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SATB1 (Special A-T rich Binding protein 1) is a cell type specific factor involved in chromatin remodelling events that participate in the regulation of the genetic network in developing T cells and neurons. In T cells, SATB1 is a key factor required for lineage commitment, VDJ recombination, development and maturation. In B cells, SATB1 is described as binding to the MARs-Eµ regions of the IgH locus. Considering that its expression varies during differentiation, the involvement of this factor needed to be clarified in B cells. Using a KO mouse model deleting SATB1 from the pro-B cell stage, we were able to examine the consequences of SATB1 deletion in naive and activated B cell subsets. Our model indicates firstly that SATB1 is not essential for B cell development and the establishment of a broad IgH repertoire. Second, we show that this factor exhibits an ambivalent function in mature B cells, acting sequentially as a positive and negative regulator of Ig gene transcription in naive and activated cells, respectively. Third, our study indicates that the negative regulatory function of SATB1 in B cells extends to the germinal center response in which this factor limits somatic hypermutation of Ig genes. This finding suggests that SATB1 may limit the introduction of unwanted mutations into B cells.

Two scaffold/matrix attachment regions (5’- and 3’-MARsEμ) flank the intronic core enhancer (cEμ) within the immunoglobulin heavy chain locus (IgH). Besides their conservation in mice and humans, the physiological role ofMARsEμis still unclear and their involvement in somatic hypermutation (SHM) has never been deeply evaluated. By analysing a mouse model devoid ofMARsEμ, we observed an inverted substitution pattern: SHM being decreased upstream fromcEμand increased downstream of it. Strikingly, the SHM defect induced byMARsEμ-deletion was accompanied by an increase of sense transcription of the IgH V region, excluding a direct transcription-coupled effect. Interestingly, by breeding to DNA repair-deficient backgrounds, we showed that the SHM defect, observed upstream fromcEμin this model, was not due to a decrease in AID deamination but rather the consequence of a defect in base excision repair-associated unfaithful repair process. Our study pointed out an unexpected “fence” function ofMARsEμregions in limiting the error-prone repair machinery to the variable region of Ig gene loci.

Efficient humoral responses rely on DNA damage, mutagenesis and error-prone DNA repair. Diversification of B cell receptors through somatic hypermutation and class-switch recombination are initiated by cytidine deamination in DNA mediated by activation-induced cytidine deaminase (AID)1 and by the subsequent excision of the resulting uracils by uracil DNA glycosylase (UNG) and by mismatch repair proteins1–3. Although uracils arising in DNA are accurately repaired1–4, how these pathways are co-opted to generate mutations and double-strand DNA breaks in the context of somatic hypermutation and class-switch recombination is unknown1–3. Here we performed a genome-wide CRISPR–Cas9 knockout screen for genes involved in class-switch recombination and identified FAM72A, a protein that interacts with the nuclear isoform of UNG (UNG2)5 and is overexpressed in several cancers5. We show that the FAM72A–UNG2 interaction controls the levels of UNG2 and that class-switch recombination is defective in Fam72a−/− B cells due to the upregulation of UNG2. Moreover, we show that somatic hypermutation is reduced in Fam72a−/− B cells and that its pattern is skewed upon upregulation of UNG2. Our results are consistent with a model in which FAM72A interacts with UNG2 to control its physiological level by triggering its degradation, regulating the level of uracil excision and thus the balance between error-prone and error-free DNA repair. Our findings have potential implications for tumorigenesis, as reduced levels of UNG2 mediated by overexpression of Fam72a would shift the balance towards mutagenic DNA repair, rendering cells more prone to acquire mutations. FAM72A interacts with UNG2 to regulate the balance between error-prone and error-free DNA repair.

Among the multiple events leading to immunoglobulin (Ig) expression in B cells, stepwise activation of the Ig heavy chain locus (IgH) is of critical importance. Transcription regulation of the complex IgH locus has always been an interesting viewpoint to unravel the multiple and complex events required for IgH expression. First, regulatory germline transcripts (GLT) assist DNA remodeling events such as VDJ recombination, class switch recombination (CSR) and somatic hypermutation (SHM). Second, productive spliced transcripts restrict heavy chain protein expression associated either with the surface receptor of developing B cells or secreted in large amounts in plasma cells. One main transcriptional regulator for IgH lies at its 3' extremity and includes both a set of enhancers grouped in a large 3' regulatory region (3'RR) and a cluster of 3'CTCF-binding elements (3'CBEs). In this focused review, we will preferentially refer to evidence reported for the murine endogenous IgH locus, whether it is wt or carries deletions or insertions within the IgH 3' boundary and associated regulatory region.

Among the multiple events leading to immunoglobulin (Ig) expression in B cells, stepwise activation of the Ig heavy chain locus (IgH) is of critical importance. Transcription regulation of the complex IgH locus has always been an interesting viewpoint to unravel the multiple and complex events required for IgH expression. First, regulatory germline transcripts (GLT) assist DNA remodeling events such as VDJ recombination, class switch recombination (CSR) and somatic hypermutation (SHM). Second, productive spliced transcripts restrict heavy chain protein expression associated either with the surface receptor of developing B cells or secreted in large amounts in plasma cells. One main transcriptional regulator for IgH lies at its 3' extremity and includes both a set of enhancers grouped in a large 3' regulatory region (3'RR) and a cluster of 3'CTCF-binding elements (3'CBEs). In this focused review, we will preferentially refer to evidence reported for the murine endogenous IgH locus, whether it is wt or carries deletions or insertions within the IgH 3' boundary and associated regulatory region.

In B-lineage cells, the cytidine deaminase AID not only generates somatic mutations to variable regions of Ig genes but also inflicts, at a lower frequency, mutations to several non-Ig genes named AID off-targets, which include proto-oncogenes. High-throughput sequencing should be in principle the method of choice to detect and document these rare nucleotide substitutions. So far, high-throughput sequencing–based methods are impaired by a global sequencing error rate that usually covers the real mutation rate of AID off-target genes in activated B cells. We demonstrate the validity of a per-base background subtraction method called detection of minor variants by error correction (DeMinEr), which uses deep sequencing data from mutated and nonmutated samples to correct the substitution frequency at each nucleotide position along the sequenced region. Our DeMinEr method identifies somatic mutations at a frequency down to 0.02% at any nucleotide position within two off-target genes: Cd83 and Bcl6. Biological models and control conditions such as AID- and UNG-deficient mice validate the specificity and the sensitivity of our method. The high resolution and robustness of DeMinEr enable us to document fine effects such as age-dependent accumulation of mutations in these oncogenes in the mouse.

