Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators

Relationships between chromatin organization and DNA methylation in determining gene expression

Chromatin is the natural substrate for the control of gene expression. Chromatin contains DNA, the transcriptional machinery and structural proteins such as histones. Recent advances demonstrate that transcriptional activity of a gene is largely controlled by the packaging of the template within chromatin. The covalent modification of chromatin provides an attractive mechanism for establishing and maintaining stable states of gene activity. DNA methylation and histone acetylation alter the nucleosomal infrastructure to repress or activate transcription. These covalent modifications have causal roles in both promoter-specific events and the global control of chromosomal activity. DNA methylation and histone acetylation have a major impact in both oncogenic transformation and normal development.

Role of histone acetylation and DNA methylation in the maintenance of the imprinted expression of the H19 and Igf2 genes

H19 and Igf2 are linked and reciprocally imprinted genes. We demonstrate that the histones associated with the paternally inherited and unexpressed H19 allele are less acetylated than those associated with the maternal expressed allele. Cell growth in the presence of inhibitors of either histone deacetylase or DNA methylation activated the silent Igf2 allele, whereas derepression of the silent H19 allele required combined inhibition of DNA methylation and histone deacetylation. Our results indicate that histone acetylation as well as DNA methylation contribute to the somatic maintenance of H19 and Igf2 imprinting and that silencing of the imprinted alleles of these two genes is maintained via distinct mechanisms.

The protein CTCF is required for the enhancer blocking activity of vertebrate insulators

An insulator is a DNA sequence that can act as a barrier to the influences of neighboring cis-acting elements, preventing gene activation, for example, when located between an enhancer and a promoter. We have identified a 42 bp fragment of the chicken beta-globin insulator that is both necessary and sufficient for enhancer blocking activity in human cells. We show that this sequence is the binding site for CTCF, a previously identified eleven-zinc finger DNA-binding protein that is highly conserved in vertebrates. CTCF sites are present in all of the vertebrate enhancer-blocking elements we have examined. We suggest that directional enhancer blocking by CTCF is a conserved component of gene regulation in vertebrates.

Targeting genes for self-excision in the germ line

A procedure is described that directs the self-induced deletion of DNA sequences as they pass through the male germ line of mice. The testes-specific promoter from the angiotensin-converting enzyme gene was used to drive expression of the Cre-recombinase gene. Cre was linked to the selectable marker Neor, and the two genes flanked with loxP elements. This cassette was targeted to the Hoxa3 gene in mouse ES cells that were in turn used to generate chimeric mice. In these chimeras, somatic cells derived from the ES cells retained the cassette, but self-excision occurred in all ES-cell-derived sperm.

Association of the 5'HS4 sequence of the chicken beta-globin locus control region with human EF1 alpha gene promoter induces ubiquitous and high expression of human CD55 and CD59 cDNAs in transgenic rabbits

Whatever its field of application, animal transgenesis aims at a high level of reproducible and stable transgene expression. In the case of xenotransplantation, prevention of hyperacute rejection of grafts of animal origin requires the use of organs expressing human inhibitors of complement activation such as CD55 (DAF) and CD59. Pigs transgenic for these molecules have been produced, but with low and variable levels of expression. In order to improve cDNA expression, a vector containing the 5'HS4 region from the LCR of the chicken beta-globin locus and the promoter and the first intron from the human EF1 alpha gene, was used to co-express human CD55 and CD59 cDNAs in transgenic rabbits. The transgenic lines with the 5'HS4 region displayed dramatically enhanced CD55 and CD59 mRNA concentrations in brain, heart, kidney, liver, lung, muscle, spleen and aortic endothelial cells in comparison with the transgenic lines without the 5'HS4 region. In the absence of the 5'HS4 region, only some of the transgenic lines displayed specific mRNAs and at low levels. Human CD55 and CD59 proteins were detectable in mononuclear cells from transgenic rabbits although at a lower level than in human mononuclear cells. On the other hand, primary aortic endothelial cells from a bi-transgenic line were very efficiently protected in vitro against human complement-dependent lysis. Transgenic rabbits harbouring the two human inhibitors of complement activation, CD55 and CD59, can therefore be used as new models in xenotransplantation. Moreover, the vector containing the 5'HS4 region from the LCR of the chicken beta-globin locus seems appropriate not only for xenotransplantation but also for any other studies involving transgenic animals in which cDNAs have to be expressed at a high level in all cell types.

