A novel enhancer in the immunoglobulin lambda locus is duplicated and functionally independent of NF kappa B

RIF1 regulates early replication timing in murine B cells

The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating murine B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin and promotes early replication, but plays a minor role in regulating replication origin activity, gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal additional layers of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.

Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS

A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific chromatin assembly that supersedes these constraints is required to configure the genome to guide gene expression changes that drive faithful lineage progression. Loss-of-function approaches in B cell precursors show that IKAROS assembles interactions across megabase distances in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries to assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains. Gain of function in epithelial cells confirms IKAROS' ability to reconfigure chromatin architecture at multiple scales. Although the compaction of the Igκ locus required for genome editing represents a function of IKAROS unique to lymphocytes, the more general function to preconfigure the genome to support lineage-specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.

Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation

Transcription enhancers are essential activators of V(D)J recombination that orchestrate non-coding transcription through complementary, unrearranged gene segments. How transcription is coordinately increased at spatially distinct promoters, however, remains poorly understood. Using the murine immunoglobulin lambda (Igλ) locus as model, we find that three enhancer-like elements in the 3' Igλ domain, Eλ3-1, HSCλ1 and HSE-1, show strikingly similar transcription factor binding dynamics and close spatial proximity, suggesting that they form an active enhancer hub. Temporal analyses show coordinate recruitment of complementary V and J gene segments to this hub, with comparable transcription factor binding dynamics to that at enhancers. We find further that E2A, p300, Mediator and Integrator bind to enhancers as early events, whereas YY1 recruitment and eRNA synthesis occur later, corresponding to transcription activation. Remarkably, the interplay between sense and antisense enhancer RNA is central to both active enhancer hub formation and coordinate Igλ transcription: Antisense Eλ3-1 eRNA represses Igλ activation whereas temporal analyses demonstrate that accumulating levels of sense eRNA boost YY1 recruitment to stabilise enhancer hub/promoter interactions and lead to coordinate transcription activation. These studies therefore demonstrate for the first time a critical role for threshold levels of sense versus antisense eRNA in locus activation.

DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations

Chromosomal translocations result from the joining of DNA double-strand breaks (DSBs) and frequently cause cancer. However, the steps linking DSB formation to DSB ligation remain undeciphered. We report that DNA replication timing (RT) directly regulates lymphomagenic Myc translocations during antibody maturation in B cells downstream of DSBs and independently of DSB frequency. Depletion of minichromosome maintenance complexes alters replication origin activity, decreases translocations, and deregulates global RT. Ablating a single origin at Myc causes an early-to-late RT switch, loss of translocations, and reduced proximity with the immunoglobulin heavy chain ( Igh ) gene, its major translocation partner. These phenotypes were reversed by restoring early RT. Disruption of early RT also reduced tumorigenic translocations in human leukemic cells. Thus, RT constitutes a general mechanism in translocation biogenesis linking DSB formation to DSB ligation.

Contribution of Immunoglobulin Enhancers to B Cell Nuclear Organization

B cells undergo genetic rearrangements at immunoglobulin gene (Ig) loci during B cell maturation. First V(D)J recombination occurs during early B cell stages followed by class switch recombination (CSR) and somatic hypermutation (SHM) which occur during mature B cell stages. Given that RAG1/2 induces DNA double strand breaks (DSBs) during V(D)J recombination and AID (Activation-Induced Deaminase) leads to DNA modifications (mutations during SHM or DNA DSBs during CSR), it is mandatory that IgH rearrangements be tightly regulated to avoid any mutations or translocations within oncogenes. Ig loci contain various cis-regulatory elements that are involved in germline transcription, chromatin modifications or RAG/AID recruitment. Ig cis-regulatory elements are increasingly recognized as being involved in nuclear positioning, heterochromatin addressing and chromosome loop regulation. In this review, we examined multiple data showing the critical interest of studying Ig gene regulation at the whole nucleus scale. In this context, we highlighted the essential function of Ig gene regulatory elements that now have to be considered as nuclear organizers in B lymphocytes.

Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer

B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.

Targeting of somatic hypermutation by immunoglobulin enhancer and enhancer-like sequences

Immunoglobulin gene enhancers have a conserved function in targeting somatic hypermutation to immunoglobulin genes, thereby supporting the production of high affinity antibodies.

Somatic hypermutation (SH) generates point mutations within rearranged immunoglobulin (Ig) genes of activated B cells, providing genetic diversity for the affinity maturation of antibodies. SH requires the activation-induced cytidine deaminase (AID) protein and transcription of the mutation target sequence, but how the Ig gene specificity of mutations is achieved has remained elusive. We show here using a sensitive and carefully controlled assay that the Ig enhancers strongly activate SH in neighboring genes even though their stimulation of transcription is negligible. Mutations in certain E-box, NFκB, MEF2, or Ets family binding sites—known to be important for the transcriptional role of Ig enhancers—impair or abolish the activity. Full activation of SH typically requires a combination of multiple Ig enhancer and enhancer-like elements. The mechanism is evolutionarily conserved, as mammalian Ig lambda and Ig heavy chain intron enhancers efficiently stimulate hypermutation in chicken cells. Our results demonstrate a novel regulatory function for Ig enhancers, indicating that they either recruit AID or alter the accessibility of the nearby transcription units.

During the B cell immune response, immunoglobulin (Ig) genes are subject to a unique mutation process known as somatic hypermutation that allows the immune system to generate high-affinity antibodies. Somatic hypermutation preferentially affects Ig genes, relative to other genes, and this is important in preventing catastrophic levels of general genomic mutations that could lead to B cell cancers. We hypothesized that this preferential targeting of somatic hypermutation is assisted by specific DNA sequences in or near Ig genes that focus the action of the mutation machinery on those genes. In this study, we show that Ig genes across species—from human, mouse, and chicken—do indeed contain such mutation targeting sequences and that they coincide with transcriptional regulatory regions known as enhancers. We show that combinations of Ig enhancers cooperate to achieve strong mutation targeting and that this action depends on well-known transcription factor binding sites in these enhancer elements. Our findings establish an evolutionarily conserved function for enhancers in somatic hypermutation targeting, which operates by a mechanism distinct from the conventional enhancer function of increasing levels of transcription. We propose that combinations of Ig enhancers target somatic mutation to Ig genes by recruiting the mutation machinery and/or by making the Ig genes better substrates for mutation.

Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci

The assembly and expression of mouse Ag receptor genes are controlled by a collection of cis-acting regulatory elements, including transcriptional promoters and enhancers. Although many powerful enhancers have been identified for Ig (Ig) and TCR (Tcr) loci, it remained unclear whether additional regulatory elements remain undiscovered. In this study, we use chromatin profiling of pro-B cells to define 38 epigenetic states in mouse Ag receptor loci, each of which reflects a distinct regulatory potential. One of these chromatin states corresponds to known transcriptional enhancers and identifies a new set of candidate elements in all three Ig loci. Four of the candidates were subjected to functional assays, and all four exhibit enhancer activity in B but not in T lineage cells. The new regulatory elements identified by focused chromatin profiling most likely have important functions in the creation, refinement, and expression of Ig repertoires.

Differential expression of the adaptor protein HSH2 controls the quantitative and qualitative nature of the humoral response

Endogenous expression of the adaptor protein hematopoietic Src homology 2-containing adaptor protein (HSH2) is regulated in a dynamic manner during B cell maturation and differentiation. Developing B cells lack detectable HSH2, whereas transitional 1 and 2 B cells in the periphery exhibit increasing levels of expression. Mature follicular B cells exhibit decreased expression of HSH2 compared with transitional 2 B cells, and expression is further downregulated in germinal center B cells. In contrast, marginal zone B cells and B1a/b B cells exhibit high-level HSH2 expression. Regulation of HSH2 expression plays a critical role in determining the outcome of the humoral immune response as demonstrated using HSH2 transgenic (Tg) mice. Constitutive expression of HSH2 in the B lineage at levels comparable to B1a/b B cells results in decreased serum Ig titers for all subclasses with the exception of IgA. HSH2 Tg mice immunized with T-dependent or T-independent Ags exhibit a moderate decrease in the production of Ag-specific IgM, whereas class-switched isotypes are decreased by ∼80-90% compared with control mice. Analysis of HSH2 Tg B cell activation in vitro demonstrated that HSH2 selectively regulates the B cell response to TNF family receptors (i.e., CD40 and BAFF-R), but not BCR- or TLR-dependent signals. These data demonstrate that changes in HSH2 expression have profound effects on the humoral immune response.

NF-kappaB family of transcription factor facilitates gene conversion in chicken B cells

Activation-induced cytidine deaminase (AID) is critical for immunoglobulin (Ig) diversification in B cells. The majority of evidence supports the model that AID modifies Ig genes at the DNA level by deaminating cytosines into uracils. The mutagenic activity is largely restricted to Ig genes to avoid genomic damage in general, but the underlying mechanism is not understood. We addressed this question in chicken B cell line DT40. We characterized a regulatory region within the Iglambda locus. This regulatory region is important for AID-mediated gene conversion at the Iglambda locus, and is capable of targeting AID activity to ectopic loci. This regulatory region contains binding sites for transcription factors NF-kappaB, Mef2 and octamer binding proteins. Mutation of these binding sites or ablation of NF-kappaB family member, p50 or c-Rel, impairs the AID targeting function of this regulatory region. These results suggest that NF-kappaB family of transcription factors contribute to AID-mediated gene conversion.

The NF-kappaB canonical pathway is involved in the control of the exonucleolytic processing of coding ends during V(D)J recombination

V(D)J recombination is essential to produce an Ig repertoire with a large range of Ag specificities. Although NF-kappaB-binding sites are present in the human and mouse IgH, Igkappa, and Iglambda enhancer modules and RAG expression is controlled by NF-kappaB, it is not known whether NF-kappaB regulates V(D)J recombination mechanisms after RAG-mediated dsDNA breaks. To clarify the involvement of NF-kappaB in human V(D)J recombination, we amplified Ig gene rearrangements from individual peripheral B cells of patients with X-linked anhidrotic ectodermal dysplasia with hyper-IgM syndrome (HED-ID) who have deficient expression of the NF-kappaB essential modulator (NEMO/Ikkgamma). The amplification of nonproductive Ig gene rearrangements from HED-ID B cells reflects the influence of the Ikkgamma-mediated canonical NF-kappaB pathway on specific molecular mechanisms involved in V(D)J recombination. We found that the CDR3(H) from HED-ID B cells were abnormally long, as a result of a marked reduction in the exonuclease activity on the V, D, and J germline coding ends, whereas random N-nucleotide addition and palindromic overhangs (P nucleotides) were comparable to controls. This suggests that an intact canonical NF-kappaB pathway is essential for normal exonucleolytic activity during human V(D)J recombination, whereas terminal deoxynucleotide transferase, Artemis, and DNA-dependent protein kinase catalytic subunit activity are not affected. The generation of memory B cells and somatic hypermutation were markedly deficient confirming a role for NF-kappaB in these events of B cell maturation. However, selection of the primary B cell repertoire appeared to be intact and was partially able to correct the defects generated by abnormal V(D)J recombination.

Chromatin opening is tightly linked to enhancer activation at the kappa light chain locus

Enhancers play an important role in chromatin opening but the temporal relationship between enhancer activation and the generation of an accessible chromatin structure is poorly defined. Recombination enhancers are essential for chromatin opening and subsequent V(D)J recombination at immunoglobulin loci. In mice, the kappa light chain locus displays an open chromatin structure before the lambda locus yet the same proteins, PU.1/PIP, trigger full enhancer activation of both loci. Using primary B cells isolated from distinct developmental stages and an improved method to quantitatively determine hypersensitive site formation, we find the kappa and lambda recombination enhancers become fully hypersensitive soon after transition to large and small pre-B-II cells, respectively. This correlates strictly with the stages at which these loci are activated. Since these cells are short-lived, these data imply that there is a close temporal relationship between full enhancer hypersensitive site formation and locus chromatin opening.

