Structure of germ line immunoglobulin alpha heavy-chain RNA and its location on polysomes

sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data

Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline 'sterile' transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built to infer the dynamics and direction of CSR. Applying sciCSR on severe acute respiratory syndrome coronavirus 2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier time point in the collected time-course, the isotype distribution of B cell receptor repertoires of subsequent time points with high accuracy (cosine similarity ~0.9). Using processes specific to B cells, sciCSR identifies transitions that are often missed by conventional RNA velocity analyses and can reveal insights into the dynamics of B cell CSR during immune response.

The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination

Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector component of antibody responses. CSR is initiated by activation-induced cytidine deaminase (AID), which targets transcriptionally active immunoglobulin heavy chain (Igh) switch donor and acceptor DNA. The 3′ Igh super-enhancer, 3′ regulatory region (3′RR), is essential for acceptor region transcription, but how this function is regulated is unknown. Here, we identify the chromatin reader ZMYND8 as an essential regulator of the 3′RR. In B cells, ZMYND8 binds promoters and super-enhancers, including the Igh enhancers. ZMYND8 controls the 3′RR activity by modulating the enhancer transcriptional status. In its absence, there is increased 3′RR polymerase loading and decreased acceptor region transcription and CSR. In addition to CSR, ZMYND8 deficiency impairs somatic hypermutation (SHM) of Igh, which is also dependent on the 3′RR. Thus, ZMYND8 controls Igh diversification in mature B lymphocytes by regulating the activity of the 3′ Igh super-enhancer.

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ZMYND8 is required for GLT of acceptor S regions and Class Switch Recombination

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ZMYND8 supports efficient somatic hypermutation of the Igh variable regions

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ZMYND8 binds B cell super-enhancers, including the 3′ Igh enhancer

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ZMYND8 modulates the transcriptional status and activity of the 3′ Igh enhancer

Long noncoding RNAs: implications for antigen receptor diversification

Noncoding RNAs (ncRNAs), both small and large, have recently risen to prominence as surprisingly versatile regulators of gene expression. In fact, eukaryotic transcriptomes are rife with RNAs that do not code for protein, though the majority of these species remains wholly uncharacterized. The functional diversity among the mere handful of validated ncRNAs hints at the vast regulatory potential of these silent biomolecules. Though the act of noncoding transcription and the resultant ncRNAs do not directly produce proteins, they represent powerful means of gene control. Here we survey the accumulating literature on the myriad functions of long ncRNAs and emphasize one curious case of noncoding transcription at antigen receptor loci in lymphocytes.

Use of chromatin immunoprecipitation (ChIP) to detect transcription factor binding to highly homologous promoters in chromatin isolated from unstimulated and activated primary human B cells

The Chromatin Immunoprecipiation (ChIP) provides a powerful technique for identifying the in vivo association of transcription factors with regulatory elements. However, obtaining meaningful information for promoter interactions is extremely challenging when the promoter is a member of a class of highly homologous elements. Use of PCR primers with small numbers of mutations can limit cross-hybridization with non-targeted sequences and distinguish a pattern of binding for factors with the regulatory element of interest. In this report, we demonstrate the selective in vivo association of NF-κB, p300 and CREB with the human Iγ1 promoter located in the intronic region upstream of the Cγ1 exons in the immunoglobulin heavy chain locus. These methods have the ability to extend ChIP analysis to promoters with a high degree of homology.

Molecular mechanism of class switch recombination: linkage with somatic hypermutation

Class switch recombination (CSR) and somatic hypermutation (SHM) have been considered to be mediated by different molecular mechanisms because both target DNAs and DNA modification products are quite distinct. However, involvement of activation-induced cytidine deaminase (AID) in both CSR and SHM has revealed that the two genetic alteration mechanisms are surprisingly similar. Accumulating data led us to propose the following scenario: AID is likely to be an RNA editing enzyme that modifies an unknown pre-mRNA to generate mRNA encoding a nicking endonuclease specific to the stem-loop structure. Transcription of the S and V regions, which contain palindromic sequences, leads to transient denaturation, forming the stem-loop structure that is cleaved by the AID-regulated endonuclease. Cleaved single-strand tails will be processed by error-prone DNA polymerase-mediated gap-filling or exonuclease-mediated resection. Mismatched bases will be corrected or fixed by mismatch repair enzymes. CSR ends are then ligated by the NHEJ system while SHM nicks are repaired by another ligation system.

