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Keywords:

  • genomics;
  • T cells;
  • transcription factors/gene regulation

Summary

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

T cells are exquisitely poised to respond rapidly to pathogens and have proved an instructive model for exploring the regulation of inducible genes. Individual genes respond to antigenic stimulation in different ways, and it has become clear that the interplay between transcription factors and the chromatin platform of individual genes governs these responses. Our understanding of the complexity of the chromatin platform and the epigenetic mechanisms that contribute to transcriptional control has expanded dramatically in recent years. These mechanisms include the presence/absence of histone modification marks, which form an epigenetic signature to mark active or inactive genes. These signatures are dynamically added or removed by epigenetic enzymes, comprising an array of histone-modifying enzymes, including the more recently recognized chromatin-associated signalling kinases. In addition, chromatin-remodelling complexes physically alter the chromatin structure to regulate chromatin accessibility to transcriptional regulatory factors. The advent of genome-wide technologies has enabled characterization of the chromatin landscape of T cells in terms of histone occupancy, histone modification patterns and transcription factor association with specific genomic regulatory regions, generating a picture of the T-cell epigenome. Here, we discuss the multi-layered regulation of inducible gene expression in the immune system, focusing on the interplay between transcription factors, and the T-cell epigenome, including the role played by chromatin remodellers and epigenetic enzymes. We will also use IL2, a key inducible cytokine gene in T cells, as an example of how the different layers of epigenetic mechanisms regulate immune responsive genes during T-cell activation.


Introduction

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

It is now well established that the chromatin landscape plays an important role in the regulation of inducible genes. The mature cells of the immune system represent an exquisitely poised system for rapid response to pathogens and have proved to be a valuable model for investigating the contribution of chromatin to the regulation of genes that respond rapidly to environmental signals. For example, activation of naive CD4+ T cells in the immunological response to infection leads to a concerted programme of proliferation and slow differentiation that results in the acquisition and regulated expression of multiple effector genes. The stimulation of T cells involves activation of protein kinase and calcium signalling pathways, including tyrosine and serine/threonine kinases and phosphatases, protein kinase C (PKC) and calcineurin, respectively; following which, numerous transcription factor families, including nuclear factor-κB and nuclear factor of activated T cells are activated and translocated into the nucleus to bind to target genes. Individual genes respond to immune stimulation in distinct temporal and cell-type-specific patterns, and this is governed by the nature of the antigenic stimulus and the interactions between the inducible transcription factors and the gene-specific chromatin environment. Chromatin can act as a barrier to the binding of transcription factors and the transcription machinery and it must therefore be modified or reorganized to facilitate changes in gene transcription. These changes may occur at a localized level or at a higher-order chromatin level. The gene expression changes that occur during T-cell activation and differentiation therefore require a co-ordinated effort from inducible transcription factors, chromatin-remodelling complexes, histone-modifying enzymes and the more recently discovered chromatin-associated signalling kinases. Herein we will focus our efforts on the chromatin events that are required to facilitate changes in gene expression programmes during T-cell activation.

Mechanisms of epigenetic control and gene expression

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

The broadest definition of epigenetics refers to gene expression that is governed by mechanisms other than the DNA sequence.[1] Eukaryotic DNA exists as chromatin; repeating units of nucleosomes where 147 base pairs of DNA are wrapped around an octameric histone complex, consisting of two each of histones H2A, H2B, H3 and H4, or variants of these core histones.[2] It has become clear that dynamic changes in chromatin structure play a key role in regulating genome functions, including transcription.[3, 4] Highly compacted chromatin structures are enriched in nucleosomes and are generally transcriptionally silent as the DNA template is inaccessible to the transcriptional apparatus. In contrast, a net loss of nucleosomes from gene-specific regulatory regions increases chromatin accessibility, enabling the binding of transcriptional regulators. This is a key initial step in gene expression. The composition of chromatin structure and biochemical modifications of histone proteins have therefore emerged as important mechanisms for the regulation of inducible immune responsive gene transcription. Figure 1 portrays the interchange between heterochromatin and euchromatin to permit binding of the transcription machinery and transcription factors. Transcriptional control is administered by mechanisms involving (i) DNA methylation, (ii) post-translational modifications of histone proteins, (iii) actions of ATP-driven chromatin-remodelling enzymes, and (iv) exchange of histone variants with canonical histones. These mechanisms function in a non-linear but inter-dependent fashion, offering multiple checkpoints for precise gene control. The role of these mechanisms in the regulation of inducible immune responsive gene transcription is discussed in detail in the following sections.