// Sandrine Le Noir 1,* , Brice Laffleur 1,* , Claire Carrion 1 , Armand Garot 1 , Sandrine Lecardeur 1 , Eric Pinaud 1 , Yves Denizot 1 , Jane Skok 2 and Michel Cogne 1 1 UMR 7276 CNRS and Universite de Limoges: Controle de la Reponse Immune B et Lymphoproliferation, Limoges, France 2 Department of Pathology, New York University School of Medicine, New York, NY, USA * These authors have contributed equally to this work Correspondence to: Michel Cogne, email: // Keywords : super-enhancer; alleles; transvection; nuclear positioning; gene regulation Received : December 20, 2016 Accepted : January 01, 2017 Published : Janaury 10, 2017 Abstract Immunoglobulin heavy chain ( IgH ) alleles have ambivalent relationships: they feature both allelic exclusion, ensuring monoallelic expression of a single immunoglobulin (Ig) allele, and frequent inter-allelic class-switch recombination (CSR) reassembling genes from both alleles. The IgH locus 3’ regulatory region (3’RR) includes several transcriptional cis -enhancers promoting activation-induced cytidine deaminase (AID)-dependent somatic hypermutation (SHM) and CSR, and altogether behaves as a strong super-enhancer. It can also promote deregulated expression of translocated oncogenes during lymphomagenesis. Besides these rare, illegitimate and pathogenic interactions, we now show that under physiological conditions, the 3’RR super-enhancer supports not only legitimate cis- , but also trans- recruitment of AID, contributing to IgH inter-allelic proximity and enabling the super-enhancer on one allele to stimulate biallelic SHM and CSR. Such inter-allelic activating interactions define transvection, a phenomenon well-known in drosophila but rarely observed in mammalian cells, now appearing as a unique feature of the IgH 3’RR super-enhancer.

International audience; The error-prone V(D)J recombination process generates considerable amounts of nonproductive immunoglobulin (Ig) pre-mRNAs. We recently demonstrated that aberrant Ig chains lacking variable (V) domains can be produced after nonsense-associated altered splicing (NAS) events. Remarkably, the expression of these truncated Ig polypeptides heightens endoplasmic reticulum stress and shortens plasma cell (PC) lifespan. Many questions remain regarding the molecular mechanisms underlying this new truncated Ig exclusion (TIE-) checkpoint and its restriction to the ultimate stage of B-cell differentiation. To address these issues, we evaluated the extent of NAS of Ig pre-mRNAs using an Ig heavy chain (IgH) knock-in model that allows for uncoupling of V exon skipping from TIE-induced apoptosis. We found high levels of V exon skipping in PCs compared with B cells, and this skipping was correlated with a biallelic boost in IgH transcription during PC differentiation. Chromatin analysis further revealed that the skipped V exon turned into a pseudo-intron. Finally, we showed that hypertranscription of Ig genes facilitated V exon skipping upon passive administration of splice-switching antisense oligonucleotides (ASOs). Thus, V exon skipping is coupled to transcription and increases as PC differentiation proceeds, likely explaining the late occurrence of the TIE-checkpoint and opening new avenues for ASO-mediated strategies in PC disorders.

Somatic hypermutation in variable heavy chain rearranged regions is abrogated in the absence of the 3′ regulatory region enhancer, whereas transcription rate in the Ig heavy chain is only partially reduced., Interactions with cognate antigens recruit activated B cells into germinal centers where they undergo somatic hypermutation (SHM) in V(D)J exons for the generation of high-affinity antibodies. The contribution of IgH transcriptional enhancers in SHM is unclear. The Eμ enhancer upstream of Cμ has a marginal role, whereas the influence of the IgH 3′ regulatory region (3′RR) enhancers (hs3a, hs1,2, hs3b, and hs4) is controversial. To clarify the latter issue, we analyzed mice lacking the whole 30-kb extent of the IgH 3′RR. We show that SHM in VH rearranged regions is almost totally abrogated in 3′RR-deficient mice, whereas the simultaneous Ig heavy chain transcription rate is only partially reduced. In contrast, SHM in κ light chain genes remains unaltered, acquitting for any global SHM defect in our model. Beyond class switch recombination, the IgH 3′RR is a central element that controls heavy chain accessibility to activation-induced deaminase modifications including SHM.

Suicidal B cells In response to an infection, immunological B cells undergo a maturation process that results in the production of immunoglobulin (Ig) that is better able to bind and clear the invading pathogen. This occurs through somatic cell hypermutation and class switch recombination of the Ig gene and requires activation-induced deaminase (AID). Péron et al. (p. 931 , published online 26 April) observed that the 3' cis-regulatory region of the heavy-chain locus is transcribed and undergoes AID-mediated mutation and recombination. The resulting deletion of the Ig heavy gene cluster generates B cells that are no longer able to express Ig on the cell surface. Because cell-surface Ig expression is essential for B cell survival, this process is termed “locus suicide recombination” (LSR) and may be important in shaping the dynamics of B effector cell differentiation and homeostasis.