Insulation of a conditionally expressed transgene in an adenoviral vector

Replication-defective recombinant adenoviruses provide an efficient system for in vivo gene transfer and numerous studies have demonstrated that this vector can accommodate tissue-specific promoters to restrict the expression of a transgene to a particular subset of cells. However, in some cases the selectivity of expression is lost when the tissue-specific promoter is placed in an adenoviral environment. In an attempt to restore the conditionality of expression of the transgene driven by the human ERBB2 promoter, we have flanked the expression cassette in 5' and 3' orientations with a 250 bp sequence containing the bovine growth hormone transcriptional stop signal for cloning into a recombinant adenovirus. The data presented here clearly demonstrate that these 'insulator' elements are able to restrict the expression of the transgene (herpes simplex thymidine kinase) to ERBB2-expressing cells and therefore to restore the selectivity mediated by the ERBB2 promoter. This approach could be generally useful to insulate expression cassettes in adenoviral vectors.

Cell cycle-regulated histone acetylation required for expression of the yeast HO gene

Expression of the yeast HO gene in late G1 of the cell cycle requires the SWI/SNF chromatin remodeling complex, the Gcn5p histone acetyltransferase, and two different sequence-specific transcriptional activators, Swi5p and Swi4p/Swi6p. We have used chromatin immunoprecipitation assays to investigate the role of each of these trans-acting factors in establishing a cell cycle-regulated domain of histone acetylation surrounding the HO upstream regulatory region. We detect a approximately 1-kb domain of H3 and H4 acetylation that is established in mid-G1, prior to and independent of HO transcription, which then declines with kinetics similar to inactivation of HO. This cell cycle burst of histone acetylation requires Gcn5p, SWI/SNF, and the Swi5p activator, but occurs in the absence of the Swi4p activator. We also find that inactivation of the Sin3p/Rpd3p deacetylase complex leads to a high level of acetylation at the HO locus throughout the cell cycle. We propose a sequential model for activation of HO in which the Swi5p-dependent recruitment of the Gcn5p acetyltransferase requires chromatin remodeling events by the SWI/SNF complex.

Cohabitation of insulators and silencing elements in yeast subtelomeric regions

In budding yeast, the telomeric DNA is flanked by a combination of two subtelomeric repetitive sequences, the X and Y' elements. We have investigated the influence of these sequences on telomeric silencing. The telomere-proximal portion of either X or Y' dampened silencing when located between the telomere and the reporter gene. These elements were named STARs, for subtelomeric anti-silencing regions. STARs can also counteract silencer-driven repression at the mating-type HML locus. When two STARs bracket a reporter gene, its expression is no longer influenced by surrounding silencing elements, although these are still active on a second reporter gene. In addition, an intervening STAR uncouples the silencing of neighboring genes. STARs thus display the hallmarks of insulators. Protection from silencing is recapitulated by multimerized oligonucleotides representing Tbf1p- and Reb1p-binding sites, as found in STARs. In contrast, sequences located more centromere proximal in X and Y' elements reinforce silencing. They can promote silencing downstream of an insulated expressed domain. Overall, our results suggest that the silencing emanating from telomeres can be propagated in a discontinuous manner via a series of subtelomeric relay elements.

Histone deacetylases: transcriptional repression with SINers and NuRDs

The DNA in eukaryotic cells is packaged into chromatin, which functions as a boundary to the transcriptional activation process. The nucleosome is the basic repeating unit of chromatin. The purification and characterization of several chromatin-remodelling complexes and the demonstration that histone acetyltransferases and histone deacetylases are regulatory components of coactivator and corepressor complexes, respectively, demonstrates that the nucleosome is not simply a static architectural feature of chromatin but, rather, plays a dynamic and integral role in the regulation of gene expression. This review focuses primarily on histone deacetylases and deacetylase-containing complexes and their role in mediating transcriptional repression.

