Deletion of germline promoter PD beta 1 from the TCR beta locus causes hypermethylation that impairs D beta 1 recombination by multiple mechanisms

Epigenetic regulation of antigen receptor rearrangement

In the mammalian immune system, V(D)J rearrangement of immunoglobulin (Ig) and T-cell receptor (TCR) genes is regulated in a lineage- and stage-specific fashion. Because each of the seven loci capable of rearrangement utilizes the same recombination machinery, it is thought that V(D)J recombination of each antigen receptor locus is regulated through the differential accessibility of each locus to the V(D)J recombination machinery. Accumulating evidence indicates that chromatin remodeling mediated by DNA methylation and demethylation plays important roles in regulating V(D)J recombination and germline transcription through the Ig and TCR loci. DNA demethylation within the antigen receptor loci appears to be regulated by cis-elements also required for coordinated V(D)J recombination and germline transcription. In this paper, we critically examine the relationship between demethylation and V(D)J recombination as well as the mechanism to regulate DNA demethylation within the antigen receptor loci.

Combinatorial control of DNase I-hypersensitive site formation and erasure by immunoglobulin heavy chain enhancer-binding proteins

DNase I-hypersensitive sites in cellular chromatin are usually believed to be nucleosome-free regions generated by transcription factor binding. Using a cell-free system we show that hypersensitivity does not simply correlate with the number of DNA-bound proteins. Specifically, the leucine zipper containing basic helix-loop-helix protein TFE3 was sufficient to induce a DNase I-hypersensitive site at the immunoglobulin heavy chain micro enhancer in vitro. TFE3 enhanced binding of an ETS protein PU.1 to the enhancer. However, PU.1 binding erased the DNase I-hypersensitive site without abolishing TFE3 binding. Furthermore, TFE3 binding enhanced transcription in the presence and absence of a hypersensitive site, whereas endonuclease accessibility correlated strictly with DNase I hypersensitivity. We infer that chromatin constraints for transcription and nuclease sensitivity can differ.

V(D)J Recombination Frequencies Can Be Profoundly Affected by Changes in the Spacer Sequence

Each V, D, and J gene segment is flanked by a recombination signal sequence (RSS), composed of a conserved heptamer and nonamer separated by a 12- or 23-bp spacer. Variations from consensus in the heptamer or nonamer at specific positions can dramatically affect recombination frequency, but until recently, it had been generally held that only the length of the spacer, but not its sequence, affects the efficacy of V(D)J recombination. In this study, we show several examples in which the spacer sequence can significantly affect recombination frequencies. We show that the difference in spacer sequence alone of two V(H)S107 genes affects recombination frequency in recombination substrates to a similar extent as the bias observed in vivo. We show that individual positions in the spacer can affect recombination frequency, and those positions can often be predicted by their frequency in a database of RSS. Importantly, we further show that a spacer sequence that has an infrequently observed nucleotide at each position is essentially unable to support recombination in an extrachromosmal substrate assay, despite being flanked by a consensus heptamer and nonamer. This infrequent spacer sequence RSS shows only a 2-fold reduction of binding of RAG proteins, but the in vitro cleavage of this RSS is approximately 9-fold reduced compared with a good RSS. These data demonstrate that the spacer sequence should be considered to play an important role in the recombination efficacy of an RSS, and that the effect of the spacer occurs primarily subsequent to RAG binding.

The T cell receptor beta enhancer promotes access and pairing of Dbeta and Jbeta gene segments during V(D)J recombination

The precise function of cis elements in regulating V(D)J recombination is still controversial. Here, we determined the effect of inactivation of the TCRbeta enhancer (Ebeta) on cleavage and rearrangement of Dbeta1, Dbeta2, Jbeta1, and Jbeta2 gene segments in CD4-CD8- [double-negative (DN)] and CD4+CD8+ [double-positive (DP)] thymocytes. In Ebeta-deficient mice, (i) Dbeta1 rearrangements were more severely impaired than Dbeta2 rearrangements; (ii) most of the Dbeta and Jbeta cleavages and rearrangements occurred in DP, rather than in DN, thymocytes; and (iii) most of the 3' Dbeta1 cleavages were coupled to 5' Dbeta2 cleavages instead of to Jbeta cleavages, resulting in nonstandard Dbeta1-Dbeta2-Jbeta2 joints. These findings suggest that the Ebeta regulates TCRbeta rearrangement by promoting accessibility of Dbeta and Jbeta gene segments in DN thymocytes and proper pairing between Dbeta1 and Jbeta gene segments for cleavage and joining in DP thymocytes.

