methylation-sensitive restriction enzyme. We then profile nine different normal tissues from two human donors relative to spleen using a custom array of genomic clones covering the euchromatic portion of human chromosome 1 and representing 8% of the human genome. We observe gross regional differences in methylation states across chromosome 1 between tissues from the same individual, with the most striking differences detected in the comparison of cerebellum and spleen. Profiles of the same tissue from different donors are strikingly similar, as are the profiles of different lobes of the brain. Comparing our results with published gene expression levels, we find that clones exhibiting extreme ratios reflecting low relative methylation are statistically enriched for genes with high expression ratios, and vice versa, in most pairs of tissues examined.

CONCLUSION

The varied patterns of methylation differences detected between tissues by our methylation profiling method reinforce the potential functional significance of regional differences in methylation levels outside of CpG islands.

Structural and functional studies on the interstitial collagen genes

An understanding of the molecular mechanisms which control expression of the type I and III collagen genes may provide a rational basis for the design of more effective therapeutic approaches to fibrotic diseases. The structure of the interstitial collagen genes is reviewed and potential sites which could control their expression are examined. One approach to the study of the regulation of these genes consists in DNA-mediated gene transfection experiments and is discussed in this paper.

Chromatin-remodelling mechanisms in cancer

Chromatin-remodelling mechanisms include DNA methylation, histone-tail acetylation, poly-ADP-ribosylation, and ATP-dependent chromatin-remodelling processes. Some epigenetic modifications among others have been observed in cancer cells, namely (1) local DNA hypermethylation and global hypomethylation, (2) alteration in histone acetylation/deacetylation balance, (3) increased or decreased poly-ADP-ribosylation, and (4) failures in ATP-dependent chromatin-remodelling mechanisms. Moreover, these alterations can influence the response to classical anti-tumour treatments. Drugs targeting epigenetic alterations are under development. Currently, DNA methylation and histone deacetylase inhibitors are in use in cancer therapy, and poly-ADP-ribosylation inhibitors are undergoing clinical trials. Epigenetic therapy is gaining in importance in pharmacology as a new tool to improve anti-cancer therapies.

A mouse gene that coordinates epigenetic controls and transcriptional interference to achieve tissue-specific expression

The mouse fpgs gene uses two distantly placed promoters to produce functionally distinct isozymes in a tissue-specific pattern. We queried how the P1 and P2 promoters were differentially controlled. DNA methylation of the CpG-sparse P1 promoter occurred only in tissues not initiating transcription at this site. The P2 promoter, which was embedded in a CpG island, appeared open to transcription in all tissues by several criteria, including lack of DNA methylation, yet was used only in dividing tissues. The patterns of histone modifications over the two promoters were very different: over P1, histone activation marks (acetylated histones H3 and H4 and H3 trimethylated at K4) reflected transcriptional activity and apparently reinforced the effects of hypomethylated CpGs; over P2, these marks were present in tissues whether P2 was active, inactive, or engaged in assembly of futile initiation complexes. Since P1 transcriptional activity coexisted with silencing of P2, we sought the mechanism of this transcriptional interference. We found RNA polymerase II, phosphorylated in a pattern consistent with transcriptional elongation, and only minimal levels of initiation factors over P2 in liver. We concluded that mouse fpgs uses DNA methylation to control tissue-specific expression from a CpG-sparse promoter, which is dominant over a downstream promoter masked by promoter occlusion.

Tissue-specific and de novo promoter methylation of the mouse glucose transporter 2

Glucose transporter 2 (GLUT2) is tissue-specifically expressed in liver and kidney, and reduced in neoplastic hepatic lesions and in most hepatoma cell lines. Here we examined the involvement of epigenetic modifications in the regulation of GLUT2. Four CpGs in the GLUT2 promoter were undermethylated in GLUT2-expressing tissues. In isolated hepatocytes, GLUT2 expression declined and the promoter was methylated de novo. This de novo methylation occurred with a similar time-course in hepatocytes cultured in a high-glucose medium that induced GLUT2 expression, suggesting that de novo methylation can be induced independently of GLUT2 expression. GLUT2 was reactivated in hepatocytes following exposure to the methylation inhibitor 5-aza-2'-deoxycytidine (AzaC) but only after the methylation had occurred. In p53-deficient mouse liver, the CpGs were methylated de novo; the GLUT2 expression declined. The GLUT2 promoter was hypermethylated in Hepa1c1c7 cells, but expression could be rescued by AzaC. Thus, it is proposed that DNA methylation has an important role in the regulation of GLUT2 in mouse tissues and liver-derived cells.