image

Figure 1. Mechanisms involved in epigenetic regulation. Chromatin-remodelling complexes can restructure, reposition and evict histone octamers using ATP to regulate access to DNA for the binding of transcriptional regulatory factors like transcription factors to their binding sites, co-activators and the basal transcription machinery including Pol II core complex. Histone tails can be modified by histone modifications like phosphorylation, acetylation and methylation. This is done through the action of histone modifiers like histone acetylases, histone methylases and histone kinases. Histone variants (H2A.Z and H3.3) flank nucleosome-free regions of actively transcribing promoters and other regulatory elements. Non-coding RNAs can target and maintain heterochromatin formation. ATP, adenosine triphosphate; ADP, adenosine diphosphate; TSS, transcriptional start site; Me, methylation; P, phosphorylation; Ac, acetylation; TF, transcription factor; RE, response elements; R, arginine; K, lysine; T, threonine; S, serine.

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Histone modifications form a key layer of epigenetic control for cellular gene expression profiles

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

The co-ordinated and dynamic changes in chromatin structure and histone modifications are considered a key underlying mechanism that directs temporal and cell-lineage-specific gene transcription. The protruding N-terminal tails of histones in particular are subjected to chemical modifications, with over a dozen different modifications now documented including acetylation, methylation, phosphorylation, ubiquitinylation, sumoylation and biotinylation.[5-7] The possible functions of these modifications can be divided into three main groups: (i) alteration of the biophysical properties of chromatin; (ii) establishment of a histone code that provides a platform to modulate binding of transcriptional regulators; or (iii) segregation of the genome into distinct domains such as euchromatin (where chromatin is maintained as accessible for transcription) or heterochromatin (chromatin regions that are less accessible for transcription). Importantly, while such modifications can be dynamic, they can also be stably inherited by daughter cells upon division. Hence, they also contribute to the maintenance of cellular identity.[8]

While particular functions have been ascribed to various histone modifications, it is becoming increasingly evident that it is the combination of histone modifications at a particular locus that is critical for transcription regulation in mammalian cells. This is most evident when considering patterns of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3) within the same promoter regions. Whereas H3K4me3 has been associated with transcriptional activation and H3K27me3 with transcriptional repression, genome-wide mapping of these two modifications in embryonic stem cells has demonstrated that regions involved in maintaining embryonic stem cell pluripotency and differentiation are enriched for both H3K4me3 and H3K27me3, and do not demonstrate significant transcriptional activity.[9] Such loci are termed “bivalent” (Fig. 2). Importantly, upon differentiation those genes that become transcriptionally active maintain the H3K4me3 modification and lose H3K27me3. Conversely, those genes that are not transcriptionally active after differentiation maintain H3K27me3, but lose H3K4me3. Together, these data suggest that bivalency is a mechanism by which genes can be rapidly activated or repressed depending on the differentiation pathway initiated. In this way, cell identity upon differentiation can be maintained by resolving specific histone modifications at key gene loci. Hence, histone modifications play a key role in forming a blueprint for the acquisition and maintenance of cellular gene expression profiles.

image

Figure 2. Interplay between histone methylation and gene expression across the promoter of active, poised and bivalent genes in human memory CD8+ T cells. The relationship between histone methylation and gene expression is characterized into four main gene groups in human memory CD8+ T cells, namely active genes, poised genes, bivalent genes and silent genes.[47] Active genes have higher levels of mRNA expression in memory T cells compared with naive T cells in the resting state. This correlates with the high levels of H3K4me3 and low levels of H3K27me3 in resting memory T cells. Both poised and bivalent genes have low gene expression in both resting naive and memory T cells. Poised genes have a similar chromatin state to the active genes but the genes are induced more highly in the activated memory cells compared with the naive cells. Bivalent genes have high levels of both H3K4me3 and H3K27me3 at gene promoters that were not expressed in the resting memory cells. Upon activation, these genes are significantly induced in activated memory cells over resting memory and activated naive cells and there was a parallel increase in H3K4me3, converting the bivalent state to an open chromatin state. In repressed genes, the resting memory cells have lower gene expression levels compared with resting naive cells and are marked by high H3K27me3 and low H3K4me3 in resting memory cells. The repressed gene expression profile remains unchanged upon activation. Hence, the differential gene expression is associated with the chromatin state present at the gene promoter. TSS, transcriptional start site; N, naive T cells; M, memory T cells.