Effect of CpG methylation on RAG1/RAG2 reactivity: implications of direct and indirect mechanisms for controlling V(D)J cleavage

It has been suggested that DNA methylation/demethylation is involved in regulating V(D)J rearrangement. Although methylated DNA is thought to induce an inaccessible chromatin structure, it is unclear whether DNA methylation can directly control V(D)J recombination independently of chromatin structure. In this study, we tested whether DNA methylation directly affects the reactivity of the RAG1/RAG2 complex. Specific methylation within the heptamer of the recombination signal sequences (RSS) markedly reduced V(D)J cleavage without inhibiting RAG1/RAG2-DNA complex formation. By contrast, methylation at other positions around the RSS did not affect the reactivity of the RAG proteins. The presence of a methyl-CpG binding-domain protein inhibited the binding of the RAG1/RAG2 complex to all the methylated CpG sites that were tested. Our findings suggest that DNA methylation around the RSS may have a previously unexpected function in regulating V(D)J recombination by directly inhibiting V(D)J cleavage, in addition to its general function of inducing an inaccessible chromatin configuration.

Gene segment selection in V(D)J recombination: accessibility and beyond

V(D)J recombination assembles genes encoding antigen receptors according to defined developmental programs in immature B and T lymphocytes. The 'accessibility hypothesis' was initially invoked to explain how a single recombinase complex could control the locus and allele specificity of V(D)J recombination. It has been since shown that recombination signal sequences themselves influence recombination efficiency and specificity in ways that had not been previously appreciated. Recent developments have increased our understanding of how the chromatin barrier to V(D)J recombination is regulated, and how chromatin control and the properties of the underlying recombination signal sequences may cooperate to create diverse, lineage-restricted and allelically excluded repertoires of antigen receptors.

A multistep mechanism for the activation of rearrangement in the immune system

Rearrangement of immune receptor loci is a developmentally controlled process that takes place exclusively in lymphoid cells. We have used a stable transfection system in pre-B cells to show that DNA methylation brings about histone underacetylation, histone H3(K9) methylation, DNaseI resistance, and strong inhibition of both transcription and recombination. Strikingly, this repression is maintained in dividing cells even after removal of the original methyl groups responsible for its establishment, but in this state, rearrangement can now be induced by reacetylation of local histones using the drug Trichostatin A. This same combination of demethylation and histone acetylation is also required to activate germline transcription and recombination from the endogenous kappa locus in vivo. These results indicate that the regulation of rearrangement is carried out by a multilayered synergistic process.

Regulation of T-cell receptor D beta 1 promoter by KLF5 through reiterated GC-rich motifs

Rearrangement of T-cell receptor (TCR) and immunoglobulin genes by a common V(D)J recombination machinery is regulated by developmentally specific chromatin changes at the target locus, a process associated with transcription. At the TCRbeta locus, the Ebeta enhancer and the Dbeta1 promoter regulate germline transcription originating near the TCR Dbeta1 gene segment. The Dbeta1 promoter contains 3 GC-rich motifs that bind a common set of nuclear proteins from pro-T-cell lines. Mutations that diminish the binding of nuclear proteins also diminish the activity of the Dbeta1 promoter in transcriptional reporter assays. Using a yeast one-hybrid approach, 3 Krüppel-like factors-KLF3, KLF5, and KLF6-and a novel zinc finger protein were identified in a thymus library, all of which bound the GC-rich motif in a sequence-specific manner. Of these genes, KLF5 mRNA was expressed in a restricted manner in lymphoid cells and tissues, with highest expression in pro-T-cell lines and Rag-deficient thymocytes. Antibody supershift studies and chromatin immunoprecipitation assay confirmed that KLF5 bound the Dbeta1 promoter. In reporter gene assays, KLF5 but not KLF6 efficiently transactivated the Dbeta1 promoter, whereas a dominant-negative KLF5 construct inhibited reporter expression. These data suggest that reiterated GC motifs contribute to germline TCRbeta transcription through binding of KLF5 and other Krüppel family members and that restricted expression of KLF5 may contribute to lineage-specific regulation of germline TCRbeta transcription.

