DNA methylation and chromatin structure regulate T cell perforin gene expression

Perforin is a cytotoxic effector molecule expressed in NK cells and a subset of T cells. The mechanisms regulating its expression are incompletely understood. We observed that DNA methylation inhibition could increase perforin expression in T cells, so we examined the methylation pattern and chromatin structure of the human perforin promoter and upstream enhancer in primary CD4(+) and CD8(+) T cells as well as in an NK cell line that expresses perforin, compared with fibroblasts, which do not express perforin. The entire region was nearly completely unmethylated in the NK cell line and largely methylated in fibroblasts. In contrast, only the core promoter was constitutively unmethylated in primary CD4(+) and CD8(+) cells, and expression was associated with hypomethylation of an area residing between the upstream enhancer at -1 kb and the distal promoter at -0.3 kb. Treating T cells with the DNA methyltransferase inhibitor 5-azacytidine selectively demethylated this area and increased perforin expression. Selective methylation of this region suppressed promoter function in transfection assays. Finally, perforin expression and hypomethylation were associated with localized sensitivity of the 5' flank to DNase I digestion, indicating an accessible configuration. These results indicate that DNA methylation and chromatin structure participate in the regulation of perforin expression in T cells.     

Mitogenic activation of EL-4 cells does not require surface Thy-1 expression

The ability of monoclonal anti-Thy-1 antibodies to stimulate IL-2 production and T-cell proliferation has raised the possibility that Thy-1 may play an important role in T-cell activation. To examine this postulated role we have produced Thy-1-negative variants of the murine T lymphoma EL-4 by mutagenesis with ethyl methanesulfonate (EMS) and subsequent negative selection with anti-Thy-1 monoclonal antibodies (mAbs) and complement. Although the parental EL-4 cell line produced interleukin-2 (IL-2) in response to concanavalin A (Con A), phytohemagglutinin, anti-Thy-1 mAbs, and an anti-T3 mAb, as well as after exposure to phorbol myristate acetate (PMA), only PMA was capable of inducing IL-2 production by several Thy-1-negative cell lines. The loss of responsiveness to cell surface stimulatory ligands appeared to be correlated with loss of Thy-1 expression because mutagenized cells selected for high levels of Thy-1 expression all responded normally to Con A. However, when Thy-1 expression was reconstituted in the "nonresponder" (Thy-1-negative) cell lines either by transfection of a Thy-1.2 gene or by 5-azadeoxycytidine treatment, the revertant cell lines were still unable to produce IL-2 when stimulated with Con A, anti-Thy-1, or anti-T3. Furthermore, several other independently derived Thy-1-negative EL-4 cell lines responded normally to mitogens and mitogenic mAbs. Taken together, these results suggest that Thy-1 expression is not required for the T-cell activation process and that the EMS mutagenesis procedure resulted in an additional mutation(s) responsible for the inability of certain Thy-1-negative cell lines to be triggered by mitogens and mitogenic mAbs. These cell lines may prove to be valuable tools for further biochemical and molecular studies of the sequence of events associated with T-cell activation.     

Methods for analyzing the role of DNA methylation and chromatin structure in regulating T lymphocyte gene expression

Chromatin structure, determined in part by DNA methylation, is established during differentiation and prevents expression of genes unnecessary for the function of a given cell type. We reported that DNA methylation and chromatin structure contributes to lymphoidspecific ITGAL (CD11a) and PRF1 (perforin) expression. We used bisulfite sequencing to compare methylation patterns in the ITGAL promoter and 5′ flanking region of T cells and fibroblasts, and in the PRF1 promoter and upstream enhancer of CD4+ and CD8+ T cells with fibroblasts. The effects of methylation on promoter function were tested using regional methylation of reporter constructs, and confirmed by DNA methyltransferase inhibition. The relationship between DNA methylation and chromatin structure was analyzed by DNaseI hypersensitivity. Herein we described the methods and results in greater detail. Published: September 16, 2004.     

H4K20 methylation regulates quiescence and chromatin compaction

The transition between proliferation and quiescence is frequently associated with changes in gene expression, extent of chromatin compaction, and histone modifications, but whether changes in chromatin state actually regulate cell cycle exit with quiescence is unclear. We find that primary human fibroblasts induced into quiescence exhibit tighter chromatin compaction. Mass spectrometry analysis of histone modifications reveals that H4K20me2 and H4K20me3 increase in quiescence and other histone modifications are present at similar levels in proliferating and quiescent cells. Analysis of cells in S, G₂/M, and G₁ phases shows that H4K20me1 increases after S phase and is converted to H4K20me2 and H4K20me3 in quiescence. Knockdown of the enzyme that creates H4K20me3 results in an increased fraction of cells in S phase, a defect in exiting the cell cycle, and decreased chromatin compaction. Overexpression of Suv4-20h1, the enzyme that creates H4K20me2 from H4K20me1, results in G₂ arrest, consistent with a role for H4K20me1 in mitosis. The results suggest that the same lysine on H4K20 may, in its different methylation states, facilitate mitotic functions in M phase and promote chromatin compaction and cell cycle exit in quiescent cells.     