Class switching and plasma cell differentiation occur at a high level within all mucosa-associated lymphoid tissues. The different classes of membrane immunoglobulin heavy chains are associated with the Igα/Igβ heterodimer within the B-cell receptor (BCR). Whether BCR isotypes convey specific signals adapted to the corresponding differentiation stages remains debated but IgG and IgA membranes have been suggested to promote plasma cell differentiation. We investigated the impact of blocking expression of the IgA-class BCR through a 'αΔtail' targeted mutation, deleting the Cα immunoglobulin gene membrane exon. This allowed us to evaluate to what extent class switching and plasma cell differentiation can be concurrent processes, allowing some αΔtail(+/+) B cells with an IgM BCR to directly differentiate into IgA plasma cells and yield serum secreted IgA in spite of the absence of membrane IgA(+) B lymphocytes. By contrast, in secretions the secretory IgA was very low, indicating that J-chain-positive plasma cells producing secretory IgA overwhelmingly differentiate from previously class-switched membrane IgA(+) memory B cells. In addition, although mucosa-associated lymphoid tissues are a major site for plasma cell accumulation, αΔtail(+/+) mice showed that the gut B-cell lineage homeostasis is not polarized toward plasma cell differentiation through a specific influence of the membrane IgA BCR.

International audience; V(D)J recombination occurs during the antigen-independent early steps of B-cell ontogeny. Multiple IgH cis-regulatory elements control B-cell ontogeny. IGCR1 (intergenic control region 1), the DQ52 promoter/enhancer, and the intronic Emu enhancer, all three located upstream of Cmu, have important roles during V(D)J recombination, whereas there is no clue about a role of the IgH regulatory region (RR) encompassing the four transcriptional enhancers hs3a, hs1,2, hs3b, and hs4 during these early stages. To clarify the role of the RR in V(D)J recombination, we totally deleted it in the mouse genome. Here, we show that V(D)J recombination is unaffected by the complete absence of the IgH RR, highlighting that this region only orchestrates IgH locus activity during the late stages of B-cell differentiation. In contrast, the earliest antigen-independent steps of B-cell ontogeny would be under the control of only the upstream Cmu elements of the locus.

International audience; The 3' regulatory region (3'RR) located downstream of the IgH gene is the master element that controls class switch recombination and sustains high-level transcription at the plasma-cell stage. This latter role suggests that the 3'RR may be involved in oncogene deregulation during the frequent IgH translocation events associated with B-cell malignancies. A convincing demonstration of the essential contribution of 3'RR in lymphomagenesis has been provided by transgenic animal models. The mouse 3'RR shares a strong structural homology with the regulatory regions located downstream of each human Cα gene. Mouse models exploring the role of the 3'RR in B-cell physiology and in malignancies should provide useful indications about the pathophysiology of human cell lymphocyte proliferation.

The immunoglobulin heavy chain locus (IgH) undergoes multiple changes along B-cell differentiation. In progenitor B cells, V(D)J assembly allows expression of μ heavy chains. In mature B cells, class switch recombination may replace the expressed constant (C)μ gene with a downstream CH gene. Finally, plasma cell differentiation strongly boosts IgH transcription. How the multiple IgH transcriptional enhancers tune these changes is unclear. Here we demonstrate that deletion of the whole IgH 3′ regulatory region (3′RR) allows normal maturation until the stage of IgM/IgD expressing lymphocytes, but nearly abrogates class switch recombination to all CH genes. Although plasma cell numbers are unaffected, we reveal the role of the 3′RR into the transcriptional burst normally associated with plasma cell differentiation. Our study shows that transcriptional changes and recombinations occurring after antigen-encounter appear mainly controlled by the 3′RR working as a single functional unit.

Significance The immunoglobulin heavy chain (IgH) 3′regulatory region ( 3′RR ) fine-tunes IgH gene expression during B cell development. One singularity of this region is its quasi-palindromic structure conserved in the 3′RR of other species. By comparing previous mouse knockout (KO) models ( 3′RR- and hs3b-4 KO) to a novel mutant devoid of the quasi-palindrome ( 3′PAL KO), we highlighted common features and differences that specify two distinct regulatory entities: ( i ) the distal module ( hs4 ) is sufficient for normal IgH expression up to the naïve B cell stage; ( ii ) during B-cell activation, the proximal module (quasi-palindrome) is important for both class switch recombination and somatic hypermutation; and ( iii ) in plasma cells, the quasi-palindrome is required for robust transcription of the IgH locus.

International audience; Molecular mechanisms underlying synapsis of activation-induced deaminase (AID)-targeted S regions during class switch recombination (CSR) are poorly understood. By using chromosome conformation capture techniques, we found that in B cells, the Emicro and 3'Ealpha enhancers were in close spatial proximity, forming a unique chromosomal loop configuration. B cell activation led to recruitment of the germline transcript (GLT) promoters to the Emicro:3'Ealpha complex in a cytokine-dependent fashion. This structure facilitated S-S synapsis because Smicro was proximal to Emicro and a downstream S region was corecruited with the targeted GLT promoter to Emicro:3'Ealpha. We propose that GLT promoter association with the Emicro:3'Ealpha complex creates an architectural scaffolding that promotes S-S synapsis during CSR and that these interactions are stabilized by AID. Thus, the S-S synaptosome is formed as a result of the self-organizing transcription system that regulates GLT expression and may serve to guard against spurious chromosomal translocations.

Activation-induced cytidine deaminase (AID), which is specific to B lymphocytes, is required for class switch recombination (CSR)--a process mediating isotype switching of immunoglobulin--and somatic hypermutation--the introduction of many point mutations into the immunoglobulin variable region genes. It has been suggested that AID may function as an RNA-editing enzyme or as a cytidine deaminase on DNA. However, the precise enzymatic activity of AID has not been assessed in previous studies. Similarly, although transcription of the target immunoglobulin locus sequences is required for both CSR and somatic hypermutation, the precise role of transcription has remained speculative. Here we use two different assays to demonstrate that AID can deaminate specifically cytidines on single-stranded (ss)DNA but not double-stranded (ds)DNA substrates in vitro. However, dsDNA can be deaminated by AID in vitro when the reaction is coupled to transcription. Moreover, a synthetic dsDNA sequence, which targets CSR in vivo in a manner dependent on transcriptional orientation, was deaminated by AID in vitro with the same transcriptional-orientation-dependence as observed for endogenous CSR. We conclude that transcription targets the DNA deamination activity of AID to dsDNA by generating secondary structures that provide ssDNA substrates.

The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus. Both the physical proximity and coupled activities of RNA helicase Mtr4 (and Senataxin) with the noncoding RNA processing function of RNA exosome determine the strand specific distribution of DNA mutations. Our study suggests that strand-specific DNA mutagenesis-associated mechanisms will play major roles in other undiscovered aspects of organismic development.