AID mediates hypermutation by deaminating single stranded DNA

Activation-induced deaminase (AID) is a protein indispensable for the diversification of immunoglobulin (Ig) genes by somatic hypermutation (SHM), class switch recombination (CSR), and gene conversion. To date, the precise role of AID in these processes has not been determined. Here we demonstrate that purified, tetrameric AID can deaminate cytidine residues in DNA, but not in RNA. Furthermore, we show that AID will bind and deaminate only single-stranded DNA, which implies a direct, functional link between hypermutation and transcription. Finally, AID does not target mutational hotspots, thus mutational targeting to specific residues must be attributed to different factors.

Epigenetic mechanisms that regulate antigen receptor gene expression

Functional immunoglobulin and T-cell receptor genes are generated from germline V, D and J gene segments by a series of site-specific recombination events. This process is regulated by the availability of recombination machinery and by the ordered accessibility of appropriate target gene segments. Recent studies highlight the importance of chromatin remodelling and locus positioning for controlling antigen receptor gene expression and recombination.

Epigenetic control during lymphoid development and immune responses: aberrant regulation, viruses, and cancer

Methylation of cytosines controls a number of biologic processes such as imprinting and X chromosomal inactivation. DNA hypermethylation is closely associated with transcriptional silencing, while DNA hypomethylation is associated with transcriptional activation. Hypoacetylation of histones leads to compact chromatin with reduced accessibility to the transcriptional machinery. Methyl-CpG binding proteins can recruit corepressors and histone deacetylases; thus, the interplay between these epigenetic mechanisms regulates gene activation. Methylation has been implicated as an important mechanism during immune development, controlling VDJ recombination, lineage-specific expression of cell surface antigens, and transcriptional regulation of cytokine genes during immune responses. Aberrations in epigenetic machinery, either by genetic mutations or by somatic changes such as viral infections, are associated with early alterations in chronic diseases such as immunodeficiency and cancer.

Promoter activation by enhancer-dependent and -independent loading of activator and coactivator complexes

Activation of the pDbeta1 promoter at the TCRbeta locus requires a functional distal enhancer, Ebeta. Here, we have analyzed the mechanism of promoter activation in thymocytes from mice containing or lacking Ebeta. We found that pDbeta1 shows a complex profile of transcription factor and chromatin remodeling complex occupancy even at Ebeta(-) alleles. The presence of Ebeta, however, results in a few specific changes in factor occupancy at the promoter. These differences correlate with localized alterations in histone modifications and in the recruitment of the basal transcriptional machinery. In addition, Ebeta is also bound by CBP and Pol II, suggesting a mechanism for delivery of a holoenzyme complex to the pDbeta1 promoter. These results illustrate a specialized, long-range function of an enhancer in the hierarchical events that regulate assembly of a cell type-specific promoter.

Access roads for RAG-ged terrains: control of T cell receptor gene rearrangement at multiple levels

Antigen-specific immune response requires the generation of a diverse antigen (Ag)-receptor repertoire. The primary repertoire is generated through somatic gene rearrangement and molded by subsequent cellular selection. Constraints during gene recombination influence the ultimate shape of the repertoire. One major control mechanism of gene rearrangement, investigated for many years, is exerted through regulated chromosomal accessibility of the recombinase to the antigen receptor loci. More recent studies began to explore the role of interactions between the recombinase and its cognate recognition DNA sequences. The emerging results suggest that formation of the primary repertoire is controlled by two, partially independent factors: chromosomal accessibility and direct recombinase-DNA interactions.

Regulation of V(D)J recombination: a dominant role for promoter positioning in gene segment accessibility

Antigen receptor gene assembly is regulated by transcriptional promoters and enhancers, which control the accessibility of gene segments to a lymphocyte-specific V(D)J recombinase. However, it remained unclear whether accessibility depends on the process of transcription itself or chromatin modifications that accompany transcription. By using T cell receptor beta substrates that integrate stably into nuclear chromatin, we show that promoter location, rather than germ-line transcription or histone acetylation, is a primary determinant of recombination efficiency. These spatial constraints on promoter positioning may reflect an RNA polymerase-independent mechanism to target adjacent gene segments for chromatin remodeling events that facilitate rearrangement.