The ubiquitously expressed DNA-binding protein late SV40 factor binds Ig switch regions and represses class switching to IgA

Ig heavy chain class switch recombination (CSR) determines the expression of Ig isotypes. The molecular mechanism of CSR and the factors regulating this process have remained elusive. Recombination occurs primarily within switch (S) regions, located upstream of each heavy chain gene (except Cdelta). These repetitive sequences contain consensus DNA-binding sites for the DNA-binding protein late SV40 factor (LSF) (CP2/leader-binding protein-1c). In this study, we demonstrate by EMSA that purified rLSF, as well as LSF within B cell extracts, directly binds both Smu and Salpha sequences. To determine whether LSF is involved in regulating CSR, two different LSF dominant negative variants were stably expressed in the mouse B cell line I.29 mu, which can be induced to switch from IgM to IgA. Overexpression of these dominant negative LSF proteins results in decreased levels of endogenous LSF DNA-binding activity and an increase in cells undergoing CSR. Thus, LSF represses class switching to IgA. In agreement, LSF DNA-binding activity was found to decrease in whole cell extracts from splenic B cells induced to undergo class switching. To elucidate the mechanism of CSR regulation by LSF, the interactions of LSF with proteins involved in chromatin modification were tested in vitro. LSF interacts with both histone deacetylases and the corepressor Sin3A. We propose that LSF represses CSR by histone deacetylation of chromatin within S regions, thereby limiting accessibility to the switch recombination machinery.

IgG2a and igA co-expression by the natural autoantibody-producing murine B lymphoma T560

The T560 B lymphoma produces polyreactive IgG2a with the features of natural autoantibody. All T560 cells bear and secrete IgG2a but a small fraction spontaneously co-express IgA. Cells secreting IgA alone cannot be detected. IgA secretion is enhanced by interaction of T560 cells either with activated T cells and cognate antigen, or with LPS, but not with cytokines, including IL-5 and TGF-beta. IgA and IgG2a mRNAs have identical V186.2. DFL 16 and JH1 sequences from framework 2 through JH1. PCR analysis reveals that previous recombination events have led to deletion of the mu, gamma3, gamma1, gamma2b constant region genes from both the productive and the unproductive chromosome but the former has retained gamma2a, epsilon and alpha, the latter only alpha. Digestion-circularization (DC)-PCR experiments provide formal proof of DNA recombination between Ca and the intron upstream of Cmu. Evidently, the productive chromosome has switched only as far as gamma2a, the unproductive all the way to the alpha constant region gene. The unproductive allele is transcriptionally active as evidenced by the presence of mRNA encoding Calphal inappropriately spliced to a cryptic splice site in the downstream intron of DQ52 (eliminated from the productive chromosome). A specific RT-PCR using oligonucleotide primers derived from the upstream initiation site of the Ialpha exon and from Calpha1 discloses that T560 cells contain alpha-germ line mRNA, presumably transcribed from the Ialpha-region of the productive chromosome, spliced to Calpha. Treatment with LPS stops production of these spliced transcripts suggesting that it may promote either DNA recombination in cells spontaneously transcribing Ialpha or a change in splicing such that Ialpha sequence is no longer joined to Calpha. Verification of the DC-PCR product by sequencing reveals that the T560 and B10.A IgA (Ig2b allotype) hinge is different from the BALB/c IgA (Ig2a allotype) hinge: it has two extra Cys and has eliminated the first Thr, a potential glycosylation site in BALB/c IgA.

CREB/ATF proteins enhance the basal and CD154- and IL-4-induced transcriptional activity of the human Igamma1 proximal promoter

To understand the underlying basis for the strong IL-4- and CD154-mediated Igamma1 promoter activity in Ramos 2G6 B cells, we carried out transient transfection assays with luciferase-based constructs containing approximately 2.2 kb and 500 bp of the human Igamma1 proximal promoter region. As a comparison, the corresponding regions of the human Igamma3 promoter were tested under identical conditions. We found that both Igamma1 and Igamma3 promoter constructs were activated upon transfection into Ramos B cells and that activity was significantly up-regulated by CD154 and IL-4 signals. However, the Igamma1 promoter was measurably stronger than the Igamma3 promoter with respect to both basal and induced responses. Sequence comparison revealed a divergent 36-bp region containing multiple putative transcription factor binding sites in the Igamma1 but not the Igamma3 promoter. A mutational "swap" of this sequence resulted in a marked decrease and increase in Igamma1 and Igamma3 basal and induced promoter activity, respectively. Gel retardation assays with Igamma1-specific probes revealed CREB-containing complexes that were not observed with the corresponding Igamma3 probes. Mutation of a single nucleotide in overlapping CREB sites in the Igamma1 sequence resulted in a significant decrease in basal activity with a corresponding reduction in the level of IL-4- and CD154-mediated transcription.