The IgH intronic enhancer region Eμ is a combination of both a 220-bp core enhancer element and two 310–350-bp flanking scaffold/matrix attachment regions named MARsEμ. In the mouse, deletion of the core-enhancer Eμ element mainly affects VDJ recombination with minor effects on class switch recombination. We carried out endogenous deletion of the full-length Eμ region (core plus MARsEμ) in the mouse genome to study VH gene repertoire and IgH expression in developing B-lineage cells. Despite a severe defect in VDJ recombination with partial blockade at the pro–B cell stage, Eμ deletion (core or full length) did not affect VH gene usage. Deletion of this regulatory region induced both a decrease of pre–B cell and newly formed B cell compartments and a strong orientation toward the marginal zone B cell subset. Because Igμ H chain expression was decreased in Eμ-deficient pre–B cells, we propose that modification of B cell homeostasis in deficient animals was caused by “weak” pre–B cell and BCR expression. Besides imbalances in B cell compartments, Ag-specific Ab responses were not impaired in animals carrying the Eμ deletion. In addition to its role in VDJ recombination, our study points out that the full-length Eμ region does not influence VH segment usage but ensures efficient Igμ-chain expression required for strong signaling through pre–B cells and newly formed BCRs and thus participates in B cell inflow and fate.

We studied the hs1,2 transcriptional enhancer identified downstream of the human alpha1 gene of the immunoglobulin H (IgH) locus, for which two different allelic configurations (a and b) were previously reported by Southern blotting. By using a polymerase chain reaction (PCR) method we amplified minisatellites within the hs1,2 core enhancer, with variable numbers of tandem repeats (VNTR) defining three 'PCR alleles' alpha1A, alpha1B and alpha1C (including one, two and three repeats, respectively). Five different alpha1 h1,2 genotypes were encountered in a population of 513 donors, representing 13.8, 34.5, 49.7, 1.3 and 0.6% for the AA, BB, AB, AC and BC genotypes, respectively. Luciferase assays showed that increasing the number of minisatellites increased the transcriptional strength of the alpha1 hs1,2 enhancer. Simultaneous determination of Southern blot alleles and VNTR alleles only showed a partial linkage between both types of polymorphism, altogether defining at least six different allelic forms of the 3'alpha1 region. In conclusion, the present study further demonstrates the genetic instability of the 3'alpha region, for which multiple alleles have been generated through inversions and internal deletions and/or duplications. This study also strengthens the hypothesis that the polymorphism at the IgH 3' regulatory region of the alpha1 gene could play a role in the outcome of diseases involving immunoglobulin secretion.

Alleles of the α1 immunoglobulin gene 3′ enhancer control evolution of IgA nephropathy toward renal failure. Background IgA nephropathy is the most common glomerular disease. Mechanisms leading to its occurrence and controlling the evolution of the disease remain largely unknown. Various genetic factors have been found, mostly implicating immunologically relevant genes (IgH, TCR, human lymphocyte antigen, and complement loci). A regulatory region recently identified downstream, the α1 gene of the IgH locus, was a likely candidate for the control of IgA1 production in patients. Alleles of this region, differing by size, sequence, and orientation of the α1 hs1,2 transcriptional enhancer, were first identified through Southern blot hybridization. Methods We established a polymerase chain reaction (PCR) method suitable for routine testing that amplifies minisatellites within the α1 hs1,2 enhancer, with variable numbers of tandem repeats (VNTR) defining the two alleles. This assay allowed the typing of 104 patients with IgAN and 83 healthy volunteers. Results from typing of α1 hs1,2 alleles were compared with long-term clinical outcome in patients. Enhancer alleles were compared in a luciferase reporter gene assay. Results The α1 hs1,2 alleles do not constitute a predictive factor for IgA nephropathy, since similar allelic frequencies were observed in healthy individuals and in unrelated European patients. In contrast, among patients, homozygosity for the weakest enhancer allele (AA genotype) was significantly correlated with a milder form of the disease, whereas the allele B was associated with severe evolution. The minisatellite region within the α1 hs1,2 enhancer carried potential transcription factor-binding sites, and its duplication increased the transcriptional strength of the α1 hs1,2 allele B over that of allele A. Conclusion Altogether, these alleles may constitute a risk factor for the prognosis of IgA nephropathy.

Transcriptional enhancers of the IgH locus include E mu and four 3' elements (C alpha3', hs1-2, hs3 and hs4), some of which are by themselves weak. We show that these weak elements behave as strong "co-enhancers" when combined, and display a stage-dependent activity which differs from that obtained when they are alone. Combinations mimicking the palindromic structure of the 3' IgH region are particularly efficient. Noticeably in pre-B cells, hs4 is boosted by the addition of elements previously considered inactive at this stage, hs1-2 and hs3. Combinations of 3' elements also strongly boost E mu at all maturation stages, but inhibitory interactions occasionally occur between E mu and incomplete 3' combinations, indicating that full transcriptional activity is mainly achieved when all 5' and 3' partners play their respective roles.

Antigen receptor gene loci are among the most complex in mammals. The IgH locus, encoding the immunoglobulin heavy chain (IgH) in B-lineage cells, undergoes major transcription-dependent DNA remodeling events, namely V(D)J recombination, Ig class-switch recombination (CSR), and somatic hypermutation (SHM). Various cis-regulatory elements (encompassing promoters, enhancers, and chromatin insulators) recruit multiple nuclear factors in order to ensure IgH locus regulation by tightly orchestrated physical and/or functional interactions. Among major IgH cis-acting regions, the large 3′ regulatory region (3′RR) located at the 3′ boundary of the locus includes several enhancers and harbors an intriguing quasi-palindromic structure. In this review, we report progress insights made over the past decade in order to describe in more details the structure and functions of IgH 3′RRs in mouse and human. Generation of multiple cellular, transgenic and knock-out models helped out to decipher the function of the IgH 3′ regulatory elements in the context of normal and pathologic B cells. Beside its interest in physiology, the challenge of elucidating the locus-wide cross talk between distant cis-regulatory elements might provide useful insights into the mechanisms that mediate oncogene deregulation after chromosomal translocations onto the IgH locus.

