Elsevier

Clinical Immunology

Volume 109, Issue 1, October 2003, Pages 37-45
Clinical Immunology

Regular article
Methylation and demethylation in the regulation of genes, cells, and responses in the immune system

https://doi.org/10.1016/S1521-6616(03)00205-5Get rights and content

Abstract

DNA methylation is a focus of epigenetic research in the immune system. This overview begins with a synopsis of the players and processes involved in DNA methylation, demethylation, methyl-CpG-recognition, histone modification, and chromatin remodeling. The role of these mechanisms in immune responses, with a focus on T lymphocytes, is then reviewed. There is evidence for epigenetic regulation of several key immune processes including thymocyte development, antigen presentation, differentiation, cytokine expression, effector function, and memory. DNA methylation contributes, along with other epigenetic mechanisms, to the establishment of transcriptional thresholds that vary between genes and T cell types. The immune system is a fertile field for studies of epigenetic regulation of cell fate and function.

Introduction

The importance of epigenetic mechanisms in the fields of developmental and cancer biology is established, and awareness in immunology is growing. While genetic information is encoded by DNA sequences, epigenetic information is encoded by differential methylation of DNA on cytosines (primarily in CpG dinucleotides), by proteins that associate with DNA and their covalent modifications, and by the chromatin structures that these form within the nucleus. DNA-associated proteins include histones—which may be modified covalently by acetylation, methylation, phosphorylation, and/or ubiquitination—methylCpG-binding proteins, and others. The primary unit of chromatin structure is the disk-shaped nucleosome, which comprises ∼165 bp of DNA wrapped around a histone octamer core, consisting of two copies each of H2A, H2B, H3, and H4. Neighboring nucleosomes are connected by short segments (∼10–80 bp) of DNA and then compacted by the linker histone H1 into ∼30-nm-diameter chromatin fibers. Variations in DNA methylation and the composition and covalent modifications of histones constitute a distinct epigenetic code that, in concert with differences in the abundance of transcription factors, regulates gene expression. For example, methylated DNA, some methylated histone forms, and condensed chromatin are associated with inaccessible DNA and repressed or silenced gene expression. Conversely, nonmethylated DNA, some acetylated histone forms, and open chromatin are associated with active or potential gene expression. Epigenetic codes are potentially heritable, thereby providing a means for propagating information from parental cells to their progeny. However, unlike information encoded in the DNA sequence, epigenetic codes can be modified, thereby providing the potential for plasticity. Recent studies, which are discussed below, are revealing the meaning of this code, new links between epigenetic mechanisms, and how the transcriptional machinery interprets epigenetic markings on DNA [for recent reviews see [1], [2], [3]].

DNA methylation has been a growing focus of epigenetic studies in the immune system for a number of reasons. First, cytosine methylation is well characterized at the chemical, enzymatic, and genetic levels in many organisms from plants to humans. Second, methylation of cytosines in CpG dinucleotides possesses a proven mechanism for heritable propagation of epigenetic information—the maintenance methyltransferase DNA methyltransferase 1 (Dnmt1) copies the pattern of CpG methylation from the parental DNA strands to their progeny strands during S phase. Gene-specific methylation patterns can thereby be faithfully transferred from parental cells to their progeny in a manner conducive to cell fate decisions. Finally, high-resolution technologies are available for comprehensive analysis of CpG methylation in small numbers of cells, and viable knockout mice for molecules associated with DNA methylation have become available. These elements have converged in recent studies on gene-specific methylation-associated processes in immune phenomena such as T-lymphocyte lineage commitment, T-cell effector function, and memory.

This review will begin with a brief description of the players and processes involved in DNA methylation-associated gene regulation and then highlight some of the most definitive and current literature on epigenetic analyses of T-cell development, differentiation, and function—as well as some of the unresolved issues awaiting elucidation. Some of these areas are the subject of topical reviews in this issue and elsewhere [1], [2], [3], [4], [5], [6], [7], [8].

Section snippets

DNA methyltransferases, maintenance methylation, and de novo methylation

Dnmt1 is ubiquitously expressed, upregulated during the S phase of cell division, and recruited to DNA replication sites by proliferating cell nuclear antigen (PCNA). Its preferred substrates are hemi-methylated CpG sites such as those generated during replication of symmetrically methylated CpG sites. Dnmt1 binds to and methylates CpGs on newly synthesized daughter strands to maintain methylation patterns that are complementary to those of the parental strand. The requirement for Dnmt1 in

Potential manifestations of epigenetic regulation of gene expression

The diversity of epigenetic players and processes outlined above is potentially compatible with quantitative, qualitative, heritable, and flexible regulation of gene expression. Through repressive methylation, histone complexes, and chromatin conformation, epigenetic mechanisms can establish quantitative thresholds for the induction of gene expression. These may be manifested as (a) the strength of stimulus needed to induce expression of a gene in a single cell, (b) the probability of gene

Epigenetic regulation of genes, cells, and fates in the immune system

During their development and differentiation, T lymphocytes make a number of sequential cell fate decisions, including irreversible commitment to the αβ or γδ TCR lineages, followed (in the case of αβ TCR lineage cells) by commitment either to the CD4 or the CD8 lineage, and, after they emerge from the thymus, they may develop polarized patterns of effector gene expression. Epigenetic mechanisms may be associated with each of these choices.

DNA methylation and other immune cells

DNA methylation and other epigenetic mechanisms are also important in the establishment and/or maintenance of diverse repertoires of clonally restricted KIR and Ly49 receptors on NK cells [118], [119], [120]. By contrast to the single receptor per cell outcome in T and B lymphocytes, the epigenetic control of receptor expression in NK cells yields unique combinations of multiple receptors on each NK cell—and a population-wide repertoire that is exquisitely responsive to changes in the MHC

Future directions

The DNA methylation field continues to benefit from the development of bisulfite sequencing as a comprehensive quantitative method for measuring CpG methylation levels [128], [129]. Further benefits can be anticipated from concurrent genome-wide mapping of methylation and mRNA patterns; however, the sensitivity of current array-based methods may need to be improved to define true transcriptional thresholds. Chromatin complex composition may be clarified by proteomic analyses that have reached

Acknowledgements

This work was supported in part by grants from the NIH (HD39454, HD18184) and March of Dimes. The authors report no relevant conflicts of interest.

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