IFN regulatory factor 4 and 8 promote Ig light chain kappa locus activation in pre-B cell development

Previous studies have shown that B cell development is blocked at the pre-B cell stage in IFN regulatory factor (IRF)4 (pip) and IRF8 (IFN consensus sequence binding protein) double mutant mice (IRF4,8(-/-)). In this study, the molecular mechanism by which IRF4,8 regulate pre-B cell development was further investigated. We show that IRF4,8 function in a B cell intrinsic manner to control pre-B cell development. IRF4,8(-/-) mice expressing a Bcl-2 transgene fail to rescue pre-B cell development, suggesting that the defect in B cell development in IRF4,8(-/-) mice is not due to a lack of survival signal. IRF4,8(-/-) pre-B cells display a high proliferation index that may indirectly inhibit the L chain rearrangement. However, forced cell cycle exit induced by IL-7 withdrawal fails to rescue the development of IRF4,8(-/-) pre-B cells, suggesting that cell cycle exit by itself is not sufficient to rescue the development of IRF4,8(-/-) pre-B cells and that IRF4,8 may directly regulate the activation of L chain loci. Using retroviral mediated gene transduction, we show that IRF4 and IRF8 function redundantly to promote pre-B cell maturation and the generation of IgM(+) B cells. Molecular analysis indicates that IRF4, when expressed in IRF4,8(-/-) pre-B cells, induces kappa germline transcription, enhances V(D)J rearrangement activity at the kappa locus, and promotes L chain rearrangement and transcription. Chromatin immunoprecipitation assay further reveals that IRF4 expression leads to histone modifications and enhanced chromatin accessibility at the kappa locus. Thus, IRF4,8 control pre-B cell development, at least in part, by promoting the activation of the kappa locus.

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.

The regulated long-term delivery of therapeutic proteins by using antigen-specific B lymphocytes

Memory lymphocytes are important mediators of the immune response. These cells are long-lived and undergo clonal expansion upon reexposure to specific antigen, differentiating into effector cells that secrete Ig or cytokines while maintaining a residual pool of memory T and B lymphocytes. Here, the ability of antigen-specific lymphocytes to undergo repeated cycles of antigen-driven clonal expansion and contraction is exploited in a therapeutic protocol aimed at regulating protein delivery. The principle of this strategy is to introduce genes encoding proteins of therapeutic interest into a small number of antigen-specific B lymphocytes. Output of therapeutic protein can then be regulated in vivo by manipulating the size of the responder population by antigen challenge. To evaluate whether such an approach is feasible, we developed a mouse model system in which Emu- and Iglambda-based vectors were used to express human erythropoietin (hEPO) gene in B lymphocytes. These mice were then immunized with the model antigen phycoerythrin (PE), and immune splenocytes (or purified PE-specific B lymphocytes) were adoptively transferred to normal or mutant (EPO-deficient) hosts. High levels of hEPO were detected in the serum of adoptively transferred normal mice after PE administration, and this responsiveness was maintained for several months. Similarly, in EPO-deficient anemic recipients, antigen-driven hEPO expression was shown to restore hematocrit levels to normal. These results show that antigen-mediated regulation of memory lymphocytes can be used as a strategy for delivering therapeutic proteins in vivo.

Analysis of Gene Expression and Ig Transcription in PU.1/Spi-B-Deficient Progenitor B Cell Lines

A number of presumptive target genes for the Ets-family transcription factor PU.1 have been identified in the B cell lineage. However, the precise function of PU.1 in B cells has not been studied because targeted null mutation of the PU.1 gene results in a block to lymphomyeloid development at an early developmental stage. In this study, we take advantage of recently developed PU.1(-/-)Spi-B(-/-) IL-7 and stromal cell-dependent progenitor B (pro-B) cell lines to analyze the function of PU.1 and Spi-B in B cell development. We show that contrary to previously published expectations, PU.1 and/or Spi-B are not required for Ig H chain (IgH) gene transcription in pro-B cells. In fact, PU.1(-/-)Spi-B(-/-) pro-B cells have increased levels of IgH transcription compared with wild-type pro-B cells. In addition, high levels of Igkappa transcription are induced after IL-7 withdrawal of wild-type or PU.1(-/-)Spi-B(-/-) pro-B cells. In contrast, we found that Iglambda transcription is reduced in PU.1(-/-)Spi-B(-/-) pro-B cells relative to wild-type pro-B cells after IL-7 withdrawal. These results suggest that Iglambda, but not IgH or Igkappa, transcription, is dependent on PU.1 and/or Spi-B. The PU.1(-/-)Spi-B(-/-) pro-B cells have other phenotypic changes relative to wild-type pro-B cells including increased proliferation, increased CD25 expression, decreased c-Kit expression, and decreased RAG-1 expression. Taken together, our observations suggest that reduction of PU.1 and/or Spi-B activity in pro-B cells promotes their differentiation to a stage intermediate between late pro-B cells and large pre-B cells.

Germline transcripts of immunoglobulin light chain variable regions are structurally diverse and differentially expressed

The murine pre-B cell line R2-bfl, which can be induced to differentiate in vitro, was used to study germline transcription of variable regions of the light chain loci. RNA from these cells was subjected to a 3'-RACE and germline transcripts from 17 individual Vkappa gene segments belonging to 12 Vkappa families were characterized. Germline transcripts of all three Vlambda regions were similarly analyzed. The synchronous differentiation of R2-bfl cells was then used to investigate the order of appearance of germline transcripts of the V and JC clusters of both light chain loci. This was taken as indicator for accessibility of a particular locus to rearrangement. Germline transcripts of the JCkappa cluster and the Vkappa family most proximal to JCkappa was detectable already at day 0, while transcripts of the most distal Vkappa family became apparent after initiation of differentiation at day 1. Transcripts of the JClambda cluster could be found at day 2, whereas transcripts of the Vlambda region were already present at day 1. Thus, the lambda locus becomes accessible to rearrangement later during development than kappa, confirming and extending our previous findings. The V and JC clusters open at the same stage of development although slight asynchronicities were found for the Vlambda and the distal Vkappa gene segments.