Cell type-specific regulation of the TGF-beta-responsive alpha2(I) collagen gene by CpG methylation

The alpha2(I) collagen gene shows cell type-specific expression, however, the mechanism behind this specificity remains to be determined. We demonstrate here that transforming growth factor-beta (TGF-beta)-mediated induction of alpha2(I) collagen gene is regulated by DNA methylation in a cell type-specific manner. Human alpha2(I) collagen mRNA and type I collagen protein were expressed in normal human fibroblasts (NHF), and also strongly enhanced by TGF-beta; they were not detected in HaCaT, HeLa, or HepG2 cells (termed "collagen-induction resistant (CIR) cells") even following stimulation with TGF-beta. On the other hand, the transcriptional activity of exogenously transfected alpha2(I) collagen promoter was clearly up-regulated by TGF-beta in the CIR cells as well as in NHF. In the CIR cells, CpG clusters around the transcription start site of the alpha2(I) collagen gene were heavily methylated, whereas no methylation was detected in NHF. Moreover, alpha2(I) collagen gene was reactivated in the CIR cells by 5-Aza-2-deoxycytidine (5-AdC) treatment to some extent. However, demethylation by 5-AdC was limited and it was unable to recover the TGF-beta responsiveness. In NHF, the alpha2(I) collagen gene has a Smad3-accessible chromatin structure and acetylated histones in the promoter regions. By contrast, in the CIR cells, Smad3 failed to bind to the chromatin and histones were not acetylated in this area. Furthermore, in vitro methylation of the reporter gene containing the alpha2(I) collagen promoter significantly reduced both basal and TGF-beta-induced enhancement of the transcriptional activity in NHF. Thus, we propose that alpha2(I) collagen gene provides the first example of the TGF-beta responsive gene whose cell type-specificity is regulated by CpG methylation.

Alterations in the regulation of expression of the alpha 1(I) collagen gene (COL1A1) in systemic sclerosis (scleroderma)

At present, the mechanisms that regulate the expression of collagen genes in normal and pathologic fibroblasts are not known. Thus, the detailed study of transcriptional regulation of COL1A1 in SSc cells will increase our current understanding of the pathophysiology of fibrotic diseases. These studies will yield valuable information regarding the important biological process of regulation of collagen gene expression under normal and pathologic conditions, a process that has remained elusive despite intense recent investigations. It is now evident that persistent overproduction of collagen is responsible for the progressive nature of tissue fibrosis in SSc. Up-regulation of collagen gene expression in SSc fibroblasts appears to be a critical event in this process. The coordinate transcriptional activation of numerous collagen genes suggests a fundamental alteration in the regulatory control of gene expression in SSc fibroblasts. Trans-acting nuclear factors which bind to cis-acting elements in enhancer (intronic) and promoter regions of the genes modulate the basal and inducible transcriptional activity of the collagen genes. The identification of the nuclear transcription factors that regulate normal collagen gene expression may provide promising approaches to the therapy of this incurable disease.

Regulation of the human alpha 2(1) procollagen gene by sequences adjacent to the CCAAT box

The human, rat, mouse and chicken alpha 2(1) procollagen promoters analysed to date all contain an inverted CCAAT box at -80. In this study we have examined the binding of nuclear proteins to the proximal promotor of the human alpha 2(1) procollagen gene, where an inverted CCAAT box is flanked by a downstream GGAGG sequence and its inverted counterpart (CCTCC) on the upstream end. Each of the GGAGG sequences is separated from the inverted CCAAT box by a single pyrimidine nucleotide (5'-CCTCCCATTGGTGGAGGCCCTTTT-3'). Electrophoretic mobility-shift assays (EMSAs) revealed that two distinct DNA-protein complexes formed on this DNA sequence. Methylation interference analysis and in vitro mutagenesis studies revealed that the integrity of the sequence 5'-CCTCCCATTGG-3' (the GGAGG/CCAAT-binding element or G/CBE) was important for the binding of the CCAAT-binding factor (CBF) (complex I). Competition studies showed that complex formation on the human G/CBE could be competed by mouse CBE and nuclear factor-Y (NF-Y) oligonucleotides, suggesting that mouse CBE and human G/CBE-binding proteins belong to the same family of CCAAT box binding proteins. Furthermore, antibodies to mouse CBF specifically supershifted the G/CBE complex (complex I) in EMSAs. The downstream GGAGG and 3'-flanking sequences (5'-GGAGGCCCTTTT-3') or collagen modulating element (CME), however, were important for the formation of a novel DNA protein complex (complex III). The formation of this complex was not competed out by CBE or NF-Y oligonucleotides, nor was DNA-protein complex formation affected by the anti-CBF antibody. Functional analysis of G/CBE and CME elements subjected to mutagenesis, using promoter-chloroamphenicol acetyl transferase constructs in transient transfection assays, showed that both these elements were essential for activity of the human promoter. These experiments identified a novel regulatory element in the human alpha 2(1) procollagen gene which is not present in the rodent gene.