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Epigenetic enzymes dynamically write or erase epigenetic signatures

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

The majority of these histone modifications are reversible through the actions of histone-modifying enzymes, contributing to the dynamic regulation of transcription. Histone acetylation on lysine residues is generally associated with transcriptional activation, and is highly dynamic. It is regulated by the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs), which have been well characterized in terms of their interacting partners and mechanisms of chromatin regulation.[10-12] Histone methylation is considerably more complex, occurring on lysine, arginine and histidine residues, of which lysine methylation is the best characterized. Histone lysine methylation has different outcomes, dependent on the residue that is modified and the extent of the modification, i.e. lysines can be mono-, di- or trimethylated. Lysine methyltransferases and the proteins that recognize and interpret the modifications have been relatively well characterized and reviewed elsewhere.[5, 13, 14] In comparison, lysine demethylases have only recently been described. The discovery of lysine demethylases revolutionized the idea that histone methylations are irreversible.[15, 16] Furthermore, new chromatin modifications and chromatin-modifying enzymes are still being described. Molecules traditionally known for their well-conserved cytoplasmic signal transduction roles are proving to be considerably more versatile than previously expected. For example, mitogen-activated protein kinases are well-characterized signal transduction molecules with thoroughly described cytoplasmic functions. More recently they have been found to regulate gene transcription, not only through phosphorylation of transcription factors and other histone modifiers, but also through modification of histones themselves, following recruitment to the promoters of target genes.[17-19] Similarly, the PKC family has been shown to have a nuclear function as epigenetic enzymes.[20, 21] In human T lymphocytes, Sutcliffe et al. demonstrated that nuclear-anchored PKCθ forms an active transcription complex with RNA polymerase II (Pol II), the histone kinase MSK1, the adaptor molecule 14-3-3ζ and the lysine demethylase, LSD1 on key immune-responsive gene promoters (Fig. 3).[21] Further results also suggest that the recruitment of PKCθ to coding genes depends on nuclear factor-κB signalling.[22] These epigenetic modifiers therefore clearly work in co-operation with other modifiers, transcription factors and the transcription machinery. Therefore future research needs to focus on the complexes of effector enzymes that form on chromatin to better understand the impact of histone modifications on gene transcription.

image

Figure 3. Multi-layered regulation of the IL2 inducible gene in T cells. The regulation of inducible genes in immune cells is a complex process involving many key epigenetic players. In the resting state, the IL2 promoter is flanked by the H2A.Z nucleosome about 150 base pairs upstream from the TSS.[21] The promoter is marked by active histone modifications like H3K9ac and H3K4me3 whereas the gene body has low levels of the transcriptional elongation mark H3K36me3.[48] The low basal gene expression is maintained through the repressive activity of miRNA such as mir-200c.[21] Upon T-cell activation, the H2A.Z nucleosome is removed, exposing the binding site for transcription factor c-Rel, which is required for chromatin remodelling of the IL2 promoter.[76] This involves loss of nucleosomes, allowing the binding of the RNA polymerase II complex for gene transcription to occur.[48, 66, 77] Histone modifiers such as PKCθ, MSK1 and LSD1 as well as the adapter protein 14-3-3ζ are recruited together with Pol II to form a transcriptional complex at the IL2 promoter.[21] While the active histone modifications were unchanged with activation, the elongation mark H3K36me3 increased indicative of transcriptional elongation hence an increase in gene expression.[48]

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Chromatin-remodelling complexes

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

In addition to the histone-modifying enzymes, a group of chromatin-remodelling complexes have been described that physically alter chromatin structure and function.[23] These complexes contain a central ATPase component that harnesses ATP hydrolysis to physically remove or slide histones from DNA. The chromatin-remodelling complexes are categorized into four distinct groups based on the sequence homology of their ATPase subunit: ISWI (Imitation SWItch), INO80/SWR1 (INOsitol requiring/Sick With Rat8 ts), CHD (chromodomain helicase DNA binding protein) and SWI/SNF (SWItch/Sucrose Non-Fermentable).

