Deletion of the CD4 silencer element supports a stochastic mechanism of thymocyte lineage commitment

The establishment and maintenance of lymphocyte identity through gene silencing

Cell identity is determined by selective gene activation and by the maintenance of other regulated genes in a silent state. Although activation mechanisms have been dissected in considerable depth, great strides towards an understanding of the molecular control of gene silencing have been made only recently. Molecular hallmarks of silent chromatin and proteins involved in its assembly and maintenance have been identified through genetic, cytological and biochemical studies in a variety of organisms. Immunologists are now beginning to use this knowledge to elucidate mechanisms underlying cell fate decisions and key developmental steps. This review surveys the current knowledge of gene silencing, with an emphasis on studies in lymphocytes that are advancing our general understanding of silencing mechanisms during development.

In vitro evidence that cytokine receptor signals are required for differentiation of double positive thymocytes into functionally mature CD8+ T cells

CD4(+)8(+) double positive (DP) thymocytes differentiate into CD4(+) and CD8(+) mature T cells in response to TCR signals. However, TCR signals that are initiated in DP thymocytes are unlikely to persist throughout all subsequent differentiation steps, suggesting that other signals must sustain thymocyte differentiation after TCR signaling has ceased. Using an in vitro experimental system, we now demonstrate that cytokine receptor signals, such as those transduced by IL-7 receptors, are required for differentiation of signaled DP thymocytes into functionally mature CD8(+) T cells as they: (a) up-regulate Bcl-2 expression to maintain thymocyte viability; (b) enhance CD4 gene silencing; (c) promote functional maturation;and (d) up-regulate surface expression of glucose transporter molecules, which improve nutrient uptake and increase metabolic activity. IL-7Rs appear to be unique among cytokine receptors in maintaining the viability of newly generated CD4(-)8(+) thymocytes, whereas several different cytokine receptors can provide the trophic/differentiative signals for subsequent CD8(+) thymocyte differentiation and maturation. Thus, cytokine receptors provide both survival and trophic/differentiative signals with varying degrees of redundancy that are required for differentiation of signaled DP thymocytes into functionally mature CD8(+) T cells.

Chromatin and CD4, CD8A and CD8B gene expression during thymic differentiation

The regulation of gene expression during thymocyte development provides an ideal experimental system to study lineage-commitment processes. In particular, expression of the CD4, CD8A and CD8B genes seems to correlate well with the cell-fate decisions that are taken by thymocytes, and elucidating the molecular mechanisms that underlie the differential expression of these genes could reveal key events in differentiation processes. Here, we review examples of how gene cis elements (such as promoters, enhancers and locus control regions) and trans elements (such as transcription factors, chromatin-remodelling complexes and histone-modification enzymes) come together to orchestrate a finely tuned sequence of events that results in the complex pattern of CD4, CD8A and CD8B gene expression that is observed during thymocyte development.

Controlling CD4 gene expression during T cell lineage commitment

T cell lineage commitment as the double-positive (DP) thymocyte matures into the single-positive (SP) T cell requires the irreversible repression or maintenance of CD4 gene expression. Signals transmitted from the T cell antigen receptor (TCR) during thymic selection are believed to be linked to the transcriptional regulation of the CD4 gene; thus, a study of the factors that control CD4 gene expression may lead to further insight into the molecular mechanisms that drive T cell development. This review discusses the work conducted to date to identify and characterize the transcriptional control elements in the CD4 locus and the factors that mediate their function. From these studies, it is clear that the molecular mechanisms controlling CD4 gene expression are very complex and are controlled by many different signals as the thymocyte develops.