International audience; Antigen receptor gene loci are among the most complex in mammals. The IgH locus, encoding the immunoglobulin heavy chain (IgH) in B-lineage cells, undergoes major transcription-dependent DNA remodeling events, namely V(D)J recombination, Ig class-switch recombination (CSR), and somatic hypermutation (SHM). Various cis-regulatory elements (encompassing promoters, enhancers, and chromatin insulators) recruit multiple nuclear factors in order to ensure IgH locus regulation by tightly orchestrated physical and/or functional interactions. Among major IgH cis-acting regions, the large 3' regulatory region (3'RR) located at the 3' boundary of the locus includes several enhancers and harbors an intriguing quasi-palindromic structure. In this review, we report progress insights made over the past decade in order to describe in more details the structure and functions of IgH 3'RRs in mouse and human. Generation of multiple cellular, transgenic and knock-out models helped out to decipher the function of the IgH 3' regulatory elements in the context of normal and pathologic B cells. Beside its interest in physiology, the challenge of elucidating the locus-wide cross talk between distant cis-regulatory elements might provide useful insights into the mechanisms that mediate oncogene deregulation after chromosomal translocations onto the IgH locus.

DREAM/KChIP-3 is a calcium-dependent transcriptional repressor highly expressed in immune cells. Transgenic mice expressing a dominant active DREAM mutant show reduced serum Ig levels. In vitro assays show that reduced Ig secretion is an intrinsic defect of transgenic B cells that occurs without impairment in plasma cell differentiation, class switch recombination, or Ig transcription. Surprisingly, transgenic B cells show an accelerated entry in cell division. Transcriptomic analysis of transgenic B cells revealed that hyperproliferative B cell response could be correlated with a reduced expression of Klf9, a cell-cycle regulator. Pulse-chase experiments demonstrated that the defect in Ig production is associated with reduced translation rather than with increased protein degradation. Importantly, transgenic B cells showed reduced expression of the Eif4g3 gene, which encodes a protein related to protein translation. Our results disclose, to our knowledge, a novel function of DREAM in proliferation and Ig synthesis in B lymphocytes.

In the mouse, the regulatory region located at the 3′ end of the IgH locus includes four transcriptional enhancers: HS3a, HS1-2, HS3b, and HS4; the first three lie in a quasi-palindromic structure. Although the upstream elements HS3a and HS1-2 proved dispensable for Ig expression and class switch recombination (CSR), the joint deletion of HS3b and HS4 led to a consistent decrease in IgH expression in resting B cells and to a major CSR defect. Within this pair of distal enhancers, it was questionable whether HS3b and HS4 could be considered individually as elements critical for IgH expression and/or CSR. Studies in HS4-deficient mice recently revealed the role of HS4 as restricted to Igμ-chain expression from the pre-B to the mature B cell stage and left HS3b as the last candidate for CSR regulation. Our present study finally invalidates the hypothesis that CSR could mostly rely on HS3b itself. B cells from HS3b-deficient animals undergo normal proliferation, germline transcription, and CSR upon in vitro stimulation with LPS; in vivo Ag-specific responses are not affected. In conclusion, our study highlights a major effect of the global ambiance of the IgH locus; enhancers demonstrated as being strongly synergistic in transgenes turn out to be redundant in their endogenous context.

International audience; B-cell malignancies, such as human Burkitt's lymphoma, often contain translocations that link c-myc or other proto-oncogenes to the immunoglobulin heavy chain locus (IgH, encoded by Igh). The nature of elements that activate oncogenes within such translocations has been a long-standing question. Translocations within Igh involve DNA double-strand breaks initiated either by the RAG1/2 endonuclease during variable, diversity and joining gene segment (V(D)J) recombination, or by activation-induced cytidine deaminase (AID, also known as AICDA) during class switch recombination (CSR). V(D)J recombination in progenitor B (pro-B) cells assembles Igh variable region exons upstream of mu constant region (Cmu) exons, which are the first of several sets of C(H) exons ('C(H) genes') within a C(H) locus that span several hundred kilobases (kb). In mature B cells, CSR deletes Cmu and replaces it with a downstream C(H) gene. An intronic enhancer (iEmu) between the variable region exons and Cmu promotes V(D)J recombination in developing B cells. Furthermore, the Igh 3' regulatory region (Igh3'RR) lies downstream of the C(H) locus and modulates CSR by long-range transcriptional enhancement of C(H) genes. Transgenic mice bearing iEmu or Igh3'RR sequences fused to c-myc are predisposed to B lymphomas, demonstrating that such elements can confer oncogenic c-myc expression. However, in many B-cell lymphomas, Igh-c-myc translocations delete iEmu and place c-myc up to 200 kb upstream of the Igh3'RR. Here we address the oncogenic role of the Igh3'RR by inactivating it in two distinct mouse models for B-cell lymphoma with Igh-c-myc translocations. We show that the Igh3'RR is dispensable for pro-B-cell lymphomas with V(D)J recombination-initiated translocations, but is required for peripheral B-cell lymphomas with CSR-associated translocations. As the Igh3'RR is not required for CSR-associated Igh breaks or Igh-c-myc translocations in peripheral B-cell lymphoma progenitors, we conclude that this regulatory region confers oncogenic activity by long-range and developmental stage-specific activation of translocated c-myc genes.