OcaB is required for normal transcription and V(D)J recombination of a subset of immunoglobulin kappa genes

OcaB, a transcriptional coactivator also known as Bob-1 or OBF-1, was isolated on the basis of its ability to enhance transcription of immunoglobulin (Ig) genes in vitro. Paradoxically, OcaB(-/-) mice showed no apparent deficiency in Ig gene transcription, only cellular immune defects including absence of germinal centers (GC) and decreased numbers of immature B cells; the genes targeted by OcaB were not determined. Here we report that OcaB is essential for V(D)J recombination of a subset of Igkappa genes. We show that OcaB modulates recombination by directly enhancing Igkappa gene transcription in vivo.

DNA methylation changes at human Th2 cytokine genes coincide with DNase I hypersensitive site formation during CD4(+) T cell differentiation

The differentiation of naive CD4(+) T lymphocytes into Th1 and Th2 lineages generates either cellular or humoral immune responses. Th2 cells express the cytokines IL-4, -5, and -13, which are implicated in asthma and atopy. Much has been published about the regulation of murine Th2 cytokine expression, but studies in human primary T cells are less common. We have developed a method for differentiating human CD45RA(+) (naive) T cells into Th1 and Th2 populations that display distinct cytokine expression profiles. We examined both CpG methylation, using bisulfite DNA modification and sequencing, and chromatin structure around the IL-4 and IL-13 genes before and after human T cell differentiation and in normal human skin fibroblasts. In naive cells, the DNA was predominantly methylated. After Th2 differentiation, DNase I hypersensitive sites (DHS) appeared at IL-4 and IL-13 and CpG demethylation occurred only around the Th2-specific DHS. Both DHS and CpG demethylation coincided with consensus binding sites for the Th2-specific transcription factor GATA-3. Although fibroblasts, like naive and Th1 cells, did not express IL-4 or IL-13, DHS and unmethylated CpG sites that were distinct from the Th2-specific sites were observed, suggesting that chromatin structure in this cluster not only varies in T cells according to IL-4/IL-13 expression but is also tissue specific.

The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution

The single crystal structure of the methylated sequence d(CCGGTACm(5)CGG) has been solved as an antiparallel stacked X Holliday junction to 1.5 A resolution. When compared with the parent nonmethylated d(CCGGTACCGG) structure, the duplexes are translated by 3.4 A along the helix axis and rotated by 10.8 degrees relative to each other, rendering the major grooves more accessible overall. A Ca(2+) complex is seen in the minor groove opposite the junction but is related to the B conformation of the stacked arms. At the junction itself, the hydrogen bond from the N4 nitrogen of cytosine C8 to the C7 phosphate at the crossover in the parent structure has been replaced by a water bridge. Thus, this direct interaction is not absolutely required to stabilize the junction at the previously defined ACC trinucleotide core. The more compact methylated junction forces the Na(+) of the protected central cavity of the nonmethylated junction into a solvent cluster that spans the space between the junction crossover and the stacked arms. A series of void volumes within the methylated and the nonmethylated structures suggests that small monovalent cations can fill and vacate this central cavity without the need to unfold the four-stranded Holliday junction completely.

A change in the structure of Vbeta chromatin associated with TCR beta allelic exclusion

To investigate chromatin control of TCR beta rearrangement and allelic exclusion, we analyzed TCR beta chromatin structure in double negative (DN) thymocytes, which are permissive for TCR beta recombination, and in double positive (DP) thymocytes, which are postallelic exclusion and nonpermissive for Vbeta to DbetaJbeta recombination. Histone acetylation mapping and DNase I sensitivity studies indicate Vbeta and DbetaJbeta segments to be hyperacetylated and accessible in DN thymocytes. However, they are separated from each other by hypoacetylated and inaccessible trypsinogen chromatin. The transition from DN to DP is accompanied by selective down-regulation of Vbeta acetylation and accessibility. The level of DP acetylation and accessibility is minimal for five of six Vbeta segments studied but remains substantial for one. Hence, the observed changes in Vbeta chromatin structure appear sufficient to account for allelic exclusion of many Vbeta segments. They may contribute to, but not by themselves fully account for, allelic exclusion of others.