IRF-4,8 orchestrate the pre-B-to-B transition in lymphocyte development

B-lymphocyte development involves sequential DNA rearrangements of immunoglobulin (Ig) heavy (mu) and light (kappa, lambda) chain loci and is dependent on transient expression of mu containing pre-antigen receptor complexes (pre-BCR). To date, genetic analysis has not identified transcription factors that coordinate the pre-B-to-B transition. We demonstrate that the related interferon regulatory factors IRF-4 (Pip) and IRF-8 (ICSBP) are required for Ig light but not heavy-chain gene rearrangement. In the absence of these transcription factors, B-cell development is arrested at the cycling pre-B-cell stage and the mutant cells fail to down-regulate the pre-BCR. On the basis of molecular analysis, we propose that IRF-4,8 function as a genetic switch to down-regulate surrogate light-chain gene expression and induce conventional light-chain gene transcription and rearrangement.

Expression of a targeted lambda 1 light chain gene is developmentally regulated and independent of Ig kappa rearrangements

Immunoglobulin light chain (IgL) rearrangements occur more frequently at Ig kappa than at Ig lambda. Previous results suggested that the unrearranged Ig kappa locus negatively regulates Ig lambda transcription and/or rearrangement. Here, we demonstrate that expression of a VJ lambda 1-joint inserted into its physiological position in the Ig lambda locus is independent of Ig kappa rearrangements. Expression of the inserted VJ lambda 1 gene segment is developmentally controlled like that of a VJ kappa-joint inserted into the Ig kappa locus and furthermore coincides developmentally with the occurrence of Ig kappa rearrangements in wild-type mice. We conclude that developmentally controlled transcription of a gene rearrangement in the Ig lambda locus occurs in the presence of an unrearranged Ig kappa locus and is therefore not negatively regulated by the latter. Our data also indicate light chain editing in approximately 30% of lambda 1 expressing B cell progenitors.

Chromatin structural analyses of the mouse Igkappa gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer

To identify new regulatory elements within the mouse Igkappa locus, we have mapped DNase I hypersensitive sites (HSs) in the chromatin of B cell lines arrested at different stages of differentiation. We have focused on two regions encompassing 50 kilobases suspected to contain new regulatory elements based on our previous high level expression results with yeast artificial chromosome-based mouse Igkappa transgenes. This approach has revealed a cluster of HSs within the 18-kilobase intervening sequence, which we cloned and sequenced in its entirety, between the Vkappa gene closest to the Jkappa region. These HSs exhibit pro/pre-B cell-specific transcriptional silencing of a Vkappa gene promoter in transient transfection assays. We also identified a plasmacytoma cell-specific HS in the far downstream region of the locus, which in analogous transient transfection assays proved to be a powerful transcriptional enhancer. Deletional analyses reveal that for each element multiple DNA segments cooperate to achieve either silencing or enhancement. The enhancer sequence is conserved in the human Igkappa gene locus, including NF-kappaB and E-box sites that are important for the activity. In summary, our results pinpoint the locations of presumptive regulatory elements for future knockout studies to define their functional roles in the native locus.

Regulation of human Ig lambda light chain gene expression by NF-kappa B

The human Iglambda enhancer consists of three separated sequence elements that we identified previously by mapping DNase I-hypersensitive regions (HSS) downstream of the C region of the Iglambda L chain genes (HSS-1, HSS-2, and HSS-3). It has been shown by several laboratories that expression of the H chain genes as well as the kappa genes, but not the lambda genes, is dependent on constitutive NF-kappaB proteins present in the nucleus. In this study we show by band-shift experiments, in vivo footprinting, and transient transfection assays that all three hypersensitive sites of the human Iglambda enhancer contain functional NF-kappaB sites that act synergistically on expression. We further show that the chicken lambda enhancer also contains a functional NF-kappaB site but the mouse lambda enhancer contains a mutated, nonfunctional NF-kappaB site that is responsible for its low enhancer activity. It is possible that the inactivating mutation in the mouse Iglambda enhancer was compensated for by an expansion of the Igkappa L chain locus, followed by a contraction of the Iglambda locus in this species.

Regulation of antigen receptor gene assembly in lymphocytes

Somatic alterations affecting the mammalian genome occur exclusively in B and T cells. Developing lymphocytes employ a series of DNA recombination events (V(D)J recombination) to assemble a diverse repertoire of immunoglobulin (Ig) and T cell receptor (TCR) variable regions from a large array of germline gene segments. V(D)J recombination is required not only for receptor diversification but also for lymphocyte development. At a molecular level, these recombination events are directed by conserved DNA sequences flanking all antigen receptor gene segments that function as recognition signals for a single recombinase activity. Despite these shared features, recombination events are controlled at the levels of stage- and tissue-specificity. Our primary research focus is to dissect the mechanisms that regulate assembly of antigen receptor loci by rendering certain gene segments accessible to a common V(D)J recombinase. This article discusses recent discoveries from the author's laboratory that address this long-standing issue. We have found that transcriptional promoters are critical cis-acting regulatory elements for targeting efficient recombination of chromosomal gene segments. We have also demonstrated that activation of NF-kappaB signaling in precursor B cells is required for global regulation of Ig light chain gene assembly. Together, these findings provide key insights into the genetic mechanisms that regulate antigen receptor diversity and the developmental pathways leading to the acquisition of lymphocyte effector function.

Germ-line transcripts of the immunoglobulin lambda J-C clusters in the mouse: characterization of the initiation sites and regulatory elements

Transcription of unrearranged immunoglobulin gene segments strongly correlates with their accessibility to the V(D)J recombination machinery. The regulatory mechanisms governing this germ-line transcription are still poorly defined. In order to identify new regulatory elements, we first carried out a detailed characterization of the transcription initiation sites for the J-C germ-line transcripts, using rapid amplification of 5' cDNA ends, assisted by a template switching mechanism at the 5'-end of the RNA. Transcripts were observed that initiated heterogeneously, starting up to 293 (lambda1), 116 bp (lambda2) and 79 bp (lambda3) upstream from the respective Jlambda gene segment. Additional RT-PCR analysis revealed the existence of germ-line transcripts of lambda and also of kappa that initiate even more upstream of these transcription initiation sites, although their frequencies were low. Promoter activity was detected in vitro 5' of Jlambda2, with the minimal promoter activity mapping to the region between positions -35 and -120. In addition, computer analysis allowed the prediction of a nuclear scaffold/matrix attachment (S/MAR) region between the two J-C gene clusters at each hemi-locus. This region between the lambda1/lambda3 clusters binds to the nuclear matrix in vitro, and J-C lambda1 germ-line transcription initiates a short distance downstream from this S/MAR element.