Burkitt lymphoma (BL) features translocations linking c-myc to an Ig locus. Breakpoints in the H chain locus (IgH) stand either close to JH or within switch regions and always link c-myc to the 3′ IgH locus control region (3′ LCR). To test the hypothesis that the 3′ LCR alone was sufficient to deregulate c-myc, we generated mice carrying a 3′ LCR-driven c-myc transgene and specifically up-regulating c-myc in B cells. Splenic B cells from mice proliferated exaggeratedly in response to various signals had an elevated apoptosis rate but normal B220/IgM/IgD expression. Although all Ig levels were lowered in vivo, class switching and Ig secretion proved normal in vitro. Beginning at the age of 12 wk, transgenic mice developed clonal lymphoblastic lymphomas or diffuse anaplastic plasmacytomas with an overall incidence of 80% by 40 wk. Lymphoblastic lymphomas were B220+IgM+IgD+ with the BL “starry sky” appearance. Gene expression profiles revealed broad alterations in the proliferation program and the Ras-p21 pathway. Our study demonstrates that 3′ IgH enhancers alone can deregulate c-myc and initiate the development of BL-like lymphomas. The rapid and constant occurrence of lymphoma in this model makes it valuable for the understanding and the potential therapeutic manipulation of c-myc oncogenicity in vivo.

The predominant path of immunoglobulin class switch recombination follows the paradigm of intra-chromosomal deletion enabling expression of another heavy chain instead of micro and delta. This was, however, challenged by observations of inter-allelic class switch recombination in rabbit or mouse IgG3- or IgA-producing B cells. Assuming that the conditions of inter-chromosomal exchange are likely present at any target S regions in stimulated B cells, we explored trans-association of VH and C genes in a model allowing all C genes to be checked simultaneously. Heterozygous mutant mice are thus studied, which carry one non-functional IgH allele inactivated by a non-translatable mutation of VDJ-CH transcripts, while the functional allele is deficient for class switching due to a truncated 3'regulatory region. A fair level of switching to all Ig classes is restored in heterozygous mice despite the fact that cis-recombination is either non productive on one allele or deficient on the other. Molecular evidence at the DNA level of trans-CSR to IgG3 was demonstrated by cloning and sequencing Smu-Sgamma3 hybrid junctions. These data demonstrate that inter-allelic recombination may broadly rescue the production of various class-switched isotypes and allow complementation between mutations located at both ends of the IgH constant gene cluster.

Studies of chimeric mice demonstrated that the core Ig heavy chain ( IgH ) intronic enhancer (iEμ) functions in V(D)J and class switch recombination at the IgH locus. To more fully evaluate the role of this element in these and other processes, we generated mice homozygous for germ-line mutations in which the core sequences of iEμ (cEμ) were either deleted (cEμ Δ/Δ mice) or replaced with a pgk-Neo R cassette (cEμ N/N mice). The cEμ Δ/Δ mice had reduced B cell numbers, in association with impaired D to J H and V H to DJ H rearrangement, whereas cEμ N/N mice had a complete block in IgH V(D)J H recombination, confirming that additional cis elements cooperate with iEμ to enforce D to J H recombination. In addition, developing cEμ Δ/Δ and cEμ N/N B lineage cells had correspondingly decreased levels of germ-line transcripts from the J H region of the IgH locus (μ0 and Iμ transcripts); although both had normal levels of germ-line V H transcripts, suggesting that cEμ may influence IgH locus V(D)J recombination by influencing accessibility of J H proximal regions of the locus. Consistent with chimera studies, peripheral cEμ Δ/Δ B cells had normal surface Ig and relatively normal class switch recombination. However, cEμ Δ/Δ B cells also had relatively normal somatic hypermutation of their IgH variable region genes, showing unexpectedly that the cEμ is not required for this process. The availability of mice with the iEμ mutation in their germ line will facilitate future studies to elucidate the roles of iEμ in V H (D)J H recombination in the context of IgH chromatin structure and germ-line transcription.

The more distal enhancers of the immunoglobulin heavy-chain 3′ regulatory region, hs3b and hs4, were recently demonstrated as master control elements of germline transcription and class switch recombination to most immunoglobulin constant genes. In addition, they were shown to enhance the accumulation of somatic mutations on linked transgenes. Since somatic hypermutation and class switch recombination are tightly linked processes, their common dependency on the endogenous locus 3′ enhancers could be an attractive hypothesis. VDJ structure and somatic hypermutation were analyzed in B cells from mice carrying either a heterozygous or a homozygous deletion of these enhancers. We find that hs3b and hs4 are dispensable both for VDJ assembly and for the occurrence of mutations at a physiologic frequency in the endogenous locus. In addition, we show that cells functionally expressing the immunoglobulin M (IgM) class B-cell receptor encoded by an hs3b/hs4-deficient locus were fully able to enter germinal centers, undergo affinity maturation, and yield specific antibody responses in homozygous mutant mice, where IgG1 antibodies compensated for the defect in other IgG isotypes. By contrast, analysis of Peyer patches from heterozygous animals showed that peanut agglutinin (PNAhigh) B cells functionally expressing the hs3b/hs4-deficient allele were dramatically outclassed by B cells expressing the wild-type locus and normally switching to IgA. This study thus also highlights the role of germinal centers in the competition between B cells for affinity maturation and suggests that membrane IgA may promote recruitment in an activated B-cell compartment, or proliferation of activated B cells, more efficiently than IgM in Peyer patches.

International audience; Four transcriptional enhancers lie downstream of the immunoglobulin heavy chain locus: Calpha3'/hs3a, hs1,2, hs3b, and hs4. Although individually weak, these elements have strong transcriptional synergies when combined and they altogether behave as a locus control region. Previous knockout experiments in the 3' region have shown that both hs3a and hs1,2 are dispensable for normal expression and rearrangement of the IgH locus but that their replacement with a transcribed neo gene severely affects class switch recombination. Here we show that even in the absence of a neo gene, joint deletion of the last two 3' enhancers, hs3b and hs4, severely impairs germline transcription and class switching to most isotypes and may in addition affect mu gene expression in resting B cells.

Although four regulatory elements are known downstream of the mouse IgH alpha gene, a single enhancer homologous to hs1,2 has been thus far described downstream of each human alpha gene (Chen, C. and Birshtein, B. K., J. Immunol. 1997. 159: 1310). We characterized a 10-kb region downstream of the human alpha 1 gene. Two B cell-specific regulatory elements homologous to the murine C alpha 3'/hs3 and hs1,2,3' enhancers were found, which are duplicated downstream of alpha 2. The hs1,2 element is in inverted orientation by comparison with a recently reported alpha 1 hs1,2 element: it appears as a common allelic variant carrying an internal tandem repeat insertion and its prevalence in the human population is 60%. As in the mouse, the human hs1,2 enhancer is flanked with long inverted repeats which may have promoted inversion events through homologous recombination. Although the palindromic organization of the region is maintained in human, sequence identity with rodents focuses on core enhancer elements rather than on flanking repeats. Concerted divergence of both sides of the dyad symmetry suggests that inverted repeats are not just evolutionary remnants but rather play an architectural role in the LCR function.

