A Role for DNA Hypomethylation and Histone Acetylation in Maintaining Allele-Specific Expression of Mouse NKG2A in Developing and Mature NK Cells

Abstract

The repertoire of receptors that is expressed by NK cells is critical for their ability to kill virally infected or transformed cells. However, the molecular mechanisms that determine whether and when NK receptor genes are transcribed during hemopoiesis remain unclear. In this study, we show that hypomethylation of a CpG-rich region in the mouse NKG2A gene is associated with transcription of NKG2A in ex vivo NK cells and NK cell lines. This observation was extended to various developmental stages of NK cells sorted from bone marrow, in which we demonstrate that the CpGs are methylated in the NKG2A-negative stages (hemopoietic stem cells, NK progenitors, and NKG2A-negative NK cells), and hypomethylated specifically in the NKG2A-positive NK cells. Furthermore, we provide evidence that DNA methylation is important in maintaining the allele-specific expression of NKG2A. Finally, we show that acetylated histones are associated with the CpG-rich region in NKG2A positive, but not negative, cell lines, and that treatment with the histone deacetylase inhibitor trichostatin A alone is sufficient to induce NKG2A expression. Treatment with the methyltransferase inhibitor 5-azacytidine only is insufficient to induce transcription, but cotreatment with both drugs resulted in a significantly greater induction, suggesting a cooperative role for DNA methylation and histone acetylation status in regulating gene expression. These results enhance our understanding of the formation and maintenance of NK receptor repertoires in developing and mature NK cells.

Evidence for high bi-allelic expression of activating Ly49 receptors

“…The half-and-half pattern of DNA methylation correlates with the mono-allelic expression of Ly49A, C and NKG2A as was subsequently shown using F1 hybrids for Ly49a and Nkg2a (22,44). If DNA methylation does not correlate with stochastic mono-allelic expression; either stochastic gene expression is maintained at the level of histone modifications only or this pattern is possibly an indication of high, if not complete, bi-allelic expression and even the lack of stochastic expression of the activating receptors.…”

“…We have shown that DNA methylation of this region correlates with expression patterns of these receptors as with the inhibitory Ly49A, Ly49C (22) and NKG2A (44). Furthermore, as in the case of Ly49a , the CpG dinucleotides downstream of the transcriptional start site of Ly49h seem to have higher levels of methylation compared to those located upstream in Ly49H-negative cells.…”

A Structural Split in the Human Genome

“…About 60% of human genes contain PCIs [9], most of which are unmethylated [11], [12]. Such PCIs are more common in widely-expressed (housekeeping) genes [13], supporting the view that non-methylated PCIs actively maintain gene transcription [14], [15].…”

Preferential Epigenetic Suppression of the Autonomous MusD over the Nonautonomous ETn Mouse Retrotransposons

“…4A). A promoter region of the housekeeping gene Hprt was amplified as an example of an active gene, and a GC-rich region of the NK cell-specific gene Nkg2a, which is deacetylated in nonexpressing cells (50), was amplified as an example of an inactive gene.…”