The best characterized of these complexes is the multi-subunit SWI/SNF complex, which contains either Brm (Brahma) or BRG1 (Brahma-related gene 1) as its ATPase subunit.[24] These ATPases are able to act alone to remodel nucleosomes in vitro; however, within cells, they are found in complexes containing up to 12 additional proteins referred to as BAFs (BRG1/Brm-associated factors). These associated BAFs are proposed to modulate the targeting and functional specificity of the SWI/SNF complexes.[25, 26] The SWI/SNF complexes are thought to be targeted to specific genes through interactions with transcription factors, co-regulators or components of the transcription machinery. Whereas BRG1 has been found to interact with a range of transcription factors, it is likely that multiple interactions are involved in the recruitment of the SWI/SNF complex to any individual promoter.[27] In addition, several components of the SWI/SNF complex, including BRG1, have bromodomains, which recognize and bind to acetylated histones.[28] Therefore, acetylated histones can act as a platform for BRG1 recruitment, but it is most likely that other interactions are also required. Regardless of the mechanism, numerous studies have now demonstrated that the recruitment of SWI/SNF complex to a target gene reorganizes the associated chromatin, thereby influencing gene activity.[29-33]

Distinct chromatin domains mark the T-cell epigenome

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

Our knowledge of the complexity of the chromatin signature has expanded exponentially in recent years and increasing data on transcriptional regulatory factors reveal a more complex picture of the epigenomic landscape. Genome-wide studies in human T cells have also characterized patterns associated with promoters, enhancers and other well-conserved genomic regulatory regions.[34-38] For example, at promoter regions, H3K4me3 exists as a double peak immediately upstream of transcriptional start sites because of nucleosome depletion or Pol II binding.[34, 37, 39-42] In contrast, enhancers are characterized by the three H3K4 methylation states as well as the histone variant, H2A.Z in human T cells.[34, 38, 41]

Bioinformatics analysis on 21 histone modifications in CD4+ T cells was used to classify genomic regions based on their regulatory functions. The study identified 14 distinct clusters of chromatin signatures for promoters.[43] A similar bioinformatics approach separated 51 functionally distinct chromatin states by using 38 histone modifications, Pol II and the insulator binding protein, CTCF (CCCTC-binding Factor). These chromatin states could be further categorized into five broad classes, namely promoter-associated states, transcription-associated states, active intergenic states, large-scale repressed states and repetitive states.[44] In addition, CpG islands have been linked with active marks like histone acetylation and H3K4me3 both in human T cells and embryonic stem cells.[35, 36, 45] Collectively, these distinct histone modifications specific to regional domains contribute to functional differences in gene regulation.