Ialpha exon-replacement mice synthesize a spliced HPRT-C(alpha) transcript which may explain their ability to switch to IgA. Inhibition of switching to IgG in these mice

Antibody class switching is regulated by transcription of unrearranged C(H) genes to produce germline (GL) transcripts which direct the choice of isotype and are required for switching. However, their role is unknown. GL transcripts are initiated at the I exons located upstream of each switch region. Although deletion of the I exon by gene targeting prevents switch recombination to that CH gene, the Ialpha exon can be replaced by an entirely different DNA segment, a minigene driven by the phosphoglycerate kinase (PGK) promoter and encoding hypoxanthine phosphoribosyl transferase (HPRT), oriented in the sense direction, without reducing antibody class switching to IgA. To understand why HPRT substitution of the Ialpha exon does not disrupt switch recombination, we have analyzed the structure of the transcript from the targeted allele in these mice. We identify a spliced transcript in which the HPRT exons are spliced to the C(alpha) gene segments, resulting in a structure similar to normal GL transcripts. The abundance of this transcript is similar to that of the normal alpha GL RNA. We also demonstrate that switching to the four IgG subclasses in B cells from these mice is reduced in comparison to wild-type mice. We discuss the possibility that the strong PGK promoter inserted at the Ig alpha locus may interfere with interaction of the promoters for gamma GL transcripts with the 3' IgH enhancer.

Somatic mutations in the Ig variable region genes and expression of novel Cmu-germline transcripts in a B-lymphoma cell line ("Farage") not producing Ig polypeptide chains

Non-Hodgkin's B-lymphomas (B-NHL) are a very heterogeneous group of B-cell neoplasias originating from the germinal centers of lymphatic follicles. Thus, they represent a suitable experimental model to study the molecular basis of certain key events which take place in the lymphatic follicles, including somatic hypermutation and heavy chain isotypic switch. An unusual B-NHL cell line ("Farage") not producing Ig polypeptide chains was previously shown to rearrange its IgH and Igkappa genes and transcribe seemingly normal size mu and kappa mRNAs. In an attempt to characterize the phenotype of Farage cells better and to elucidate the molecular basis of the failure of Farage cells to synthesize Ig chains, we sequenced its VH and Vkappa rearranged gene segments by PCR and RT-PCR. It was found that both V genes are somatically, heavily mutated compared to their germline counterparts. In addition, this rearranged VDJ gene of the heavy chain is not transcribed. Instead, the Farage cells express a low level of a new family of germline transcripts starting with a VH like sequence, continuing with a small segment of the 3'VH germline flanking region, and ending within the Cmu region. These transcripts lack D and J segments and do not contain the open reading frame of the full-length Cmu protein. Thus, Farage cells fail to produce mu heavy chains due to silencing of the expression of the conventional VDJCmu transcript and expression of unusual Cmu-germline transcripts. In contrast to the IgH genes, the rearranged VJ gene of Farage is transcribed and gives rise to a full-size kappa-mRNA. This transcript, however, is not translated to a full-length kappa-chain, as it contains a stop codon in its coding region. All the above show that Farage cells are unable to produce Ig polypeptide chains, due to somatic mutations altering the kappa-chain gene, and mutations and/or regulatory events that shutoff the transcription of the IgH gene. The heavily mutated Vkappa and Vkappa genes found, support the conclusion that the Farage cell line originated either from germinal center cells or from the mantle zone of the lymphoid follicle.

Structural analysis of human gamma 3 intervening regions and switch regions: implication for the low frequency of switching in IgG3-deficient patients

High and low serum concentrations of IgG3 are associated with the human G3m(b) and G3m(g) allotypes, respectively. In the present study, we analyzed the structure of the S gamma 3 and I gamma 3, the switch frequency, switch breakpoints and the levels and initiation sites of I gamma 3 transcripts both in normal blood donors expressing (b) or (g) allotypes as well as IgG3-deficient (D) patients. A low switch frequency to gamma 3 was found in the (g) allotype IgG3D patients which may be caused in part by the allotype-associated mutations in the S gamma 3 region and in part by additional individual mutations observed in the A (SNAP) and B (SNIP/ NF-kappa B) sites in the S gamma 3 repeat region. A higher I gamma 3 germ-line (GL) transcriptional rate was seen in cells from the IgG3D patient, suggesting that low levels of GL I gamma 3 transcripts are not a major contributing factor to the defect. However, individual mutations in the I gamma 3 region and differential splicing of GL I gamma 3 transcripts were found which may affect the switching process.