DNA methylation: biology and significance

The modification of DNA by cytosine methylation is crucial for normal development. DNA methylation patterns are distinctive between tissues and are maintained with high fidelity during cell division. DNA methylation probably exerts its effects through alterations in chromatin structure, with a resultant effect on genetic transcription. 5-methylcytosine is also prone to spontaneous hydrolytic deamination to thymine. Whilst most G:T mismatches so produced are repaired, failure of mismatch repair leads to established mutation. Indeed, mutations that are the result of 5-methylcytosine transitions account for a disproportionate number of genetic mutations described in malignant and non-malignant disease. There is also evidence for substantial deregulation of DNA methylation in malignancy. Whether this deregulation is crucial for the transformation process, or simply an epiphenomenon associated with it, is still not established.

Pathogenesis of scleroderma. Collagen

It is now evident that persistent overproduction of collagen and other connective tissue macromolecules results in excessive tissue deposition, and is responsible for the progressive nature of fibrosis in SSc. Up-regulation of collagen gene expression in SSc fibroblasts appears to be a critical event in the development of tissue fibrosis. The coordinate transcriptional activation of a number of extracellular matrix genes suggests a fundamental alteration in the regulatory control of gene expression in SSc fibroblasts. Trans-acting nuclear factors that bind to cis-acting elements in enhancer and promoter regions of the genes modulate the basal and inducible transcriptional activity of the collagen genes. The identity of the nuclear transcriptional factors that regulate normal collagen gene expression remains to be firmly established, and to date, no alterations in the level or in the activity of such DNA binding factors has been demonstrated in SSc fibroblasts. In addition to important interactions between fibroblasts and the extracellular matrix, cytokines and other cellular mediators can positively and negatively influence fibroblast collagen synthesis. Some of these signaling molecules may have physiologic roles, and their aberrant expression, or altered responsiveness of SSc fibroblasts to them, may result in the acquisition of the activated phenotype. The rapid expansion of knowledge regarding the effects of cytokines on extracellular matrix synthesis has led to an appreciation of the enormous complexity of regulatory networks that operate in the physiologic maintenance of connective tissue and which may be responsible for the occurrence of pathologic fibrosis. The ubiquitous growth factor TGF beta is the most potent inducer of collagen gene expression and connective tissue accumulation yet discovered. The expression of TGF beta in activated infiltrating mononuclear cells suggests a role for this cytokine as a mediator of fibroblast activation in SSc. Furthermore, the recognition that TGF beta is capable of inducing its own expression in a variety of cell types, coupled with the demonstration that a subpopulation of SSc dermal fibroblasts produces TGF beta, indicates the existence of a possible autocrine loop whereby lymphocyte-derived TGF beta in early SSc not only signals biosynthetic activation of fibroblasts in a paracrine manner, but autoinduces endogenous TGF beta production by the target fibroblasts themselves. Such an autocrine loop involving TGF beta may explain the persistent activation of collagen gene expression in SSc fibroblasts, and could be responsible for the progressive nature of fibrosis in SSc. Numerous other cytokines, as well as cell-matrix interactions, also modify collagen gene expression and can significantly influence the effects of TGF beta. Although their physiologic function in tissue remodeling or their involvement in abnormal fibrogenesis has not yet been conclusively demonstrated, the study of the biologic effects of these cytokines may provide important clues to understanding the pathogenesis of SSc, and to the development of rational drug therapy aimed at interrupting the abnormal fibrogenic process in this disease.