Transcription factor NF-kappa B regulates Ig lambda light chain gene rearrangement

The tissue- and stage-specific assembly of Ig and TCR genes is mediated by a common V(D)J recombinase complex in precursor lymphocytes. Directed alterations in the accessibility of V, D, and J gene segments target the recombinase to specific Ag receptor loci. Accessibility within a given locus is regulated by the functional interaction of transcription factors with cognate enhancer elements and correlates with the transcriptional activity of unrearranged gene segments. As demonstrated in our prior studies, rearrangement of the Igkappa locus is regulated by the inducible transcription factor NF-kappaB. In contrast to the Igkappa locus, known transcriptional control elements in the Iglambda locus lack functional NF-kappaB binding sites. Consistent with this observation, the expression of assembled Iglambda genes in mature B cells has been shown to be NF-kappaB independent. Nonetheless, we now show that specific repression of NF-kappaB inhibits germline transcription and recombination of Iglambda gene segments in precursor B cells. Molecular analyses indicate that the block in NF-kappaB impairs Iglambda rearrangement at the level of recombinase accessibility. In contrast, the activities of known Iglambda promoter and enhancer elements are unaffected in the same cellular background. These findings expand the range of NF-kappaB action in precursor B cells beyond Igkappa to include the control of recombinational accessibility at both L chain loci. Moreover, our results strongly suggest the existence of a novel Iglambda regulatory element that is either directly or indirectly activated by NF-kappaB during the early stages of B cell development.

Urine free light chains in SLE: clonal markers of B-cell activity and potential link to in vivo secreted Ig

As a marker of in vivo B-cell activity, urine levels of free light chain (FLC) were measured twice weekly by radioimmunoassay (RIA) and correlated with disease activity over periods of 5-10 months in seven patients with systemic lupus erythematosus (SLE). In addition, RIA-measured urine albumin was used to track glomerular injury, and alpha1-microglobulin (alpha1-M) levels, 28- to 32-kDa protein, provided control measurements on excretion of low-molecular-weight proteins. As controls, urine FLC levels were obtained from healthy normals and in subjects with acute pharyngitis, sickle-cell anemia, and acute sepsis or pneumonia. The control results showed that with acute sepsis/pneumonia had marked increases in urine FLC, while pharyngitis and sickle-cell controls had normal FLC levels. In SLE, active patients receiving intravenous cyclophosphamide and high-dose steroids exhibited highly increased urine FLC that fluctuated widely during therapy and fell to normal range levels with disease remission. During active SLE, urine albumin often was increased, while alpha1-M levels remained in normal range. In contrast to the increased FLC of active disease, inactive patients on low-dose maintenance therapy had predominantly normal FLC levels throughout the collection period. These results support our hypothesis that longitudinal levels of urine FLC can be used to track disease-related B-cell activity in SLE. Furthermore, we suggest that the urine FLC of active SLE would share LC idiotype with the clonal associated in vivo secreted Ig, and thus permit the identification of these antibodies that are targeted to the culprit immunogen(s) responsible for the pathogenesis of SLE.

Comparison of CMV, RSV, SV40 viral and Vlambda1 cellular promoters in B and T lymphoid and non-lymphoid cell lines

Determining the activity of viral and cellular regulatory elements in B or T lymphoid cell lines would facilitate appropriate utilization of the regulatory sequences for gene transfer- and expression-dependent applications. We have compared the activity of the CMV, RSV and SV40 viral promoter/enhancers as well as the Vlambda1 cellular promoter, in three B cell lines (REH, SMS-SB, C3P), three T cell lines (CEM, Jurkat, ST-F10), and two non-lymphoid cell lines (K-562, HeLa) using the luciferase reporter gene. In B cell lines, the activity of the CMV promoter/enhancer construct was the highest ranging from 10- to 113-fold greater than that of SV40. In contrast, in T cell lines the RSV promoter/enhancer activity was 11-65-fold higher than that of SV40. The Vlambda1 promoter activity was close to that of SV40 promoter/enhancer in most of the cell lines tested. We conclude that CMV and RSV promoter/enhancers contain stronger regulatory elements than do the SV40 and Vlambda1 for expression of genes in lymphoid cell lines.

B cells are programmed to activate kappa and lambda for rearrangement at consecutive developmental stages

Kappa and lambda, the two types of immunoglobulin light (L) chains present in mammals, contribute differently to the L chain pool of each species. Here we show that the extreme preponderance of kappa in the mouse results from programmed sequential activation of the kappa and lambda loci. Activation--a prerequisite of rearrangement--was monitored by analyzing transcription of unrearranged J-C clusters. Upon in vitro differentiation of a rearrangement-deficient pro/pre-B line, germ-line transcripts of the lambda J-C clusters, that are newly described here, became detectable 2 days later than their counterparts of J-C kappa. Clear differences could also be observed in vivo: germ-line transcripts of kappa were already present in large B220+ CD25+ pre B-II cells whereas germ-line lambda transcripts first became detectable at the consecutive developmental stage of small B220+ CD25+ pre-B-II cells. This activation pattern was found to be identical in mice which can not rearrange kappa due to a targeted deletion or inactivation of kappa. This suggests that pre-B-II cells follow a hit-and-run mechanism of development which includes programmed transitions and differential activation of the L chain loci, i.e. kappa first, then lambda. Thus, privileged activation of kappa might be the decisive factor in setting the 10:1 ratio of kappa to lambda present in the mouse.

A human immunoglobulin lambda locus is similarly well expressed in mice and humans

Transgenic mice carrying a 380-kb region of the human immunoglobulin (Ig) lambda light (L) chain locus in germline configuration were created. The introduced translocus on a yeast artificial chromosome (YAC) accommodates the most proximal Iglambda variable region (V) gene cluster, including 15 Vlambda genes that contribute to >60% of lambda L chains in humans, all Jlambda-Clambda segments, and the 3' enhancer. HuIglambdaYAC mice were bred with animals in which mouse Igkappa production was silenced by gene targeting. In the kappa-/- background, human Iglambda was expressed by approximately 84% of splenic B cells. A striking result was that human Iglambda was also produced at high levels in mice with normal kappa locus. Analysis of bone marrow cells showed that human Iglambda and mouse Igkappa were expressed at similar levels throughout B cell development, suggesting that the Iglambda translocus and the endogenous kappa locus rearrange independently and with equal efficiency at the same developmental stage. This is further supported by the finding that in hybridomas expressing human Iglambda the endogenous L chain loci were in germline configuration. The presence of somatic hypermutation in the human Vlambda genes indicated that the Iglambda-expressing cells function normally. The finding that human lambda genes can be utilized with similar efficiency in mice and humans implies that L chain expression is critically dependent on the configuration of the locus.

Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers

Gene expression in higher eukaryotes appears to be regulated by specific combinations of transcription factors binding to regulatory sequences. The Ets factor PU.1 and the IRF protein Pip (IRF-4) represent a pair of interacting transcription factors implicated in regulating B cell-specific gene expression. Pip is recruited to its binding site on DNA by phosphorylated PU.1. PU.1-Pip interaction is shown to be template directed and involves two distinct protein-protein interaction surfaces: (i) the ets and IRF DNA-binding domains; and (ii) the phosphorylated PEST region of PU.1 and a lysine-requiring putative alpha-helix in Pip. Thus, a coordinated set of protein-protein and protein-DNA contacts are essential for PU.1-Pip ternary complex assembly. To analyze the function of these factors in vivo, we engineered chimeric repressors containing the ets and IRF DNA-binding domains connected by a flexible POU domain linker. When stably expressed, the wild-type fused dimer strongly repressed the expression of a rearranged immunoglobulin lambda gene, thereby establishing the functional importance of PU.1-Pip complexes in B cell gene expression. Comparative analysis of the wild-type dimer with a series of mutant dimers distinguished a gene regulated by PU.1 and Pip from one regulated by PU.1 alone. This strategy should prove generally useful in analyzing the function of interacting transcription factors in vivo, and for identifying novel genes regulated by such complexes.

Molecular Mechanisms and Selection Influence the Generation of the Human VλJλ Repertoire

To define the λ light chain repertoire in humans, a single-cell PCR technique using genomic DNA obtained from individual peripheral B cells was employed. Of the 30 known functional Vλ genes, 23 were detected in either the nonproductive or productive repertoires. Specific Vλ genes, including 2A2, 2B2, 1G, and 4B, were overexpressed in the nonproductive repertoire, whereas some Vλ genes, such as 3R, 2A2, 2B2, 1C, 1G, and 1B, were overexpressed in the productive repertoire. Comparison of the nonproductive and productive repertoires indicated that no Vλ genes were positively selected, whereas a number of Vλ genes, including 4C, 1G, 5B, and 4B, were negatively regulated. All four of the functional Jλ segments were found in both repertoires, with Jλ7 observed most often. Evidence of terminal deoxynucleotidyltransferase activity was noted in nearly 80% of nonproductive VλJλ rearrangements, and exonuclease activity was apparent in the majority. Despite this, the mean CDR3 length was 30 base pairs in both productive and nonproductive repertoires, suggesting that it was tightly regulated at the molecular level. These results have provided new insights into the dimensions of the human Vλ repertoire and the influences that shape it.

The immunoglobulin lambda light chain enhancer consists of three modules which synergize in activation of transcription

V(D)J rearrangement, high level expression and somatic hypermutation of assembled Ig genes is tightly controlled by a number of regulatory sequence elements located in the vicinity of the J-, (D)-, and C-gene segments. During B cell maturation these elements become accessible to binding of trans-acting factors, reflecting the opening of the chromatin structure through an as yet unidentified mechanism. The mapping of regions of an altered chromatin structure (DNase I hypersensitivity) therefore is a powerful approach in identifying regulatory sequence elements. We here show that the human Ig lambda enhancer consists of three modules previously identified by us as DNase I-hypersensitive sites HSS-1, -2, and -3. The three sequence elements synergize in transcriptional activation of a reporter gene and together constitute a powerful tissue-specific enhancer which is a much stronger transcriptional activator than the kappa enhancers alone or in combination. We further show that the accessibility of the kappa and lambda enhancer elements for DNase I in the chromatin of a pre-B cell line (207) correlates with the transcriptional enhancer activities of kappa and lambda enhancer constructs. This finding is in support of an ordered model for Ig light chain activation (kappa before lambda).

The immunoglobulin light chain in poikilothermic vertebrates

The immunoglobulin light chains are classified as kappa or lambda in mammals and birds (homeothermic vertebrates), but the traditional criteria for this classification are not applicable to the light chains found in poikilothermic vertebrates. Still it is possible to find some relationships between Ig light chain sequences in these animals and in those of the homeothermic animals. It is generally accepted that the Ig light chains contribute to the antigen binding capacity of antibodies and the variability is approximately similar in all studied vertebrate species except the elasmobranchs. This might be explained by the organisation of the Ig light chain locus in these animals and the fact that the variable and joining DNA segments are joined in the genome. These conclusions are limited by the small number of species studied in this respect.

Mef2 Proteins, Required for Muscle Differentiation, Bind an Essential Site in the Ig λ Enhancer

The Ig λ light chain gene enhancer has two unique essential motifs, λA and λB. The transcription factors that bind the λB motif have been identified as Pu.1 and Pu.1-interacting partner (Pip). We report here that the λA site includes a binding site for the myocyte-specific enhancer factor 2 (Mef2) family of transcription factors. Mef2 proteins were first described in muscle cells and, in vertebrates, include four known members designated A to D. Using a λA electrophoretic-mobility shift assay (EMSA), in conjunction with a high affinity Mef2 binding site and anti-Mef2 Abs, we show that members of the Mef2 family are present in nuclear extracts of λ-producing B cells and bind the λA site. Functional assays using the chloramphenicol acetyltransferase (CAT) reporter construct containing three copies of the λA motif demonstrate that the λA sequence can function as an enhancer in conjunction with the thymidine kinase (TK) promoter and is regulated by Mef2 proteins. Extrapolating from other systems where transcriptional regulation by Mef2 has been studied, other transcription factors may be involved along with Mef2 in transcriptional regulation at the λA site.