The chicken beta-globin 5'HS4 boundary element blocks enhancer-mediated suppression of silencing

A constitutive DNase I-hypersensitive site 5' of the chicken beta-globin locus, termed 5'HS4 or cHS4, has been shown to insulate a promoter from the effect of an upstream enhancer and to reduce position effects on mini-white expression in Drosophila cells; on the basis of these findings, it has been designated a chromatin insulator. We have examined the effect of the cHS4 insulator in a system that assays both the level of gene expression and the rate of transcriptional silencing. Because transgenes flanked by insulator elements are shielded from position effects in Drosophila cells, we tested the ability of cHS4 to protect transgenes from position effects in mammalian cells. Flanking of an expression vector with the cHS4 insulator in a colony assay did not increase the number of G418-resistant colonies. Using lox/cre-based recombinase-mediated cassette exchange to control integration position, we studied the effect of cHS4 on the silencing of an integrated beta-geo reporter at three genomic sites in K562 erythroleukemia cells. In this assay, enhancers act to suppress silencing but do not increase expression levels. While cHS4 blocked enhancement at each integration site, the strength of the effect varied from site to site. Furthermore, at some sites, cHS4 inhibited the enhancer effect either when placed between the enhancer and the promoter or when placed upstream of the enhancer. These results suggest that the activity of cHS4 is not dominant in all contexts and is unlikely to prevent silencing at all genomic integration sites.

Functional determinants for the tetracycline-dependent transactivator tTA in transgenic mouse embryos

Tetracycline-dependent transgenes promise to be an important tool for investigating the time dependence of gene function during mouse development. The pivotal element of this approach is the recombinant tetracycline-dependent transactivator tTA. Using a modified gene trap approach we successfully generated mouse lines expressing tTA in a wide spread manner during embryogenesis. The transgenic model system which we established allowed us to depict transactivator and target gene expression patterns with high resolution by histochemical means. Our data provide evidence that with decreasing concentrations of tTA protein the state of chromatin acetylation becomes an increasingly important determinant for tTA function. The observation of tTA-dependent position effects on tetO-linked target genes suggests that transcription patterns can be encoded at the level of promoter preactivation.

DNA methylation and chromatin modification

DNA methylation and chromatin modification are two global mechanisms that regulate gene expression. Recent studies provide insight into the mechanism of transcriptional silencing by a methyl-CpG binding protein, MeCP2. MeCP2 is shown to interact with the Sin3/histone deacetylase co-repressor complex. Thus, this interaction can provide a mechanistic explanation for the long-known relationship between DNA methylation and chromatin structure. Moreover, several studies have shown that inhibition of histone deacetylases by specific inhibitors can reactivate endogenous genes or reporter constructs previously silenced by DNA methylation. Taken together, the data strongly suggest that DNA methylation can pattern chromatin modification.

Activation by locus control regions?

On the basis of homologous recombination experiments to delete the murine beta-globin locus control region (LCR) in embryonic stem cells, it was recently suggested that the LCR is not required for the activation of the murine beta-globin locus. This conclusion is in direct contradiction to the findings and conclusions that have been obtained with the human beta-globin LCR; thus the murine and human LCR may functionally be different or there may be a different interpretation of the results.

Stopped at the border: boundaries and insulators

Boundaries in chromatin are often marked by the presence of insulator elements. New results in Drosophila have identified an insulator with a proven boundary function essential for development. Other studies suggest a connection between the activity of some insulators and Drosophila trithorax-Group and Polycomb-Group genes. Several examples of vertebrate insulators have now been found; their locations suggest important boundary functions. Enhancer-blocking studies in oocytes and position-effect studies in transformed cells shed new light on insulator mechanisms.

Slow and Steady Wins The Race? Progress in the Development of Vectors for Gene Therapy of β-Thalassemia and Sickle Cell Disease

The cloning of the human β-globin genes more than 20 years ago led to predictions that β-thalassemia and sickle cell disease would be among the first monogenic diseases to be successfully treated by gene replacement therapy. However, despite the worldwide enrollment of more than 3,000 patients in approved gene transfer protocols, none have involved therapy for these diseases. This has been due to several technical hurdles that need to be overcome before gene replacement therapy for β-thalassemia and sickle cell disease can become practical. These problems include inefficient transduction of hematopoietic stem cells and an inability to achieve consistent, long-term, high-level expression of transferred β-like globin genes with current gene transfer vectors. In this review we highlight the relationships between understanding the fundamental mechanisms of β-globin gene locus function and basic vector biology and the development of strategies for β-globin gene replacement therapy. Despite slow initial progress in this field, recent advances in a variety of critical areas provide hope that clinical trials may not be far away.