Advanced glycation end products modulate transcriptional regulation in mesangial cells

Advanced glycation end products (AGEs) stimulate synthesis of extracellular matrix (ECM) in a receptor-mediated manner on mesangial cells. In the present study, we examined the transcriptional regulation of the gene for type IV collagen [(IV)collagen], which is one of the major components of mesangial sclerosis, after stimulation of AGEs on mesangial cells. The methylation pattern of the promoter/enhancer region of (IV)collagen gene was similar in AGE-treated and control cells. AGEs significantly increased the transcriptional activity of the (IV)collagen gene, as measured by transient transfection assays using the reporter gene construct containing (IV)collagen promoter/enhancer and the chloramphenicol acetyltransferase gene. AGEs also increased smooth muscle alpha-actin mRNA levels as well as its transcriptional activity. Nuclear factor binding of the promoter of (IV)collagen gene was stimulated by AGEs. Furthermore, AGEs dramatically decreased the mRNA levels of (IV)collagen promoter binding protein (MSW), a larger subunit of DNA replication complex, AP1. These results suggest that AGEs increase expression of (IV)collagen gene by modulating the levels of promoter binding proteins. These transcriptional events may play a critical role in ECM accumulation in response to AGEs.

Differentiation of smooth muscle phenotypes in mouse mesangial cells

Smooth muscle alpha-actin (SMA) mRNA, a marker of vascular smooth muscle cells, was identified in the normal glomerular mesangium both in vivo and in vitro. Several populations of mesangial cells were studied to determine if SMA and basement membrane collagen were regulated together. The levels of SMA expression, which could be linked to the stage of differentiation, were different for the differing cell populations. One cell population had high SMA and type IV collagen levels at its early passages. The others expressed both interstitial and basement membrane collagens. The first population developed these phenotypic features at later passages. The levels of SMA and alpha 1(IV) collagen expression were regulated together in concert, whereas the alpha 2(I) collagen levels were expressed inversely to SMA and alpha 1(IV) collagen. Both SMA and type IV collagen were controlled by the methylation states of the cis-regulators; however, type I collagen was mainly regulated by the trans-acting regulators. Treatment with 5-azacytidine converted the cells of a fibroblast-phenotype to a smooth muscle cell-like phenotype. These cell lines may be useful for studying the differentiation process in vitro.

Methylation status of CpG sites in the mouse and human CFTR promoters

To determine whether a relationship exists between DNA methylation and CFTR gene expression, we investigated the methylation status of CpG sites in the mouse and human CFTR promoters. Tissues and previously characterized cell lines that vary with respect to CFTR expression were selected for analysis using the methylation sensitive restriction endonuclease Hha I. We find that CpG sites are not methylated in high and low CFTR-expressing cell lines, whereas in the very low or non-CFTR-expressing cell lines, the CpG sites are partially or completely methylated. However, none of these sites were methylated in any of the tissues examined irrespective of the state of CFTR expression. Therefore, we conclude that the CFTR promoter belongs to the class of CpG-rich promoters in which the associated CpG sites are not methylated in tissues and that an inverse correlation between methylation and CFTR expression can only be found in cell lines.

The CpG-rich promoter of human LDH-C is differentially methylated in expressing and nonexpressing tissues

A comparison of nucleotide sequences of murine Ldh-a and Ldh-c genes and human LDH-A, LDH-B, and LDH-C reveals that mouse Ldh-c has lost the CpG "island" present in the genes for the somatic isozymes. However, the human LDH-C gene has a CpG-rich region of 230 bp surrounding its promoter. Endonuclease sensitivity coupled with polymerase chain reaction (PCR) demonstrate the presence of nine heavily methylated sites in this region in different somatic cells. The same sites are specifically hypomethylated in expressing tissues. 3' sites bordering the CpG-rich region appear to be methylated in both expressing and nonexpressing tissues. Furthermore, the methylated promoter forms a specific complex in vitro with a methyl-DNA binding protein. Evolutionary and functional implications of these observations are discussed.

De novo methylation of an MHC class I transgene following transformation with human adenoviruses is not correlated with its altered expression