Differential requirements for Runx proteins in CD4 repression and epigenetic silencing during T lymphocyte development

T lymphocytes differentiate in discrete stages within the thymus. Immature thymocytes lacking CD4 and CD8 coreceptors differentiate into double-positive cells (CD4(+)CD8(+)), which are selected to become either CD4(+)CD8(-)helper cells or CD4(-)CD8(+) cytotoxic cells. A stage-specific transcriptional silencer regulates expression of CD4 in both immature and CD4(-)CD8(+) thymocytes. We show here that binding sites for Runt domain transcription factors are essential for CD4 silencer function at both stages, and that different Runx family members are required to fulfill unique functions at each stage. Runx1 is required for active repression in CD4(-)CD8(-) thymocytes whereas Runx3 is required for establishing epigenetic silencing in cytotoxic lineage thymocytes. Runx3-deficient cytotoxic T cells, but not helper cells, have defective responses to antigen, suggesting that Runx proteins have critical functions in lineage specification and homeostasis of CD8-lineage T lymphocytes.

Evidence for distinct CD4 silencer functions at different stages of thymocyte differentiation

An intronic silencer within the CD4 gene is the critical cis regulatory element for T cell subset-specific expression of CD4. We have combined transfection studies with gene targeting in mice to identify several key sequences within the silencer core that are required for gene silencing during thymocyte development. In mice, mutations in individual sites resulted in variegated, but heritable, derepression of CD4 in mature CD8(+) T lymphocytes, whereas compound mutations resulted in full derepression. These results indicate that there is partial redundancy in recruiting a chromatin remodeling machinery that results in epigenetic silencing. Mutations in single sites also resulted in partial derepression of CD4 in immature double-negative thymocytes, but there was no apparent variegation. These findings suggest two distinct modes of CD4 silencer function at different developmental stages: active repression in CD4(-)CD8(-) thymocytes, in which silencing must be reversible, and epigenetic gene silencing upon differentiation to the CD8(+) cytotoxic T cell lineage.

Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes

Thymic development produces two sub-lineages of T cells expressing either CD4 or CD8 co-receptors that assist antibody production and mediate cell killing, respectively. The mechanisms for mutually exclusive co-receptor expression remain poorly defined. We find that mutations in the high mobility group (HMG) domain of BAF57--a DNA-binding subunit of the mammalian SWI/SNF-like chromatin-remodelling BAF complexes--or in the BAF complex ATPase subunit Brg, impair both CD4 silencing and CD8 activation. Brg is haploinsufficient for CD8 activation, but not for CD4 silencing, whereas BAF57 mutations preferentially impair CD4 silencing, pointing to target- and subunit-specific mechanisms of chromatin remodelling. BAF complexes directly bind the CD4 silencer, but the BAF57 HMG domain is dispensable for tethering BAF complexes to the CD4 silencer or other chromatin loci in vivo, or for remodelling reconstituted templates in vitro, suggesting that chromatin remodelling in vivo requires HMG-dependent DNA bending. These results indicate that BAF complexes contribute to lineage bifurcation by reciprocally regulating lineage-specific genes, reminiscent of the role of the yeast SWI/SNF complex in mediating mating-type switching.

T cell development: bottoms-up

An important but laborious approach to understanding the concepts underlying T cell lineage commitment is to characterize the cis-acting control elements governing the expression of CD4 and CD8. Previous studies on the CD4 gene have shown that lineage commitment information is directed by the intronic silencer; however, a similarly simple mechanism for controlling CD8 gene expression has not been uncovered. In this issue of Immunity, two groups have investigated the role of putative enhancers in the CD8 locus. The deletion of three different elements in the intergeneic region between CD8 beta and CD8 alpha provides evidence for control at the level of chromatin accessibility.

T-cell development and the CD4-CD8 lineage decision

Cell-fate decisions are controlled typically by conserved receptors that interact with co-evolved ligands. Therefore, the lineage-specific differentiation of immature CD4+ CD8+ T cells into CD4+ or CD8+ mature T cells is unusual in that it is regulated by clonally expressed, somatically generated T-cell receptors (TCRs) of unpredictable fine specificity. Yet, each mature T cell generally retains expression of the co-receptor molecule (CD4 or CD8) that has an MHC-binding property that matches that of its TCR. Two models were proposed initially to explain this remarkable outcome--'instruction' of lineage choice by initial signalling events or 'selection' after a stochastic fate decision that limits further development to cells with coordinated TCR and co-receptor specificities. Aspects of both models now appear to be correct; mistake-prone instruction of lineage choice precedes a subsequent selection step that filters out most incorrect decisions.