Involvement of the E2A basic helix-loop-helix protein in immunoglobulin heavy chain class switching

The basic helix-loop-helix (bHLH) transcriptional factor E2A has previously been shown to play a critical role in early B cell development, with E2A knockout mice and Id1 transgenic mice showing an arrest at the pro-B cell stage of development. More recent data suggest that E2A, through an interaction with the immunoglobulin heavy chain 3' enhancer, might also regulate later events in B cell development such as heavy chain class switching. The patterns of E2A protein expression in secondary lymphoid tissues support a role in later stages of B cell maturation. In particular, immunostaining reveals upregulation of E2A protein in cells of the dark zone of the germinal center, the site of immunoglobulin heavy chain class switching. To examine the role of E2A in class switching, the inhibitory HLH protein Id1 was expressed in B cell lines which normally undergo spontaneous and inducible switching from IgM to IgA. The forced expression of Id1 in these cell lines effectively blocked class switching. This Id1 blockade of class switching did not occur via downregulation of immunoglobulin heavy chain germline transcription or through inhibition of cell cycling. Furthermore, Id1 inhibited spontaneous and, to a lesser degree, cytokine inducible class switching. From these data, we conclude that E2A plays an important role in the class switching process.

Molecular characterization of an unusual non-Hodgkin's B-lymphoma cell line ("Farage") lacking the ability to produce immunoglobulin polypeptide chains

"Farage" is a cell line derived from a patient who had a diffuse and mixed type malignant lymphoma. In a previous study it was shown that Farage cells expressed B-cell markers, but not membrane IgM. Karyotypic analysis showed that in contrast to most follicular cell lymphomas, Farage did not have the 14;18 chromosomal translocation. In the present work Farage was further characterized by Southern and Northern blot analyses. Two rearranged heavy chain alleles and one rearranged kappa chain gene were detected. The cells expressed both mu and kappa mRNA, even though at a 3-7 fold lower level than that found in the control Daudi and DG-75 Burkitt lymphomas. Farage cells did not express the terminal deoxynucleotydyl transferase gene (TdT), nor the recombination activating genes RAG-1 and RAG-2, known as markers of the pre-B cell stage. These results show that Farage represents a mature B-cell rather than a pre-B cell. Despite the presence of C kappa and C mu RNAs, no Ig polypeptide chains were produced by Farage as judged by immunoblotting and biosynthesis labeling assays. Ig mRNAs were detected on the polysomal fraction, but at a lower level relative to Daudi cells. Our combined results suggest that in Farage cells translation of Ig mRNA is not fully blocked at the stage of translation initiation. Farage cells may express "germline" or mutated variants of Ig mRNAs. The unusual phenotype of Farage may reflect a normal as yet unknown stage of B-cell differentiation, or it may be due to an aberrant expression developed after malignant transformation.

Translatable immunoglobulin germ-line transcript

During B cell differentiation, the functional genes encoding immunoglobulin (Ig) heavy (H) and light (L) chains are generated by two rearrangement processes--VDJ rearrangement generates the exon encoding the Ig variable (V) regions, and the class switch reconstructs a rearranged IgH gene by exchanging the segment encoding the constant (C) region, which determines the Ig class. Both types of rearrangement are preceded by transcripts originating from a transcriptional start site 5' of the I exon, which is then spliced to the C exons. These germ-line transcripts, which are thought to be necessary for the initiation of both types of rearrangement, are said to be sterile. We demonstrate here that the mu germ-line transcript is translatable into a polypeptide chain, to which we assign the symbol psi. Thus, protein products of these transcripts might be part of or signal to the recombinases that catalyze Ig gene rearrangement.