The biological importance of class I histocompatibility antigens in a large variety of immune mechanisms is widely recognized, and their role in tumor rejection has been proven in several experimental tumor systems. Reduced expression of class I antigens, which is correlated with enhanced tumorigenicity, was shown in these systems to be mainly the result of transcriptional down-regulation. Mouse embryonal fibroblasts expressing H-2 antigens and the product of a miniature swine class I transgene, transformed by adenovirus 12, exhibit low levels of all class I antigens on the cell surface. Half of the cell lines demonstrate a suppressed level of class I mRNAs. Cell lines derived from transformation with the early region of adenovirus 5 express a high level of class I antigens. DNAs from adenovirus-transformed cells are extensively hypermethylated both in the 5' and the coding regions of the transgene compared to DNAs from immortalized cell lines and primary embryonal fibroblasts. Nevertheless, hypermethylation of these sequences is not correlated with mRNA level or cell-surface expression of the transgene product. Treatment of the transformed cells with high concentration of 5-azacytidine (5 Aza-C) induced merely a minor enhancement in the expression of class I mRNAs and class I antigens. Thus, this system is a perfect example of where viral transformation is associated with induced methylation of a class I gene, but hypermethylation does not affect its expression. The role of de novo methylation of genes in this system might be associated with transformation, or generation of mutations in CpG-rich sequences.

An X-linked human collagen transgene escapes X inactivation in a subset of cells

Transgenic mice carrying one complete copy of the human alpha 1(I) collagen gene on the X chromosome (HucII mice) were used to study the effect of X inactivation on transgene expression. By chromosomal in situ hybridization, the transgene was mapped to the D/E region close to the Xce locus, which is the controlling element. Quantitative RNA analyses indicated that transgene expression in homozygous and heterozygous females was about 125% and 62%, respectively, of the level found in hemizygous males. Also, females with Searle's translocation carrying the transgene on the inactive X chromosome (Xi) expressed about 18% transgene RNA when compared to hemizygous males. These results were consistent with the transgene being subject to but partially escaping from X inactivation. Two lines of evidence indicated that the transgene escaped X inactivation or was reactivated in a small subset of cells rather than being expressed at a lower level from the Xi in all cells, (i) None of nine single cell clones carrying the transgene on the Xi transcribed transgene RNA. In these clones the transgene was highly methylated in contrast to clones carrying the transgene on the Xa. (ii) In situ hybridization to RNA of cultured cells revealed that about 3% of uncloned cells with the transgene on the Xi expressed transgene RNA at a level comparable to that on the Xa. Our results indicate that the autosomal human collagen gene integrated on the mouse X chromosome is susceptible to X inactivation. Inactivation is, however, not complete as a subset of cells carrying the transgene on Xi expresses the transgene at a level comparable to that when carried on Xa.

DNA methylation inhibits transcription of procollagen alpha 2(I) promoters

Our previous studies have demonstrated that a 2-[N-(acetoxyacetyl)amino]fluorene-transformed rat epithelial-like cell line, W8, contains a transcriptionally inactive alpha 2(I) gene with a hypermethylated promoter/first-exon region. We have cloned the rat promoter/first-exon region (-211 to +207) from W8 cells and their parent cell line, K16, which expresses alpha 2(I) collagen. There were no sequence differences between the clones from the two cell lines, indicating that a mutation was not responsible for transcriptional inhibition. The alpha 2(I) rat promoters were cloned upstream of the chloramphenicol acetyltransferase gene. Both constructs were equally active in both cell lines, suggesting that trans-activating factors for alpha 2(I) transcription are present in W8 cells. Finally, methylation of plasmids at all CpG sites with SssI methylase completely inhibited transcription using alpha 2(I) promoters, but methylation did not inhibit simian-virus-40 promoter-driven transcription. Certain methylation sites partially inhibit promoter activity. An HhaI methylation site inhibited transcriptional activity of the alpha 2(I) promoter 8-fold, whereas methylation at the HpaII site in the rat alpha 2(I) promoter did not decrease transcriptional activity. This provides further evidence that methylation at specific sites in the collagen alpha 2(I) promoter is responsible for the inactivation of transcription in W8 cells.

Evolution of the primate beta-globin gene region: nucleotide sequence of the delta-beta-globin intergenic region of gorilla and phylogenetic relationships between African apes and man

A 6.0-kb DNA fragment from Gorilla gorilla including the 5' part of the beta-globin gene and about 4.5 kb of its upstream flanking region was cloned and sequenced. The sequence was compared to the human, chimpanzee, and macaque delta-beta intergenic region. This analysis reveals four tandemly repeated sequences (RS), at the same location in the four species, showing a variable number of repeats generating both intraspecific (polymorphism) and interspecific variability. These tandem arrays delimit five regions of unique sequence called IG for intergenic. The divergence for these IG sequences is 1.85 +/- 0.22% between human and gorilla, which is not significantly different from the value estimated in the same region between chimpanzee and human (1.62 +/- 0.21%). The CpG and TpA dinucleotides are avoided. CpGs evolve faster than other sequence sites but do not confuse phylogenetic inferences by producing parallel mutations in different lineages. About 75% of CpG doublets have become TpG or CpA since the common ancestor, in agreement with the methylation/deamination pattern. Comparison of this intergenic region gives information on branching order within Hominoidea. Parsimony and distance-based methods when applied to the delta-beta intergenic region provide evidence (although not statistically significant) that human and chimpanzee are more closely related to each other than to gorilla. CpG sites are indeed rich in information by carrying substitutions along the short internal branch. Combining these results with those on the psi eta-delta intergenic region, shows in a statistically significant way that chimpanzee is the closest relative of human.