Chromatin signatures define gene activation states in T cells

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

Given the distinct chromatin states that govern specific regions of the genome, it is likely that genes with comparable transcription profiles possess similar epigenetic landscapes. Genome-wide studies in human T cells have extensively characterized a large number of histone modifications using chromatin immunoprecipitation assays (ChIP) combined with massively parallel sequencing (ChIP-Seq) and have been particularly informative in identifying modification patterns associated with active and inactive genes.[34-38, 46, 47] In general, promoters with an active chromatin signature have intermediate to high gene expression levels but genes with low expression levels are associated with promoters with repressed chromatin signatures.[43] A major study focusing on 37 histone acetylation and methylation marks in human CD4+ T cells has shown that genes with different basal expression levels are associated with specific combinations of histone modifications.[38] A common backbone of histone modifications consisting of: histone variant H2A.Z, H2BK5ac, H2BK12ac, H2BK20ac, H2BK120ac, H3K4ac, H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K18ac, H3K27ac, H3K36ac, H4K5ac, H4K8ac, H4K91ac and H3K9ac was identified at a large number of promoters and tended to correlate with higher expression levels. Complimentary human T-cell ChIP-Seq data revealed that a similar chromatin signature marks not only active genes but also inducible genes, and the enrichment of these marks distinguishes them from their non-responsive counterparts with similar basal expression levels, especially in the lower basal expression group.[48] In general, active genes have H3K4me1/2/3, H3K9me1 and H3 acetylation at the promoter region and H2BK5me1, H3K9me2/3, H3K27me1, H3K36me3, H3K27me1 and H4K20me1 distributed throughout transcribed regions.[34, 38, 39, 47, 49] Conversely, inactive genes are enriched with high levels of H3K9me2/3, H3K27me3 and H3K79me3 but low levels of H3K9me1, H3K27me1, H3K36me3, H4K20me1 and H3K4me.[34, 47, 50, 51] Bivalent promoters (having both H3K4me3 and H3K27me3) are also present in T cells though not to the same extent as in embryonic stem cells.[35, 47, 52-54] Poised genes are generally indicated by the active markers like H3K9ac and H3K4me3 but not the repressive methylation marker, H3K27me3 at the promoter in the resting state (summarized in Fig. 2).[35, 38, 47, 48] This chromatin signature does not change upon gene activation, suggesting that these genes may have a chromatin structure that is epigenetically primed for activation.[48, 55, 56] This was unexpected as haematopoietic stem cells show dynamic changes in chromatin structure upon differentiation.[57] The discrepancy in these results could indicate that the chromatin structure of inducible genes is set up before gene transcription and this feature is unique to T cells.[48, 55, 56] Having a similar chromatin signature may help in co-ordinating and co-regulating transcriptional events for efficient and rapid activation of genes.

The active chromatin acetylation signature has recently been proposed to be maintained by constitutive transcription factors such as Sp1 recruiting histone acetylases, such as p300, to promoters of primary response genes. Upon induction, inducible transcription factors such as nuclear factor-κB recruit distinct acetylases that modify a set of lysines, specifically H4K5/8/12, to generate optimal gene activation.[58] Genome-wide mapping of HATs and HDACs in human CD4+ T cells has shown that transcriptionally silent genes with H3K4me3 are primed for future activation by the cycling of transient acetylation by HATs and deacetylation by HDACs.[59] During T-cell activation, elongating phosphorylated Pol II recruits both HATs and HDACs to the transcribed regions of active genes that alter the acetylation levels within the transcribed region to facilitate transcriptional elongation.[59] Indeed, acetylation increases within the transcribed region of the highly inducible IL2 gene upon T-cell activation.[60] It would be of great interest to examine the involvement of HATs and HDACs with other histone modifications in inducible genes specific to T cells.

The active chromatin state detected in the resting state of inducible genes could be a result of past transcriptional activity. Indeed, the active histone modifications of constitutively active genes were shown to be retained through cell division.[61] This could explain how inducible genes acquire active chromatin signature, so enabling a fast and effective transcription of these genes in daughter cells. For example, genes encoding signalling molecules have a repressive chromatin state in naive T cells but a permissive chromatin state in memory T cells, hence these genes in memory T cells are able to respond more quickly to T-cell activation.[47] Furthermore, gene promoters in memory T cells have increased histone acetylation levels when compared with naive T cells. Increased acetylation levels were retained even after numerous cell divisions.[62, 63] There is currently intense interest in determining the mechanisms responsible for the inheritance of permissive chromatin states in memory T cells, as this is an essential step in mediating a faster gene expression response that is required to combat re-infection.

Structural chromatin changes at inducible genes during T-cell activation

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

Although the particular histone patterns that mark inducible genes described above and the changes to histone modifications that occur during gene activation have been characterized relatively recently, changes to chromatin structure have long been thought to accompany gene activation in T cells. The appearance of inducible DNase I hypersensitive (DH) sites have been well documented concomitant with gene activation in T cells.[64, 65] These DH sites coincide with regulatory regions and have long been presumed to represent regions at which chromatin structure is reorganized. Further studies have revealed that the DH sites at the granulocyte–macrophage colony-stimulating factor (GM-CSF) and interleukin-2 (IL-2) promoters represent regions of increased chromatin accessibility,[64-66] and coincide with depletion of the core histones H3 and H4 from the promoter region upon T-cell activation.[60, 67] Genome-wide analysis of histone occupancy and positioning in human CD4+ T cells also documented extensive reorganization at gene promoters and enhancers in response to T-cell activation.[68]

