X Inactivation, DNA Methylation, and Differentiation Revisited. In: Razin A, Cedar H, Riggs AD, editors. DNA Methylation. New York: Springer; 1984. pp. 269-78. [DOI: 10.1007/978-1-4613-8519-6_13]

Cytological evaluation of global DNA methylation in mouse testicular genome

Global methylation of DNA from different testicular cell types has been studied by DNA end-labeling and nick translation of fixed chromatin (in situ), following digestion with cytosine methylation-sensitive restriction enzymes. Both at the level of chromatic (chromosome) and naked DNA, there is extensive methylation of the genome. Although the extent of methylation was nearly the same among different cell types in the MspI, HpaII, and HhaI digested end-labelled DNA, in the chromosome preparations the digestion patterns varied in cell type-specific manner, pachytene being the most sensitive and spermatids and sperm the most resistant. The differential sensitivity is attributable to the difference in the chromatin organisation in different testicular cell types though no specific region could be identified as particularly more sensitive or resistant to the enzymes. Pachytene bivalents do not reveal a consistent segmental pattern of digestion, but the perichiasmate regions of diplotene/diakinesis and metaphase I chromosomes show hypersensitivity to the enzymes.

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

The constitutive DNase I hypersensitive site at the 5' end of the chicken beta-globin locus marks the boundary of the active chromatin domain in erythroid cells. The DNA sequence containing this site has the properties of an insulator, as shown by its ability in stable transformation experiments to block enhancer-promoter interaction when it lies between the two, but not when it lies outside, and to protect against position effects in Drosophila. We now show that the chicken insulator can protect a stably integrated gene, which is otherwise subject to great variability of expression, from chromatin-mediated repression in cell culture. When the integrated reporter gene is surrounded by insulator elements, stably transformed cell lines display consistent enhancer-dependent expression levels, in accord with the strength of the enhancer. In the absence of insulators, long-term nonselective propagation of cells carrying the integrated reporter gene results in gradual extinction of the reporter's expression, with expression patterns from tandemly repeated inserted genes suggesting that the extinction of adjacent genes is coupled. We show that the uninsulated reporter genes, in addition to becoming transcriptionally inactive, lose several epigenetic hallmarks of active chromatin, including nuclease accessibility, DNA hypomethylation, and histone hyperacetylation during time in culture. Treatment with inhibitors of histone deacetylase or DNA methylation reverses the extinction of the uninsulated genes. Extinction is completely prevented by flanking the reporter construct with insulators. Furthermore, in contrast to the uninsulated reporter genes, chromatin over the insulated genes retains nuclease accessibility and histone hyperacetylation. However, there is no clear correlation between the presence of the insulators and the level of DNA methylation. This leads us to propose a model for the insulator's ability to protect against extinction in the transformed cell lines and to function as a chromatin boundary for the chicken beta-globin locus in normal erythroid cells.

Role of T cell DNA methylation in lupus syndromes

Current theories postulate that exposure to certain environmental agents will induce lupus in genetically predisposed individuals. However, the mechanisms by which environmental agents interact with the immune system to trigger lupus is unclear. Recent work has shown that some environmental agents associated with lupus, such as procainamide, hydralazine and ultraviolet light, will inhibit T cell DNA methylation, increase LFA-1 expression and induce autoreactivity. In addition, T cells isolated from patients with active lupus have hypomethlated DNA, diminished DNA methyltransferase activity and overexpress LFA-1 on an autoreactive subset of cells which spontaneously lyses autologous macrophages. More recent work has shown that the adoptive transfer of murine T cells made autoreactive with DNA methylation inhibitors is sufficient to cause a lupus-like disease in otherwise healthy syngeneic recipients. Together, these results support a new model of autoimmunity, in which certain environmental agents modify T cells by inhibiting DNA methylation and altering expression of certain genes, thereby inducing autoreactivity. The autoreactive cells then interact with the host to produce a lupus-like disease.

Gene silencing in mammalian cells by direct incorporation of electroporated 5-methyl-2'-deoxycytidine 5'-triphosphate

DNA methylation is an important process contributing to transcriptional regulation in animal and plant cells. We observed that electroporation of Chinese hamster V-79 cells in the presence of millimolar concentrations of 5-methyl-2'-deoxycytidine 5'-triphosphate (5mdCTP) led to high-level direct incorporation of this nucleotide into DNA polymer. Under optimum conditions, approximately 2 x 10(8) molecules of 5 mdCTP were calculated to have been incorporated into each unit genome (6 pg of DNA). Since a diploid mammalian genome contains approximately 1.2-1.5 x 10(9) cytosines, this level of 5 mdCTP incorporation corresponds to substitution of up to 16.6% of total cytosines by 5-methylcytosine, or about 100-150 new methylated cytosines per average gene. The pattern of genomic methylation produced under these conditions differed from that produced physiologically in that 5mdCTP was substituted into DNA at random cytosines, superimposing a novel methylation pattern upon that derived from the normal enzyme-driven postreplicational process. This novel pattern of methylation showed no preference for CpG dinucleotides, but was nevertheless found capable of silencing HPRT gene expression and producing a condition of resistance to 6-thioguanine. The epigenetic nature of this gene silencing event was shown by the very high level of reexpression of HPRT mRNA following exposure of HPRT cells to the demethylating agent 5-azadeoxycytidine.

DNA methylation and cell memory

In this paper we address the question: How do replicating mammalian cells remember with high fidelity their proper state of differentiation? Several possible mechanisms for cell memory are discussed, and it is concluded that only mechanisms involving DNA methylation are supported by strong experimental evidence. This evidence is reviewed. The establishment and modulation of methylation patterns are discussed and a hemimethylation model for stem cells is presented. The overall conclusion is that, although little is yet known about the details, there should be little doubt about the existence of a methylation system functioning at least to aid cell memory.

DNA methylation: a secondary event in globin gene switching?

Changes in gamma-globin gene methylation accompany the fetal to adult globin switch in man. Using somatic cell hybrids made by fusing mouse erythroleukemia and human fetal erythroid cells, we asked whether methylation is a cause or a consequence of gamma-gene inactivation during development. These hybrids initially express human gamma-globin but switch with time in culture to adult globin gene production. In hybrids before the switch, the gamma-genes are unmethylated. After completion of the switch, the hybrids contain methylated gamma-globin genes. However, during the time that the gamma----beta switch is occurring, hybrids are found that no longer express gamma-globin, yet still possess unmethylated gamma-globin genes. This suggests that methylation is not a primary event in gamma-gene inactivation during human development.

Structure of transcriptionally active chromatin

Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.