Expression and methylation of the beta-subunit gene of prolyl 4-hydroxylase: in erythrocytes, tendon and cornea of chick embryos

It has recently been demonstrated that the beta-subunit of prolyl 4-hydroxylase (E.C. 1.14.11.2) is the same gene product as protein disulfide isomerase (PDI) and cellular thyroid hormone binding protein (THP). Therefore, it is very likely that the beta-subunit of the prolyl 4-hydroxylase gene serves as a house keeping gene in most cell types. In the present study, we examined the distribution of the chicken beta-subunit of prolyl 4-hydroxylase/protein disulfide isomerase (CPH beta/PDI) in erythrocytes, corneas and tendons of 13-, 17-, and 19-day-old chick embryos by immunohistochemistry using antibodies against CPH beta/PDI. Our data indicate that erythrocytes do not express the CPH beta/PDI gene whereas tendon cells express CPH beta/PDI at all developmental stages examined. The basal cells of corneal epithelium express CPH beta/PDI, but the superficial cell layers of stratified corneas of 19-day-old chick embryos do not. The expression of the CPH beta/PDI gene is also confirmed by in situ hybridization with cDNA encoding CPH beta/PDI. The results indicate that the expression of CPH beta/PDI in cornea is probably developmentally regulated. It has been suggested that methylation of genomic DNA is one of many possible regulatory mechanisms for gene expression. In order to examine whether methylation of genomic DNA may play any role in the expression of the beta-subunit gene, genomic DNA was isolated from corneas, tendons, and erythrocytes of individual 13-, 17-, and 19-day-old chick embryos. DNA samples were digested with Sma I and Eco RI, or Pst I and Sma I and followed by either Msp I, Hpa II, or Hha I and were then subjected to Southern hybridization with 32P-labeled genomic DNA fragments of CPH beta/PDI. Our results indicate that the CPH beta/PDI gene is methylated at the Hha I site in the 4th exon in erythrocytes whereas the same sites in tendon and cornea are hypomethylated. Examination of 5'-end flanking sequences of exon 1 of the CPH beta/PDI gene with the methylation sensitive endonucleases, Hha I and Hpa II did not reveal any difference in erythrocyte, cornea and tendon cells. Thus, our results indicated that DNA methylation may not play an important role in the expression of CPH beta/PDI.

DNA methylation changes in human testicular cancer

We previously reported an X/Y imbalance with a relative excess of X- and a relative deficiency of Y-chromosomal DNA in three out of nine testicular tumors of germ cell origin. To study the implications of those changes the methylation status of DNA from seven of the tumors was explored by HpaII/MspI analysis. The 5' regions of the hypoxanthine phosphoribosyltransferase (HPRT) and the phosphoglycerate kinase (PGK) gene loci exhibited main patterns suggestive of active X chromosomes in the tumors. However, a minority of the HPRT loci of one teratocarcinoma with an increased dosage of the X chromosome, as well as one additional teratocarcinoma, revealed patterns analogous to inactive X chromosomes in females. Using probes from several chromosomes it was subsequently found that the teratocarcinoma tumors (3/3) were characterized by generalized hypermethylation. On the contrary, the seminomas showed variable hypomethylation (4/5) or virtually complete demethylation (1/5). The seminoma with the most extensive hypomethylation was disseminated (stage III), whereas the other seminomas were local (stage I). These findings suggest that DNA methylation may play a role in the developmental pathways leading to different histologic types of testicular tumors of germ cell origin. The HPRT results imply that the consequences of extra X chromosomes--a frequent finding in testicular tumors--may be modulated by mechanisms, such as DNA methylation, that control gene activity.