There are several mechanisms that may underlie the reorganization of chromatin associated with T-cell activation that has been described in such studies. First, chromatin-remodelling complexes such as the SWI/SNF complex have been demonstrated to contribute to chromatin changes during T-cell activation. Early studies examining the BRG1 ATPase component demonstrated its increased association with chromatin in response to T-cell activation,[69] and ChIP-Seq analysis has demonstrated increased association of BRG1 with promoters of a set of inducible genes following T-cell activation.[70] Second, chromatin composition can be altered by the exchange of the canonical histones for histone variants,[71] which can affect nucleosome stability and also high-order chromatin structure.[72] Analysis of the inducible CD69 and heparanase genes in T cells demonstrated that both promoters display increased accessibility in response to T-cell activation, but that rather than histone depletion, this reflects exchange of H3 for H3.3,[73] which has been reported to destabilize nucleosomes.[74] A concomitant decline in H2A.Z was also observed at the promoter, particularly of the CD69 gene.[73] Enrichment of H2A.Z near the transcription start site and depletion concomitant with induction have also been reported for other inducible genes,[55, 75] the suggestion being that incorporation of H2A.Z decreases the stability of the nucleosome.

IL2: a paradigm for epigenetic regulation of gene expression

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References

Complex programmes of transcriptional regulation orchestrate the carefully co-ordinated expression of signature immune-responsive genes in response to T-cell activation. The molecular switches that mediate such precise and intricate control have been best characterized for the key T-cell cytokine, IL-2. Given its cell-specific expression, rapid transcription response and importance in T-cell biology, IL2 is considered as a model gene for unravelling epigenetic switches. As summarized in Fig. 3, extensive analysis of the IL2 gene allows us to put forward a model of the complex multilayered hierarchy of gene regulatory processes that are likely to drive immune-responsive genes. In resting T cells, when no IL2 transcription occurs, the IL2 gene exhibits low levels of chromatin accessibility and is decorated by H3/H2A.Z nucleosomes with H2A.Z flanking its transcription start site.[66, 73] Moreover, silent IL2 transcription is reinforced by the repressive activity of the microRNA, mir-200c and transcription factor, Zeb-1.[21] Chromatin remodelling accompanies high levels of IL2 transcription in activated T cells and histone variant exchange takes place in the promoter regions with a loss of histone H3 and a gain of H3.3. In addition, a concomitant decline of H2A.Z levels accompanied gene induction. H3.3 carries active histone post-translational modifications such as K9ac across the IL2 gene.[73] The accessible chromatin state across the IL2 promoter in activated T cells exposes the binding sites for transcription factors such as c-Rel for chromatin remodelling and Pol II to initiate IL2 expression.[48, 66, 76, 77] Transcription of IL2 is dependent on the formation of the active transcription complex with PKCθ, MSK1 and LSD1 as well as the adapter protein 14-3-3ζ with Pol II[21] and increase in the elongation marker H3K36me3.[48] Overall, as illustrated in Fig. 3, IL2 regulation perfectly depicts the multi-layered process from all levels of the chromatin, ranging from chromatin accessibility, histone modifications, microRNAs and transcription factors. This holds particular significance in T-cell biology as the level of IL2 dictates the outcome of the T-cell immune response.

In summary, to understand the multi-layered process of transcriptional regulation, it is necessary to combine research from the systematic approach of bioinformatics and bench top experiments. Given the rapid advancement in technology, we are in a timely position to unravel the contribution of these regulatory mechanisms to T-cell-specific gene expression. Unveiling novel mechanisms will undoubtedly provide new insights into T-cell-mediated diseases.

References

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of epigenetic control and gene expression
  5. Histone modifications form a key layer of epigenetic control for cellular gene expression profiles
  6. Epigenetic enzymes dynamically write or erase epigenetic signatures
  7. Chromatin-remodelling complexes
  8. Distinct chromatin domains mark the T-cell epigenome
  9. Chromatin signatures define gene activation states in T cells
  10. Structural chromatin changes at inducible genes during T-cell activation
  11. IL2: a paradigm for epigenetic regulation of gene expression
  12. Acknowledgements
  13. Disclosure
  14. References