A stepwise epigenetic process controls immunoglobulin allelic exclusion

Changes in immunoglobulin–nucleoprotein complex structure mapped by chromatin immunoprecipitation

Transcription factor-mediated immunoglobulin (Ig) enhancer activation has been analyzed extensively outside the physiological constraints of chromatin. Towards understanding the role sequence-specific DNA binding proteins identified by these methods play in activating Ig genes during B cell development, we have investigated in vivo interaction between the Ig enhancer activator PU.1 and two target elements, the Igmu and kappa3' enhancers, by chromatin immunoprecipitation (ChIP). By using two antibodies recognizing different PU.1 epitopes in murine B cells, these analyses demonstrate that ChIP results may depend on the availability of the epitope(s) targeted by the immunoprecipitating antibody. Specifically, PU.1 epitope availability at the mu and kappa3' enhancers does not accurately quantitate total PU.1 association. This result suggests the nucleoprotein complexes formed at these various active enhancers is cell type-specific. Interestingly, RAG1-/- but not RAG2-/- pro-B cells lack PU.1/kappa3' association, probably due to limited accessibility of the kappa locus in the former. The more robust association of PU.1 with the kappa3' versus mu enhancer in all but RAG1-/- B lineage cells is not explained by differences in PCR primer efficiency, but likely reflects the different structures formed by the complexes at mu versus kappa3' enhancers. Finally, PU.1 is not associated with an inaccessible mu or kappa3' enhancer chromatin structure in macrophages, again emphasizing the importance cellular protein context plays in PU.1/Ig enhancer association. The demonstration that changes in epitope availability, hence nucleoprotein structure, can be monitored by ChIP suggests using this technique to monitor biologically important changes in nucleoprotein complex structure/composition in situ.

Differential regulation of chromatin structure of the murine 3′ IgH enhancer and IgG2b germline promoter in response to lipopolysaccharide and CD40 signaling

Class switch recombination (CSR) of murine immunoglobulin heavy chain (IgH) is controlled by germline transcription-coupled modification of the accessibility of the highly repetitive switch regions (S) located upstream of the constant region genes. Activation of the 3' IgH enhancer (3'E) is believed to regulate CSR during B cell terminal differentiation, although the detailed molecular mechanism remains unclear. Here, we show that BAF57 and BRG1, two essential subunits of murine SWI/SNF complex, differentially associate with the DNase I hypersensitive region HS1/2 of 3'E and the IgG2b germline promoter in response to LPS activation or CD40 engagement. Both LPS and CD40 signaling cause SWI/SNF complex to dissociate from HS1/2 and associate with their responsive IgG2b germline promoter, suggesting the potential fluidity of chromatin structure and specific regulatory mode for the ATP-dependent chromatin remodeler during CSR. More interesting, increase in histone acetylation is either inverse or parallel with the action of SWI/SNF complex at HS1/2 enhancer or IgG2b germline promoter, respectively. Chromatin immunoprecipitation experiments show that alteration of histone H3 and H4 acetylation has overall similarities in response to LPS and CD40 signaling, with H3 hyperacetylated and H4 hypoacetylated at the HS1/2 enhancer and reversed modification patterns at the IgG2b germline promoter. Finally, the specificity of LPS and CD40 signaling in control of CSR could be partially coded by the specific acetylation marking of H3 and H4. Our results further strengthen the notion that chromatin remodeling plays a critical role in CSR.

Epigenetics and human disease: translating basic biology into clinical applications

Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Research has shown that epigenetic mechanisms provide an "extra" layer of transcriptional control that regulates how genes are expressed. These mechanisms are critical components in the normal development and growth of cells. Epigenetic abnormalities have been found to be causative factors in cancer, genetic disorders and pediatric syndromes as well as contributing factors in autoimmune diseases and aging. In this review, we examine the basic principles of epigenetic mechanisms and their contribution to human health as well as the clinical consequences of epigenetic errors. In addition, we address the use of epigenetic pathways in new approaches to diagnosis and targeted treatments across the clinical spectrum.