Altered methylation of versican proteoglycan gene in human colon carcinoma

We show for the first time that DNA isolated from human colon carcinoma tissue exhibits a selective hypomethylation of versican gene, which encodes a large chondroitin sulfate proteoglycan. The degree of methylation of CpG sequences of versican gene locus, as determined by isoschizomeric endonucleases and Southern hybridization, is about three times lower than that found in either normal colon or ulcerative colitis tissues. Hypomethylation can be observed in both benign and malignant colonic neoplasms; however, there is no correlation with increased expression since versican mRNA levels do not significantly vary between normal and neoplastic tissues. We further show that versican gene locus from malignant tissue, but not from normal or ulcerative colitis tissues, contains Hind III hypersensitive sites which also comprise hypomethylated CpG sequences. Analysis of versican methylation status in colon carcinoma cells and benign mesenchymal cells derived from human colon suggests that the changes observed in vivo derive from demethylating events involving host stromal cells rather than tumor cells themselves. These findings demonstrate that changes in versican gene methylation are specific for colonic neoplasms, that these changes may precede malignant transformation, and that inflammation and tissue remodelling alone are not enough to generate these changes in proteoglycan gene methylation and nuclease hypersensitivity.

High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines

CpG islands are normally methylation free in cells of the animal, even when the associated gene is transcriptionally silent. In mouse NIH 3T3 and L cells, however, over half of the islands are heavily methylated. Near identity of the methylated subset in the two cell lines suggested that methylation is confined to genes that are nonessential in culture. In agreement with this, islands at several tissue-specific genes, but not at housekeeping genes, have become methylated in many human and mouse cell lines. At the chromatin level, methylated islands are Mspl resistant compared with their nonmethylated counterparts. We suggest that mutation-like gene inactivation due to CpG island methylation is widespread in many cell lines and could explain the loss of cell type-specific functions in culture.

DNA methylation and demethylation events during meiotic prophase in the mouse testis

The genes encoding three different mammalian testis-specific nuclear chromatin proteins, mouse transition protein 1, mouse protamine 1, and mouse protamine 2, all of which are expressed postmeiotically, are marked by methylation early during spermatogenesis in the mouse. Analysis of DNA from the testes of prepubertal mice and isolated testicular cells revealed that transition protein 1 became progressively less methylated during spermatogenesis, while the two protamines became progressively more methylated; in contrast, the methylation of beta-actin, a gene expressed throughout spermatogenesis, did not change. These findings provide evidence that both de novo methylation and demethylation events are occurring after the completion of DNA replication, during meiotic prophase in the mouse testis.

DNA methylation and demethylation events during meiotic prophase in the mouse testis

The genes encoding three different mammalian testis-specific nuclear chromatin proteins, mouse transition protein 1, mouse protamine 1, and mouse protamine 2, all of which are expressed postmeiotically, are marked by methylation early during spermatogenesis in the mouse. Analysis of DNA from the testes of prepubertal mice and isolated testicular cells revealed that transition protein 1 became progressively less methylated during spermatogenesis, while the two protamines became progressively more methylated; in contrast, the methylation of beta-actin, a gene expressed throughout spermatogenesis, did not change. These findings provide evidence that both de novo methylation and demethylation events are occurring after the completion of DNA replication, during meiotic prophase in the mouse testis.

Induction of class II major histocompatibility complex antigens in murine placenta by 5-azacytidine and interferon-gamma involves different cell populations

Class II MHC antigen expression is required for recognition of an alloantigen and generation of immune response. In rodents as well as in humans primary trophoblasts do not express class II MHC antigens. In this study we focused our interest on the mechanism(s) of class II antigen suppression on murine trophoblasts. First, we examined the possibility of gene inactivation by methylation and second the possibility of lymphokine regulation of the class II genes. The first possibility was tested by treatment of placental cells with 5-azacytidine (5-AzaC), a cytidine analog which upon incorporation into the DNA inhibits further methylation, thus leading to gene activation. In order to test the second possibility we treated placental cells with interferon-gamma (IFN-gamma) or interleukin 4 (IL4) which are known to induce class II antigen expression in many systems. We showed that treatment with 5-AzaC or IFN-gamma but not IL4 significantly increased class II expression on cytokeratin-positive and vimentin-negative adherent placental cells. Following placental cell fractionation we distinguished three cell subsets with different responsiveness to 5-AzaC and IFN-gamma. The first, characterized as placental macrophages, were induced to express class II MHC antigens only after IFN-gamma treatment. The other two subsets, characterized as trophoblasts, were isolated from the labyrinthine- and spongio-trophoblast layer of the placenta and showed class II inducibility to 5-AzaC and IFN-gamma, respectively. The results show that depending on the anatomical localization of trophoblasts within the placenta, various regulatory elements control gene expression, so that the placental barrier provides fetal protection at different levels.