Variegated expression of CD8 alpha resulting from in situ deletion of regulatory sequences

The developmental and subset-specific expression of the CD8 genes is under the control of a complex array of regulatory elements distributed along the locus and characterized by DNaseI hypersensitivity. Here we describe the phenotype of mice in which hypersensitive sites 1 and 2 (HSS1 and 2) of DNaseI hypersensitive Cluster II (CII), which are located upstream of the CD8 alpha gene, were deleted by targeted homologous recombination of the endogenous locus. Knockout mice exhibit a variegated expression of the CD8 alpha gene, particularly among the immature CD4(+)8(+) TCR(lo) thymocyte population. We propose that HSS Cluster II regulatory elements are essential in ensuring initiation of chromatin remodeling and establishment of an open configuration in all developing thymocytes that undergo the double-negative to double-positive transition. Furthermore, these sequences contribute to the levels of expression of the CD8 alpha gene.

Combined deletion of CD8 locus cis-regulatory elements affects initiation but not maintenance of CD8 expression

Developmental stage-, subset-, and lineage-specific CD8 enhancers have been identified recently by transgenic reporter analyses. Enhancer E8(II) (CIV-4,5) is active in both immature double-positive thymocytes (DP) and mature CD8 single-positive (SP) thymocytes and T cells, whereas E8(I) (CIII-1,2) directs expression only in mature cells. In mice lacking either E8(I) (CIII-1,2) or E8(II) (CIV-4,5), there was no effect on CD8 expression in DP thymocytes. However, deletion of both enhancers resulted in variegated expression of CD8, with appearance of CD4(+)CD8(-) SP thymocytes expressing surface markers characteristic of DP thymocytes. Consequently, fewer mature CD8(+) T cells developed from the reduced pool of DP cells. These results suggest that the initiation of CD8 expression is mediated by cis-regulatory elements that are distinct from any that may be involved in maintenance of expression.

On the brink of becoming a T cell

Recent studies provide fresh insight into the mechanisms by which precursor cells are committed to and develop within the T-lymphocyte lineage. Precursor/product studies have identified developmental stages between that of the pluripotent hematopoietic stem cell and thymocytes committed to the T lineage. Specific ligands and signaling pathways interacting with the Notch-1 receptor and its ability to influence commitment within the lymphoid lineage have been described. Although the structural features or putative ligands endowing the pre-TCR with constitutive signaling capacity remain elusive, numerous distal mediators of pre-TCR signaling have been identified. It remains for the future to determine what roles they may have in survival, proliferation, lineage commitment and allelic exclusion of TCR genes. Receptor editing and lineage commitment of alphabeta T cells still represent controversial topics that need further study.

New perspectives on a developmental dilemma: the kinetic signaling model and the importance of signal duration for the CD4/CD8 lineage decision

Double-positive thymocytes are short-lived bipotential cells whose developmental fate is determined by the specificity of their TCRs. A relatively small number of double-positive thymocytes undergo positive selection in the thymus and these are signaled to differentiate either into CD4(+) or CD8(+) mature T cells. The mechanism by which double-positive thymocytes determine their appropriate CD4/CD8 fate has been the subject of intense theoretical debate and rigorous experimental analysis. In the last year, 'signal duration' has been offered as a replacement for 'signal strength' as a major determinant of the CD4/CD8 decision, a deceptively minor refinement that requires a major change in our understanding of how signaled double-positive thymocytes differentiate into mature T cells. Indeed, the kinetic signaling model provides a radically new perspective on the mechanism by which the CD4/CD8 lineage decision is made.