Accessibility control of V(D)J recombination

Mammals contend with a universe of evolving pathogens by generating an enormous diversity of antigen receptors during lymphocyte development. Precursor B and T cells assemble functional immunoglobulin (Ig) and T cell receptor (TCR) genes via recombination of numerous variable (V), diversity (D), and joining (J) gene segments. Although this combinatorial process generates significant diversity, genetic reorganization is inherently dangerous. Thus, V(D)J recombination must be tightly regulated to ensure proper lymphocyte development and avoid chromosomal translocations that cause lymphoid tumors. Each genomic rearrangement is mediated by a common V(D)J recombinase that recognizes sequences flanking all antigen receptor gene segments. The specificity of V(D)J recombination is due, in large part, to changes in the accessibility of chromatin at target gene segments, which either permits or restricts access to recombinase. The chromatin configuration of antigen receptor loci is governed by the concerted action of enhancers and promoters, which function as accessibility control elements (ACEs). In general, ACEs act as conduits for transcription factors, which in turn recruit enzymes that covalently modify or remodel nucleosomes. These ACE-mediated alterations are critical for activation of gene segment transcription and for opening chromatin associated with recombinase target sequences. In this chapter, we describe advances in understanding the mechanisms that control V(D)J recombination at the level of chromatin accessibility. The discussion will focus on cis-acting regulation by ACEs, the nuclear factors that control ACE function, and the epigenetic modifications that establish recombinase accessibility.

Receptor editing can lead to allelic inclusion and development of B cells that retain antibodies reacting with high avidity autoantigens

Receptor editing is a major B cell tolerance mechanism that operates by secondary Ig gene rearrangements to change the specificity of autoreactive developing B cells. In the 3-83Igi mouse model, receptor editing operates in every autoreactive anti-H-2K(b) B cell, providing a novel receptor without additional cell loss. Despite the efficiency of receptor editing in generating nonautoreactive Ag receptors, we show in this study that this process does not inactivate the autoantibody-encoding gene(s) in every autoreactive B cell. In fact, receptor editing can generate allelically and isotypically included B cells that simultaneously express the original autoreactive and a novel nonautoreactive Ag receptors. Such dual Ab-expressing B cells differentiate into transitional and mature B cells retaining the expression of the autoantibody despite the high avidity interaction between the autoantibody and the self-Ag in this system. Moreover, we find that these high avidity autoreactive B cells retain the autoreactive Ag receptor within the cell as a consequence of autoantigen engagement and through a Src family kinase-dependent process. Finally, anti-H-2K(b) IgM autoantibodies are found in the sera of older 3-83Igi mice, indicating that dual Ab-expressing autoreactive B cells are potentially functional and capable of differentiating into IgM autoantibody-secreting plasma cells under certain circumstances. These results demonstrate that autoreactive B cells reacting with ubiquitous membrane bound autoantigens can bypass mechanisms of central tolerance by coexpressing nonautoreactive Abs. These dual Ab-expressing autoreactive B cells conceal their autoantibodies within the cell manifesting a superficially tolerant phenotype that can be partially overcome to secrete IgM autoantibodies.

Helix-loop-helix proteins and lymphocyte development

Helix-loop-helix (HLH) proteins are transcriptional regulators that control a wide variety of developmental pathways in both invertebrate and vertebrate organisms. Results obtained in the past decade have shown that HLH proteins also contribute to the development of lymphoid lineages. A subset of HLH proteins, the 'E proteins', seems to be particularly important for proper lymphoid development. Members of the E protein family include E12, E47, E2-2 and HEB. The E proteins contribute to B lineage- and T lineage-specific gene expression programs, regulate lymphocyte survival and cellular proliferation, activate the rearrangement of antigen receptor genes and control progression through critical developmental checkpoints. This review discusses HLH proteins in lymphocyte development and homeostasis.

Natural antisense transcripts: sound or silence?

Antisense RNA was a rather uncommon term in a physiology environment until short interfering RNAs emerged as the tool of choice to knock down the expression of specific genes. As a consequence, the concept of RNA having regulatory potential became widely accepted. Yet, there is more to come. Computational studies suggest that between 15 and 25% of mammalian genes overlap, giving rise to pairs of sense and antisense RNAs. The resulting transcripts potentially interfere with each other’s processing, thus representing examples of RNA-mediated gene regulation by endogenous, naturally occurring antisense transcripts. Concerns that the large-scale antisense transcription may represent transcriptional noise rather than a gene regulatory mechanism are strongly opposed by recent reports. A relatively small, well-defined group of antisense or noncoding transcripts is linked to monoallelic gene expression as observed in genomic imprinting, X chromosome inactivation, and clonal expression of B and T leukocytes. For the remaining, much larger group of bidirectionally transcribed genes, however, the physiological consequences of antisense transcription as well as the cellular mechanism(s) involved remain largely speculative.