Loss of alpha I type I collagen gene expression in rat clonal bone cell lines is accompanied by DNA methylation

Four clonal cell lines subcloned from a clonal population of fetal rat calvaria cells show a loss of type I collagen synthesis. Northern blot analysis showed that the level of alpha 1(I) collagen mRNA expression in each of the clonal populations parallels the level of collagen protein expression in each of these cell lines. The methylation pattern of the collagen gene in these clonal cell lines was determined using the restriction endonucleases MspI and HpaII. It was found that the loss in collagen type I expression correlated positively with the degree of methylation of alpha 1(I) procollagen genes, indicating that methylation of CpG may be an important mechanism of collagen gene regulation.

Demethylation by 5-azacytidine results in the expression of hepatitis B virus surface antigen in transgenic mice

In 14p3HB transgenic mice, which carry three tandem copies of hepatitis B virus (HBV) DNA, the HBV DNA was significantly methylated and no viral proteins were produced. To analyze the causal relationship between hypermethylation and gene inactivity, 5-azacytidine was injected into the mice to demethylate HBV DNA. When postnatal 14p3HB mice were treated with the drug, hepatitis virus surface antigen was produced in these mice by 3 weeks of age, and the integrated HBV DNA of the liver was less heavily methylated. Our results suggest that injection of 5-azacytidine can be used to efficiently activate a silent transgene such as HBV DNA in transgenic mice.

Complete structure of the gene for human keratin 18

The complete sequence of the human keratin 18 (K18) gene was determined. The K18 gene is 3791 bp in length and the K18 protein is coded for by seven exons. The exon structure of K18 has been conserved compared to that of other keratin genes, with the exception of a single 3' terminal exon that codes for the tail domain of the protein that is represented by two exons in epidermal keratins. The K18 gene contains an unusual AG/GC donor splice site of intron 3 instead of the consensus AG/GT sequence. This variation is not seen in any other intermediate filament genes. The promoter region of the gene contains a TATA box, six potential SP1 binding sites, and 10 copies of CACCC boxes but lacks any CCAAT boxes and is surprisingly different from the immediately 5' flanking region of the homologous mouse Endo B gene. However, both genes contain small CpG islands surrounding the 5' end of exon 1 and, in addition, conserve repetitive Alu potential transcription units approximately 300 nt upstream of the transcriptional start site.

Transcriptional unit of the murine Thy-1 gene: different distribution of transcription initiation sites in brain

Structural analysis of the mouse Thy-1.2 gene has shown that the major promoter of the gene is characterized by a tissue-specific DNase I-hypersensitive site and is located within a methylation-free island. The gene is regulated at the transcriptional level, and steady-state mRNA analysis reveals that the previously reported exon Ib contributes at most 5% of the total mRNA. The major promoter uses several transcription initiation sites within a region of 100 base pairs. The frequency of usage of these sites in brain is markedly different from that in other tissues.

Location and methylation pattern of a nuclear matrix associated region in the human pro alpha 2(I) collagen gene

Using both a 25 mM Lithium di-iodosalicylic acid (LIS) and a 2M NaCl extraction procedure to extract nuclear matrices from white cells we have identified a 0.9 kb nuclear matrix associated region (MAR) in the human pro alpha 2(I) collagen gene. The MAR is located towards the 3' coding end of the gene, it is completely associated with the matrix in transcriptionally inactive white cells but is incompletely associated with the matrix in transcriptionally active fibroblasts. Furthermore the methylation state of the fibroblast gene in the region coinciding with the MAR showed unique differences when compared to adjacent sites in the fibroblast gene and corresponding sites of the white cell gene.

Transcriptional unit of the murine Thy-1 gene: different distribution of transcription initiation sites in brain

Structural analysis of the mouse Thy-1.2 gene has shown that the major promoter of the gene is characterized by a tissue-specific DNase I-hypersensitive site and is located within a methylation-free island. The gene is regulated at the transcriptional level, and steady-state mRNA analysis reveals that the previously reported exon Ib contributes at most 5% of the total mRNA. The major promoter uses several transcription initiation sites within a region of 100 base pairs. The frequency of usage of these sites in brain is markedly different from that in other tissues.