DNA methylation and chromatin structure: a view from below

An understanding of the function and control of DNA methylation in eukaryotes has been elusive. Studies of Neurospora crassa have led to a model that accounts for the chromosomal distribution of methylation and suggests a basic function for DNA methylation in eukaryotes.     

DNA methylation regulates tissue-specific expression of Shank3

Tissue-specific gene expression can be controlled by epigenetic modifications such as DNA methylation. SHANK3, together with its homologues SHANK1 and SHANK2, has a central functional and structural role in excitatory synapses and is involved in the human chromosome 22q13 deletion syndrome. In this report, we show by DNA methylation analysis in lymphocytes, brain cortex, cerebellum and heart that the three SHANK genes possess several methylated CpG boxes, but only SHANK3 CpG islands are highly methylated in tissues where protein expression is low or absent and unmethylated where expression is present. SHANK3 protein expression is significantly reduced in hippocampal neurons after treatment with methionine, while HeLa cells become able to express SHANK3 after treatment with 5-Aza-2'-deoxycytidine. Altogether, these data suggest the existence of a specific epigenetic control mechanism regulating SHANK3, but not SHANK1 and SHANK2, expression.     

MD1 expression regulates development of regulatory T cells

Intense interest has centered around the role of a subset of regulatory T cells, CD4+CD25+ Treg, in controlling the development of autoimmune disorders, allograft rejection, infection, malignancy, and allergy. We previously reported that MD1, a molecule known to be important in regulation of expression of RP105, also was important in regulating alloimmunity, and that blockade of expression of MD1 diminished graft rejection in vivo. One mechanism by which an MD1-RP105 complex exerts an effect on immune responses is through interference with an LPS-derived signal delivered through the CD14-MD-2-TLR4 complex. We show below that LPS signaling for Treg induction occurs at higher LPS thresholds that for effector T cell responses. In addition, blockade of MD1 functional activity in dendritic cells (using anti-MD1 mAbs, MD1 antisense deoxyoligonucleotides, or responder cells from mice with deletion of the MD1 gene), resulted in elevated Treg induction in response to allogeneic stimulation (in vivo or in vitro) in the presence of LPS. These data offer one mechanistic explanation for the augmented immunosuppression described following anti-MD1 treatment.     

Effect of an inhibitor of DNA methylation on T cells. I. 5-Azacytidine induces T4 expression on T8+ T cells

Maturing thymocytes express a series of cell surface glycoproteins which can be identified by monoclonal antibodies. The stage II or common thymocyte expresses the phenotype T4+T8+T6+T3-. In response to unknown signals, but presumably involving interactions with products of the major histocompatibility complex, the thymocyte suppresses either the T8 or T4 gene, becoming committed to the T4+T8- or T4-T8+ phenotype. With maturation, the thymocyte also becomes T6-T3+. To study whether DNA methylation may be involved in regulating expression of these determinants in mature T cells, we treated cloned interleukin 2-dependent T8- and T4-bearing T cells with 5-azacytidine (5-azaC), a nucleoside analog which inhibits methylation of newly synthesized DNA. In this report, we show that T8+ T cells treated with 5-azaC express the phenotype T8+T4+T6-T3+. Treatment of the same cells with hydroxyurea, an inhibitor of DNA synthesis, failed to induce T4 on T8+ cells. These results suggest that expression of the T4 gene may be suppressed by DNA methylation in mature T8+ cells.     

Overall DNA methylation and chromatin structure of normal and abnormal X chromosomes

DNA methylation patterns were studied at the chromosome level in normal and abnormal X chromosomes using an anti-5-methylcytosine antibody. In man, except for the late-replicating X of female cells, the labeled chromosome structures correspond to R- and T-bands and heterochromatin. Depending on the cell type, the species, and cell culture conditions, the late-replicating X in female cells appears to be more or less undermethylated. Under normal conditions, the only structures that remain methylated on the X chromosomes correspond to pseudoautosomal regions, which harbor active genes. Thus, active genes are usually hypomethylated but are located in methylated chromatin. Structural rearrangements of the X chromosome, such as t(X;X)(pter;pter), induce a Turner syndrome-like phenotype that is inconsistent with the resulting triple-X constitution. This suggests a position effect controlling gene inactivation. The derivative chromosomes are always late replicating, and their duplicated short arms, which harbor pseudoautosomal regions, replicate later than the normal late-replicating X chromosomes. The compaction or condensation of this segment is unusual, with a halo of chromatin surrounding a hypocondensed chromosome core. The chromosome core is hypomethylated, but the surrounding chromatin is slightly labeled. Thus, unusual DNA methylation and chromatin condensation are associated with the observed position effect. This strengthens the hypothesis that DNA methylation at the chromosome level is associated with both chromatin structure and gene expression.