The positional effect of Eβ on Vβ genes of TCRβ chain in the ordered rearrangement and allelic exclusion

In the TCRbeta gene locus, the Vbeta, Dbeta and Jbeta gene segments are assembled in a tightly ordered manner. To investigate the positional effects of TCRbeta enhancer (Ebeta) on the recombination processes of the Vbeta genes, we utilized beta(LD) mice lacking 70% of the TCRbeta locus, leaving four Vbeta genes at the 5' side and, consequently, the Vbeta10 gene moves into the Ebeta regulatory region. In this mutant mouse, the Vbeta10 gene showed direct Vbeta-to-Dbeta and Vbeta-to-Jbeta recombination, although the Dbeta-to-Jbeta joining was still predominant. Interestingly, these two aberrant recombination processes were barely suppressed when beta(LD) mice were crossed with TCRbeta transgenic mice, whereas V(D)J recombination of the Vbeta10 gene was sufficiently suppressed. These results suggest that the positional effects of Ebeta on the Vbeta genes may enable the recombination potential to increase prior to Dbeta-to-Jbeta joining and that such aberrant recombination may be free from allelic suppression.

Silence of the genes--mechanisms of long-term repression

A large fraction of genes in the mammalian genome is repressed in every cell throughout development. Here, we propose that this long-term silencing is carried out by distinct molecular mechanisms that operate in a global manner and, once established, can be maintained autonomously through DNA replication. Both individually and in combination these mechanisms bring about repression, mainly by lowering gene accessibility through closed chromatin structures.

Transcriptional networks in developing and mature B cells

The development of B cells from haematopoietic stem cells proceeds along a highly ordered, yet flexible, pathway. At multiple steps along this pathway, cells are instructed by transcription factors on how to further differentiate, and several check-points have been identified. These check-points are initial commitment to lymphocytic progenitors, specification of pre-B cells, entry to the peripheral B-cell pool, maturation of B cells and differentiation into plasma cells. At each of these regulatory nodes, there are transcriptional networks that control the outcome, and much progress has recently been made in dissecting these networks. This article reviews our current understanding of this exciting field.

Epigenetic control in the immune response

Helper T cells engaged in an immune response confront a prevalent challenge for developmentally regulated gene expression: How does a cell give rise to daughter cells with different fates? Additionally, lymphocyte function is intimately associated with the processes of cell division and migration. This imposes an additional burden for daughter cells, to remember inductive events from which they are temporally and spatially removed. An emerging view is that helper T cells use epigenetic mechanisms tied to the structure of chromatin and its covalent modifications to achieve at least two important features of their programmed gene expression. Epigenetic effects organize the ability of signal transduction pathways to generate a restricted set of progeny from a multi-potent progenitor. In addition, epigenetic effects seem to allow dividing cells to memorize, or imprint, signaling events that occurred earlier in their development. Beyond helper T cells, the use of epigenetic effects is emerging as a common strategy in development and function of the mammalian immune system, suggesting that epigenetic effects may play a more prominent role in metazoan cell differentiation than previously appreciated. Lymphocytes are, thus, becoming a tractable system for genetic and biochemical dissection of the ways in which the genome is embedded with regulatory information to achieve developmental complexity.

Visualization of looping involving the immunoglobulin heavy-chain locus in developing B cells

The immunoglobulin heavy-chain (IgH) locus undergoes large-scale contraction in B cells poised to undergo IgH V(D)J recombination. We considered the possibility that looping of distinct IgH V regions plays a role in promoting long-range interactions. Here, we simultaneously visualize three subregions of the IgH locus, using three-dimensional fluorescence in situ hybridization. Looping within the IgH locus was observed in both B- and T-lineage cells. However, monoallelic looping of IgH V regions into close proximity of the IgH DJ cluster was detected in developing B cells with significantly higher frequency when compared with hematopoietic progenitor or CD8+ T-lineage cells. Looping of a subset of IgH V regions, albeit at lower frequency, was also observed in RAG-deficient pro-B cells. Based on these observations, we propose that Ig loci are repositioned by a looping mechanism prior to IgH V(D)J rearrangement to facilitate the joining of Ig variable, diversity, and joining segments.