// Alexis Saintamand 1 , Pauline Rouaud 1 , Armand Garot 1 , Faten Saad 1 , Claire Carrion 1 , Christelle Oblet 1 , Michel Cogne 1, 2, 3 , Eric Pinaud 1 , Yves Denizot 1 1 CNRS, CRIBL, UMR 7276, Limoges, France 2 Universite de Limoges, CRIBL, UMR 7276, Limoges, France 3 Institut Universitaire de France, Paris, France Correspondence to: Yves Denizot, e-mail: yves.denizot@unilim.fr Keywords: BCR, B cell fate, IgH 3’ regulatory enhancers, knock-out mice Received: December 17, 2014 Accepted: December 21, 2014 Published: March 03, 2015 ABSTRACT We report that the IgH 3’ regulatory region (3’RR) has no role on μ chain transcription and pre-BCR expression in B cell progenitors. In contrast, analysis of heterozygous IgH a Δ3’RR /b wt mice indicated that the 3’RR controls μ chain transcripts in mature splenocytes and impacts membrane IgM density without obvious effect on BCR signals (colocalisation with lipid rafts and phosphorylation of Erk and Akt after BCR crosslinking). Deletion of the 3’RR modulates the B cell fate to less marginal zone B cells. In conclusion, the 3’RR is dispensable for pre-BCR expression and necessary for optimal commitments toward the marginal zone B cell fate. These results reinforce the concept of a dual regulation of the IgH locus transcription and accessibility by 5’ elements at immature B cell stages, and by the 3’RR as early as the resting mature B cell stage and then along further activation and differentiation.

By introducing frequent point mutations into the variable regions of immunoglobulin (Ig) genes, somatic hypermutation (SHM, initiated by the AID deaminase) is a driving force for antibody affinity maturation. It is now admitted that AID-induces mutations in germinal centre B cells could affect in parallel to their Ig genes physiological targets, illegitimates targets (including oncogenes) so calles "off targets" (such as Bcl6 with frequent point mutation in B lymphomas). The high risk of "collateral damage" in the B cell genome implies that remodeling events are precisely surveyed. Among cisregulatory elements involved (transcriptional enhancers and chromatin isolators and anchors...), one best candidate is the intronic region including the cEμ enhancer and iths flanking MARsEμ regions that we have been studying extensively using mouse KO model. We recently showed that MARsEμ deletion decreases SHM not only at Ig Heavy chain locus IgH (physiological cis effect) but surprisingly also at the Ig Light chain Kappa locus Ig, located on a different chromosome (trans effect). To extend the study of this intriguing trans effect, we developed a bioinformatic tool called DeMinEr that unveiled that MARsEμ regions were also involved in AID-induced collateral damages to "off-targets". Using FISH 3D, we show that MARsEμ regions harboured the potential not only to locally recruit SHM but also to cause dynamic changes of nuclear structures. The surprising cis and trans effect of MARsEμ deletion, impacting simultaneously nuclear positioning and SHM, revealed an additional level of regulation for targeting mutations to Ig and "off-targets" genes., En introduisant fréquemment des mutations ponctuelles dans les régions variables des gènes d'immunoglobulines (Ig), le processus d'hypermutation somatique (SHM, initié par la déaminase AID) est essentiel pour augmenter l'affinité des anticorps. En marge de ses cibles physiologiques (les gênes d'Ig), AID peut induire des "dommages collatéraux" au niveau de cibles "illégitimes" qui sont appelées "off targets" (dont certains oncogènes, tel que Bcl6 fréquemment muté dans les lymphomes B). Le risque élevé de dommages collatéraux dans le génome des cellules B implique que les remaniements géniques soient précisément surveillés. Parmi les éléments cis-régulateurs impliqués dans cette surveillance, on compte l'activateur cEμ au locus des chaînes lourdes des Ig (IgH) et ses régions flanquantes d'attachement à la matrice nucléaire MARsEμ (étudiés en détails dans nos modèles de souris KO). Nous montrons que la délétion des régions MARsEμ diminue non seulement les mutations au locus des chaines lourdes des Ig (effet physiologique en cis) mais également au locus des chaines légères Ig situé sur un chromosome différent (effet de trans). A l'aide d'une outil bioinformatique (DeMinEr) que nous avons développé dans le but d'identifier des mutations rares, nous montrons également que les régions MARsEμ sont impliquées dans les dommages collatéraux infligés aux "off targets" des cellules B. Grâce à la technique de FISH 3D, nous proposons que les régions MARsEμ participent à la régulation de la SHM en influençant la position des cibles de AID dans le noyau des cellules B. Notre étude met en évidence un niveau de régulation spatiale du processus de SHM médié par les régions MARsEμ du locus IgH.