Stepwise activation of the immunoglobulin mu heavy chain gene locus

The immunoglobulin heavy chain (IgH) gene locus spans several megabases. We show that IgH activation during B-cell differentiation, as measured by histone acetylation, occurs in discrete, independently regulated domains. Initially, a 120 kb domain of germline DNA is hyperacetylated, that extends from D(FL16.1), the 5'-most D(H) gene segment, to the intergenic region between Cmu and Cdelta. Germline V(H) genes were not hyperacetylated at this stage, which accounts for D(H) to J(H) recombination occurring first during B-cell development. Subsequent activation of the V(H) locus happens in at least three differentially regulated domains: an interleukin-7-regulated domain consisting of the 5' J558 family, an intermediate domain and the 3' V(H) genes, which are hyperacetylated in response to DJ(H) recombination. These observations lead to mechanisms for two well-documented phenomena in B-cell ontogeny: the sequential rearrangement of D(H) followed by V(H) gene segments, and the preferential recombination of D(H)-proximal V(H) genes in pro-B cells. We suggest that stepwise activation may be a general mechanism by which large segments of the genome are prepared for expression.

A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival

The role of DNA methylation and of the maintenance DNA methyltransferase Dnmt1 in the epigenetic regulation of developmental stage- and cell lineage-specific gene expression in vivo is uncertain. This is addressed here through the generation of mice in which Dnmt1 was inactivated by Cre/loxP-mediated deletion at sequential stages of T cell development. Deletion of Dnmt1 in early double-negative thymocytes led to impaired survival of TCRalphabeta(+) cells and the generation of atypical CD8(+)TCRgammadelta(+) cells. Deletion of Dnmt1 in double-positive thymocytes impaired activation-induced proliferation but differentially enhanced cytokine mRNA expression by naive peripheral T cells. We conclude that Dnmt1 and DNA methylation are required for the proper expression of certain genes that define fate and determine function in T cells.

Distinct control of the frequency and allelic exclusion of the V beta gene rearrangement at the TCR beta locus

Ag receptor gene loci contain many V gene segments, each of which is recombined and expressed at a different frequency and is subject to allelic exclusion. To probe the parameters that mediate the different levels of regulation of V gene rearrangement, a Vbeta gene segment together with 3.6-kb 5' and 0.7-kb 3' flanking sequences was inserted 6.8 kb upstream of the Dbeta1 gene segment in the murine TCRbeta locus. Despite its proximity to the Dbeta gene segments and the Ebeta enhancer, the inserted Vbeta segment underwent VDJ recombination at the same frequency as the natural copy located 470 kb upstream. However, the inserted Vbeta segment was no longer under allelic exclusion control as it recombined at a similar frequency in the presence of a TCRbeta transgene. These results suggest that while the inserted fragment contains the necessary cis-regulatory elements for determining the frequency of Vbeta rearrangement, additional cis-regulatory elements are required for mediating Vbeta allelic exclusion. Interestingly, most of the inserted Vbeta rearrangements were not transcribed and expressed in the presence of a TCRbeta transgene, suggesting that TCRbeta allelic exclusion can also be achieved by blocking the transcription of the rearranged gene segments. These findings provide strong evidence for distinct control of the frequency and allelic exclusion of Vbeta gene rearrangement.

Normal TCRbeta transcription and recombination in the absence of the Jbeta2-Cbeta2 intronic cis element

The developmental regulation of antigen receptor gene transcription and recombination are mediated by cis regulatory elements. At the T cell receptor beta chain locus (TCRbeta), two DNase I hypersensitive sites within the Jbeta2-Cbeta2 intron contained binding sites for NF-kappaB and additional nuclear factors and were postulated to be involved in controlling TCRbeta transcription and V(D)J recombination. To test this possibility, we deleted these elements from the mouse genome by homologous recombination and assayed the effect on transcription of both the germline and rearranged TCRbeta locus, and on TCRbeta rearrangement in T and B lymphocytes. We found that TCRbeta transcription and V(D)J recombination and T cell development were normal in these mutant mice. Therefore, the Jbeta2-Cbeta2 intronic elements are dispensable for TCRbeta assembly and function.