Germ-line human epsilon heavy chain gene RNA transcripts utilize the full range of alternative 3' splicing seen in productive epsilon mRNA

An early step in immunoglobulin isotype switching involves the initiation of active transcription of downstream heavy chain loci while they are still in germ-line configuration. This results in the production of 'sterile' germ-line RNA transcripts that do not contain VDJ sequences, the role of which in isotype switching is under intense scrutiny. We investigated whether such human epsilon germ-line transcripts employ the full complement of complex alternative 3' RNA splicing, splicing we have recently reported occurring with productive epsilon mRNA transcripts. Using a reverse transcriptase polymerase chain reaction (RT-PCR) strategy, in which the 5' primer was located in the I region of the epsilon gene, a region expressed in germ-line but not productive (VDJ containing) epsilon transcripts, we showed that the full range of alternative 3' epsilon splices occur with germ-line transcripts. These results demonstrate that epsilon 3' splicing events are independent of 5' isotype DNA switching. Additionally, we showed that, just as with mature epsilon mRNA, the relative production of the various epsilon germ-line mRNA isoforms was responsive to modulation by stimuli such as interleukin-10 (IL-10). Thus B cells, when stimulated to produce epsilon germ-line transcripts, generate a family of germ-line mRNA that differ not only in their initiation sites but, more importantly, also differ in their 3' sequences, sequences that could be important in regulation of the parent gene itself. Furthermore, by discontinuous or trans-splicing, cells could utilize these various epsilon germ-line transcripts to produce the full range of mature IgE proteins prior to undergoing deletional recombination of isotype switching.

Alternatively spliced, germline J alpha 11-2-C alpha mRNAs are the predominant T cell receptor alpha transcripts in mouse kidney

We recently reported the expression of a truncated T cell receptor (TCR) alpha mRNA in kidney and brain of normal mice. In the kidney, the truncated TCR alpha transcript was expressed by bone marrow-dependent, non-T large interstitial cells located predominantly in the medulla. Here, we report the molecular characterization of the truncated TCR alpha transcript from kidney. Using a modified anchored-PCR (A-PCR) technique and directional cloning, 37 cDNA clones extending 5' of the C alpha region were generated. cDNA sequencing showed that 29 of the clones (78%) originated in the J alpha 11-2 region. Of these clones, 17 started upstream or in the J alpha 11-2 exon and contained the entire J alpha 11-2 sequence correctly spliced to the first C alpha exon. Analysis of the sequence revealed the presence of multiple stop codons in all three reading frames. The other 12 clones originated further upstream of the J alpha 11-2 exon and did not include the J alpha 11-2 exon, but rather arose from the joining of a cryptic splice donor signal to the usual TCR alpha C splice acceptor. This alternatively spliced transcript contained an open reading frame extending from the upstream J alpha 11-2 region to 82 nucleotides downstream of the beginning of the TCR C alpha region, and potentially encoded a 36 amino acid polypeptide. The remaining eight clones all contained the J alpha TA61 region correctly spliced to C alpha with two of these extending upstream of the J alpha TA61 exon. The predominance of J alpha 11-2-C alpha containing clones was confirmed by RNase protection assay using total RNA from kidney and spleen of scid mice. The 3' region of the transcript contained a fully conserved, correctly spliced TCR alpha C region which was polyadenylated at the 3' end. The truncated TCR alpha mRNA could be detected in preparations of cytoplasmic RNA, indicating that this transcript follows a normal RNA processing pathway. Our results demonstrate that the truncated TCR alpha mRNA expressed in normal mouse kidney is a germline J-C transcript resulting from transcription initiated predominantly upstream of the J alpha 11-2 region. This germline transcript in the kidney is undergoing alternative splicing leading to the appearance of an open reading frame coding for a short polypeptide. These results suggest that the product of this transcript may be functionally relevant.

DNA binding sites 5' of the IgG1 switch region comprising IL4 inducibility and B cell specificity

Immunoglobulin class switch recombination is directed to the same switch region on both chromosomes of a B cell by an as yet unknown mechanism. The cytokine interleukin 4 (IL4) targets recombination in activated B lymphocytes to the gamma 1 switch region (s gamma 1). Here we report two DNA-binding-proteins which bind to a sequence 5' of s gamma 1. One protein is B cell specific, while binding of the other one is induced by IL4. These two proteins bind to a region 700 bp upstream of the putative promoter region of the gamma 1 germline transcripts and may be involved in the process of recombination and/or transcription.