Immunoglobulin (Ig) gene expression in B cells depends on multiple genetic rearrangements named V(D)J recombination, class switch recombination (CSR) and somatic hypermutation (SHM). These events are controlled by cis-regulatory elements which are, especially numerous within the IgH locus. Major IgH regulatory elements are Eµ composed of a core enhancer flanked by nuclear matrix attachment regions MARsEµ and the regulatory region located at the 3’end of the locus (3’RR), composed of 4 enhancers (hs3a; hs1-2; hs3b; hs4) harbouring a highly conserved quasi-palindromic structure. To study these regulatory regions, we analyzed multiple mice models carrying endogenous deletions of either the entire Eµ region, MARsEµ only or various parts of the 3’RR. These models revealed unsuspected functions for all IgH regulatory regions, at various stages of B cell development. Beyond its role to control accessibility prior DH to JH rearrangements, we identified the window of activity for Eµ region and its particular role on transcription and expression of the µ heavy chain from pre-B to the transitional stages. Indeed, the Eµ enhancer modulates pre-BCR and BCR expression and consequently modulates the mature B cell fate toward marginal zone and follicular compartments. Our study also indicated that the absence of Eµ has no effect on VH segment usage during V to DJ recombination. We also showed that MARsEµ are implicated in the targeting of Ig genes by SHM. The mechanism by which MARsEµ enhances SHM remains to be clarified but we showed that the process does not depend on transcription. Surprisingly MARsEµ also modulates SHM occuring on genes located on different chromosomes: the Ig light chain loci (Igκ) and AID off-targets loci (Bcl6 and Cd83).In a study comparing a new mouse model devoid of the 3’ IgH quasi-palindromic region (hs3a to hs3b) to previous relevant models available in our laboratory (3’RR KO and hs3b-hs4 KO), we identified two complementary functional modules within the 3’RR. The distal module (hs4), which regulates Ig heavy chain expression (and therefore BCR expression) from the immature to mature naïve B cell stages and the proximal module (hs3a to hs3b and its quasi-palindromic structure) required at mature stages for SHM, CSR to most isotypes in activated B cells, and antibody production in plasma cells., L’expression des immunoglobulines (Ig) par les cellules B est dictée par de multiples remaniements géniques appelées recombinaisons V(D)J, commutation de classe (CSR) et hypermutation somatique (SHM). Tous ces événements sont contrôlés par des éléments cis-régulateurs notamment au locus IgH. Les mieux décrits sont la région intronique Eµ et ses régions d’attachement à la matrice nucléaire MARsEµ et la région régulatrice en 3’ du locus IgH (3’RR), constituée de 4 éléments activateurs (hs3a ; hs1,2 ; hs3b ; hs4) et possédant une structure quasi-palindromique très conservée. Afin d’étudier ces régions régulatrices, nous avons analysé plusieurs modèles murins présentant la délétion de la totalité de la région Eµ, des MARsEµ, et de diverses parties de la 3’RR. Ces modèles ont mis au jour des fonctions insoupçonnées de ces régions régulatrices, à divers stades du développement B. Au delà de son rôle régulateur des réarrangements précoces de DH vers JH, nous avons précisé la fenêtre d’action de région Eµ et son rôle sur la transcription et l’expression de la chaîne lourde µ du stade pré-B jusqu’au stade B transitionnel. L’activateur Eµ module en effet l’expression du pré-BCR et du BCR et par conséquent conditionne l’orientation des cellules B matures vers les compartiments de la zone marginale et folliculaire. Notre étude indique également que Eµ n’influence pas le choix des segments VH au cours de la recombinaison VDJ. Nous montrons que les régions MARsEµ, sont impliquées dans le ciblage des gènes d’Ig par l’hypermutation somatique. Le mode d’action de ces régions MARsEµ reste à définir mais nous décrivons qu’il est découplé de la transcription et qu’il affecte également des loci situés sur des chromosomes différents : loci codant les chaînes légères d’Ig (Ig) et loci des cibles illégitimes de AID (Bcl6 et Cd83).Une étude comparant un nouveau modèle murin déficient pour la région quasi-palindromique 3’IgH (de hs3a à hs3b) à deux autres modèles de notre laboratoire (3’RR KO et hs3b-hs4 KO) nous a permis d’identifier deux modules fonctionnels complémentaires dans la région 3’RR. Le module distal (hs4) impliqué dans la régulation de l’expression de la chaîne lourde du stade B immature au stade B naïf et le module proximal (de hs3a à hs3b) nécessaire aux stades matures pour la SHM et la CSR vers la majorité des isotypes après activation, mais également pour la synthèse des anticorps par les plasmocytes.

Class Switch Recombination (CSR) is a key step during the immune response. CSR results in a switch to a more specific Ig isotype in response to a specific antigen. Plasma cells, the ultimate stage of B cell lineage differentiation, will synthesize this Ig. During plasma cell disorders, the production of an abnormal monoclonal Ig can lead to pathogenic situations. The aim of the first part of this study is to determine the minimal requirements for CSR induction with a mouse model in which we inserted a “switch cassette” composed of two transcribed S regions into a kappa locus which is naturally targeted by AID. However, despite efficient transcription and AID targeting of S regions, the “switch cassette” was not sufficient to induce effective CSR. We also developed a mouse model of HCDD (Heavy Chain Deposition Disease) which reproduced typical Randall-type renal lesions due to production of a pathogenic truncated heavy chain. This model demonstrated that the effective response to proteasome inhibitors observed in patients, is the consequence of the presence of a truncated HC that sensitizes plasma cells to this type of therapy through an elevated unfolded protein response (UPR)., La commutation de classe (CSR) est une étape clef de la réponse immunitaire. Ce phénomène va permettre de changer le type d’immunoglobuline (Ig) produite en réponse à un antigène donné. Ces Ig seront ensuite produites par les plasmocytes, qui constituent le stade ultime de la différenciation de la lignée cellulaire B. Lors de dérèglements de la prolifération de ces cellules, certaines Ig monoclonales anormales peuvent être produites et conduire à des situations pathologiques. La première partie de ce travail s’inscrit dans une logique de compréhension des éléments minima requis pour l’établissement de ce phénomène de CSR. Grace à un modèle animal d’insertion dirigée dans le locus kappa murin, naturellement ciblé par l’enzyme AID responsable de ce phénomène, nous avons mis en évidence que la présence de deux régions « switch » transcrites et fortement mutées par AID, n’était pas suffisante pour permettre ce phénomène. Un modèle murin reproduisant une maladie due à une Ig anormale a aussi été établi. Ce modèle de HCDD (Heavy Chain Deposition Disease) nous a permis de mettre en évidence la nécessité de la délétion du CH1 des chaînes lourdes d’Ig pour la génération des dépôts et nous a également permis de montrer que l’efficacité des thérapies à base d’inhibiteur de protéasome observée chez les patients atteint de HCDD, était en partie due à l’Ig pathogène elle-même, qui induit une élévation du stress du réticulum endoplasmique (UPR) au sein des plasmocytes producteurs de ces Ig.