A λ 3′ Enhancer Drives Active and Untemplated Somatic Hypermutation of a λ1 Transgene

Somatic hypermutation is a highly regulated process that targets mutations to the rearranged Ig genes. Little is known about the cis-elements required for somatic hypermutation of the λ light chain gene. We have studied somatic hypermutation of a rearranged λ1 transgene under the control of either a λ2-4 or κ 3′ enhancer. The mutations in the transgenes were analyzed by sequencing DNA amplified from hypermutating Peyer’s patch B cells. The results indicate that the λ 3′ enhancer can drive active hypermutation of a λ1 transgene in Peyer’s patch cells. The λ1 transgene under analysis carried two marked Vλ2 genes immediately upstream that could serve as sequence donors in possible gene conversion events. There was no evidence of sequence transfer to the hypermutated λ1 gene, suggesting that gene conversion is not a major mechanism for somatic hypermutation in mice.

Somatic hypermutation in mouse lambda chains

The frequency and distribution of somatic hypermutation in immunoglobulin genes and the effect of amino acid substitution on the structure/function of antibodies were studied using hybridomas that secrete anti-(4-hydroxy-3-nitrophenyl)acetyl (NP) monoclonal antibodies bearing lambda 1 chains. A high frequency of mutation was observed in V-J exons and J-C introns of rearranged and active lambda 1 chains but not in the 5'-non-coding regions of these chains. Since a similar distribution was observed in inactive lambda 2 chain genes, 5'-non-coding regions containing a promoter were considered to be protected from mutation in view of their apparent importance. Using transgenic mice carrying chloramphenicol acetyl transferase transgenes driven by the VH promoter and heavy-chain intron enhancer, it was also revealed that these cis-acting elements are important in the induction of somatic hypermutation and are capable of inducing mutation even in non-immunoglobulin genes. Affinity of anti-NP Abs to NP increased with time after immunization to approximately 8,000-fold (affinity maturation); however, fine specificity, such as heteroclicity, remained unchanged. Memory B cells, which are responsible for affinity maturation, were analyzed in terms of the mutation from Trp to Leu at position 33, a change known to raise affinity about 10-fold and considered to be a memory B-cell marker. These cells were found predominantly in the early stage (2-3-week) hybridomas but rarely in late stage (> 12-week) ones, suggesting that a dynamic change in the memory B-cell population occurs during the immunization process.

A stage-specific enhancer of immunoglobulin J chain gene is induced by interleukin-2 in a presecretor B cell stage

Interleukin-2 (IL-2)-induced transcription of the J chain gene was used as a model for analyzing cytokine regulation during B cell development. To determine whether IL-2 signals are targeted to a J chain gene enhancer as well as to its promoter, the sequences flanking the J chain gene were first examined for DNase I hypersensitivity. Of six sites identified, two strong ones, 7.5 kb upstream of the J chain gene, were found to be associated with an enhancer that is active only during the antigen-driven stages of B cell development. Further analyses of the enhancer in the IL-2-responsive presecretor BCL1 cells showed that the enhancer is activated at this stage by an IL-2 signal that functions by opening the enhancer chromatin and stimulating STAT5 to bind to a STAT5 element critical for the enhancer induction. Moreover, after this early induction stage, the enhancer was shown to be constitutively open and active in terminally differentiated plasma cells.

Mechanism of antigen-driven somatic hypermutation of rearranged immunoglobulin V(D)J genes in the mouse

Available data relevant to the mechanism of somatic hypermutation have been critically evaluated in the context of alternative models: (i) error-generating reverse transcription (RT) followed by homologous recombination; and (ii) error-prone DNA replication/repair. A set of basic principles concerning somatic hypermutation has also been formulated and a revised and expanded "RT-Mutatorsome" concept (analogous to telomerase) is presented which is consistent with these principles and all data on the distribution of somatic mutations in normal and Ig transgenic mice carrying particular V(D)J and flanking region constructs. It is predicted that in the mouse VH and Vk loci. the J-C intronic Enhancer-Nuclear Matrix Attachment Region (Ei/MAR) contains a unique sequence motif or secondary structure which ensures that only V(D)J sequences mutate whilst other regions of the genome are not mutated.

Bone Marrow and Thymus Expression of Interferon-γ Results in Severe B-Cell Lineage Reduction, T-Cell Lineage Alterations, and Hematopoietic Progenitor Deficiencies

Interferon-γ (IFN-γ) is an immunoregulatory lymphokine that is primarily produced by T cells and natural killer cells. It has effects on T-cell, B-cell, and macrophage differentiation and maturation. We have developed transgenic mice that express elevated levels of IFN-γ mRNA and protein by inserting multiple copies of murine IFN-γ genomic DNA containing an Ig λ-chain enhancer in the first intron. The founder line carrying eight copies of this transgene has eightfold to 15-fold more IFN-γ–producing cells in the bone marrow and spleen than do nontransgenic littermates. Transgenic mice show a pronounced reduction in B-lineage cells in the bone marrow, spleen, and lymph nodes. In addition, single positive (CD4+,CD8− and CD4−,CD8+) thymocyte numbers are increased twofold, yet the number of splenic T cells is reduced by 50%. There is also a twofold to threefold decrease in the frequency and total number of myeloid progenitors in the bone marrow. Granulomatous lesions and residual degenerating cartilaginous masses are also present in the bones of these mice. Overall, our data show that the abnormal expression of IFN-γ in these transgenic mice results in multiple alterations in the immune system. These animals provide an important model to examine the role of IFN-γ expression on lymphoid and myeloid differentiation and function.

Rescue of thymocytes from glucocorticoid-induced cell death mediated by CD28/CTLA-4 costimulatory interactions with B7-1/B7-2

During the differentiation of thymocytes to mature T cells the processes of positive and negative selection result in signals that either protect thymocytes from cell death, or delete, through apoptosis, thymocytes with self-reactive T cell receptors (TCR). Glucocorticoids have been shown to induce thymocyte apoptosis and are produced within the thymic microenvironment. Furthermore, steroid-induced apoptosis of thymocytes has been suggested as a potential mechanism for removal of nonselected thymocytes. In this report, we demonstrate that thymocytes can be rescued from glucocorticoid-induced apoptosis by incubation with cells that express high levels of B7-1 or B7-2. In addition, the ability to be rescued by B7-1 and/or B7-2 can precede expression of the TCR. We demonstrate that CD3(+)-depleted or CD3+/ TCR-beta(+)-doubly depleted thymocytes can be rescued from glucocorticoid-induced apoptosis through the interaction of CD28 or CTLA-4 on thymocytes with cells bearing high levels of B7-1 or B7-2. Furthermore, these transfected cells are major histocompatibility complex (MHC) class II negative and, while they may express MHC class I, there is no preferential rescue of CD8+ thymocytes in the presence of glucocorticoids. Together, these data suggest that the rescue of thymocytes from glucocorticoids can be independent of the TCR. We also demonstrate that, in addition to CD28, CTLA-4 is expressed on thymocytes, suggesting that rescue from glucocorticoid-induced cell death can be mediated by both CD28 and CTLA-4. A CTLA-4Ig fusion protein which binds to both B7-1 and B7-2 was shown to completely block the rescue of thymocytes from glucocorticoid-induced cell death. Therefore, we conclude that interactions between B7-1/B7-2 and CD28/CTLA-4 are sufficient and necessary for rescue of thymocytes from glucocorticoid-induced cell death.

The human lambda immunoglobulin enhancer is controlled by both positive elements and developmentally regulated negative elements

We have recently reported the localization of the first transcriptional enhancer in the human lambda (lambda) immunoglobulin light chain locus. Enhancer activity was contained on a 1.2 kb SstI fragment, with partial activity retained on a core 111 bp PstI-SstI fragment. This enhancer is located 11.7 kb downstream of C lambda 7, the most 3' lambda constant region gene. Using a chloramphenicol acetyl transferase (CAT) assay system, we have now determined the boundaries of the complete enhancer and find it is two- to four-fold as active as the core fragment in both pre-B and B cell lines. Interestingly, a larger fragment, containing the complete enhancer as well as 5' and 3' flanking sequences has four- to eight-fold reduced activity when tested in pre-B cell lines, but full activity in B cell lines. This suggests the presence of developmentally regulated negative elements flanking the human lambda enhancer which prevent or reduce its activity at a developmentally incorrect time. By using in vivo footprinting we have begun to examine the protein interactions within this enhancer in a more physiologically relevant manner and have identified motifs which are shared with the murine lambda enhancers, as well as motifs unique to the human lambda enhancer.

Tissue-specific deoxyribonuclease I-hypersensitive sites in the vicinity of the immunoglobulin C lambda cluster of man

During B cell development, the onset of DNA rearrangements, expression, and somatic hypermutation of Ig genes are regulated through the complex interaction of cis-acting elements with trans-acting factors. Our aim is to identify DNA elements required during activation of the human Ig lambda light chain genes. Determination of deoxyribonuclease (DNase) I-hypersensitive sites in complex regulated genes can lead to the identification of sequence elements which would have been overlooked by employing transient transfection protocols. We have therefore investigated the chromatin structure of human J-C lambda genes and identified three DNase I-hypersensitive sites (HSS-1, -2, and -3) within an 8-kb region downstream of the J-C lambda 7 gene. HSS-2 and HSS-3 are B cell specific. The DNase I-hypersensitive sites are also present in kappa-producing cell lines which have not rearranged the Ig lambda locus and produce germ-line J-C lambda transcripts. We conclude that in mature B cells, both kappa and lambda loci are in an active structure regardless of the type of light chain they produce. This suggests that the chromatin structure of both loci is opened early in B cell development and that the active structure persists in mature B cells. The observed temporal order (first kappa, then lambda) of activation can be explained by consecutive synthesis of the appropriate regulating factors and the tight regulation of the recombination machinery through the products of L chain gene rearrangements.

A compilation of composite regulatory elements affecting gene transcription in vertebrates

Over the past years, evidence has been accumulating for a fundamental role of protein-protein interactions between transcription factors in gene-specific transcription regulation. Many of these interactions run within composite elements containing binding sites for several factors. We have selected 101 composite regulatory elements identified experimentally in the regulatory regions of 64 genes of vertebrates and of their viruses and briefly described them in a compilation. Of these, 82 composite elements are of the synergistic type and 19 of the antagonistic type. Within the synergistic type composite elements, transcription factors bind to the corresponding sites simultaneously, thus cooperatively activating transcription. The factors, binding to their target sites within antagonistic type composite elements, produce opposing effects on transcription. The nucleotide sequence and localization in the genes, the names and brief description of transcription factors, are provided for each composite element, including a representation of experimental data on its functioning. Most of the composite elements (3/4) fall between -250 bp and the transcription start site. The distance between the binding sites within the composite elements described varies from complete overlapping to 80 bp. The compilation of composite elements is presented in the database COMPEL which is electronically accessible by anonymous ftp via internet.

Various V-J rearrangement efficiencies shape the mouse lambda B cell repertoire

The diversity of the B cell repertoire of C kappa knockout mice is limited by the expression of four lambda light chain types. Among the spleen B cells, lambda 1 is expressed by the majority (58%) of cells, and lambda 3 by the minority (8%), while lambda 2 (V2) and lambda 2 (Vx) are expressed in intermediate quantities (18% and 16%, respectively). To assess the influence of mechanistic pressures on the lambda subtype distribution, the proportions of the different lambda rearrangements were determined in various B cell subpopulations divided on the basis of the lambda subtype expressed, and the V lambda J lambda junction sequences were studied at different steps of B cell differentiation (pre-B, immature and mature B cells). The data show that (1) the ratio of productive/non-productive VJ junctions is determined by the nature of the lambda segments that are rearranged as can be observed in the pre-B cells, (2) V1-J1 non-productive rearrangements are often found in the lambda 1-negative B cells in the periphery, and (3) V1J3 junctions are often non-productive regardless of the nature of the cells analyzed. Our results, therefore, suggest that a strong probability of initiating a V1-J1 rearrangement and a weak probability of giving a productive V1J3 junction are responsible for the lambda 1 dominance and the lambda 3 under-expression, respectively. The intermediate proportion of lambda 2(V2) subtype is most likely due to a probability of obtaining a productive joint that is better than that for V1J3 and a probability of initiating a rearrangement that is lower than that for V1J1. However, the lambda 2(Vx) cell proportion cannot be determined only by these parameters.