Structure and expression of mouse germline immunoglobulin gamma 3 heavy chain transcripts induced by the mitogen lipopolysaccharide

Germline immunoglobulin heavy chain gene transcription is though to direct isotype switching by modulating the accessibility of specific switch regions to a recombinase. In this study, cloned cDNA copies of mouse germline Igh-8 RNAs have been used to characterize the Igh-8 transcription unit. The 5' end of these transcripts are derived from an exon denoted Ig3, located 1 kilobase 5' of the Igh-8 switch region. Sequence analysis of cDNA and genomic clones reveals that these RNAs are noncoding. In splenic B cell cultures treated with lipopolysaccharide (LPS), germline Igh-8 transcript levels are upregulated after 8 h due to increased transcription. This induction is consistent with the identification of a putative binding site for the LPS inducible transcription factor NF-kappa B approximately 150 nucleotides upstream of the sites of transcript initiation. Furthermore, nucleotide sequence comparisons reveal that the region encompassing the site of germline Igh-8 transcription initiation is highly homologous to part of the Ig2b exon, and is also conserved upstream of the Igh-1 switch region. The implications of these findings for the control of germline Igh-8 transcription is discussed.

Early occurrence of immunoglobulin isotype switching in human fetal liver

A cDNA library prepared from a human fetal liver of the first trimester of gestation was screened with Ig C mu, C gamma, C kappa and C lambda probes. Ten heavy chain clones were isolated and characterized by restriction mapping and partial sequencing. The absence of Ig light chain clone and the presence of pre-B-specific lambda-like transcripts suggest that the immune compartment of this cDNA library was mostly derived from pre-B cells. Three transcripts of mu, gamma 2 and gamma 4 isotypes contained a V-D-J-C region with an open reading frame and used members of the VHIV, VHIII and VHI families, respectively. Seven clones were derived from sterile transcripts, one C mu and six C gamma. In addition to C mu exons, the sterile mu transcript contained the 5' flanking germline region. By contrast, the gamma sterile transcripts used a 5' sequence that was spliced from the I gamma 1 region onto the first C gamma 1 exon. In addition several of these transcripts were derived from alternative splicing. The simultaneous expression of both sterile and functional gamma transcripts suggests that the switch mechanism operates in normal fetal liver very early in ontogeny.

Expression of a novel type of immunoglobulin C lambda transcripts in human mature B lymphocytes producing kappa light chains

Ordered rearrangement of immunoglobulin genes (heavy chain then kappa and eventually lambda genes) is observed during B lymphocyte ontogeny. Unexpectedly, we found that human mature B cells producing kappa chains and having germ-line lambda genes contain lambda mRNA consisting of an invariant 5' region (herein termed X) and of one of the classical C lambda exons. The X region of these transcripts originates from a unique exon located 5 kb upstream of the J-C lambda 1 gene segment. X-C lambda mRNA expression occurs without somatic DNA rearrangement. The use of the X DNA fragment as a probe allows definition of a family of human genes that comprises at least four members and includes the first exon of the lambda 14.1 gene. The latter is selectively transcribed in pre-B lymphocytes and directs the synthesis of a lambda-like chain. In contrast, the X-C lambda transcripts do not appear to encode a C lambda-related polypeptide in mature B cells. Thus, despite a 73% homology extending far beyond the exon sequences, the X and lambda 14.1 genes are expressed at different stages of B cell development and might serve different functions.

Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region

A deletion DNA rearrangement is associated with immunoglobulin class switching from IgM to IgG, IgA or IgE This recombination occurs in immunoglobulin switch regions, which are complex, highly repetitive regions of DNA. As switch regions become transcriptionally active just before switch recombination, analysis of the behaviour of these sequences during transcription could elucidate the mechanism of switch recombination. Here, we report that transcription of a supercoiled plasmid containing the murine IgA switch region (S alpha) leads to a loss of superhelical turns. The resulting series of less supercoiled plasmids is stabilized by RNA-DNA hybrids formed by the nascent RNA transcripts, which remain base-paired with their DNA templates.

Induction of germ-line immunoglobulin heavy chain transcripts by mitogens and interleukins prior to switch recombination

It has recently been postulated that immunoglobulin class switching is preceded by transcription from unrearranged heavy chain genes. In this report, we have investigated the conditions under which RNA transcribed from unrearranged C gamma 3, C gamma 1, C gamma 2b, C gamma 2a, C epsilon and C alpha genes are induced in normal spleen cells by mitogens and/or interleukin (IL) 4, IL 5 and interferon-gamma. Lipopolysaccharide (LPS) plus IL 4 induced germ-line gamma 1 and epsilon transcripts. LPS induced gamma 2b and gamma 3 transcripts and high doses of IL 4 suppressed these LPS-induced transcripts. Interferon-gamma induced low levels of germ-line gamma 2a transcripts and profoundly suppressed the gamma 1 and epsilon transcripts induced by LPS and IL 4. IL 5 alone or in combination with IL 4 and/or LPS did not induce germ-line alpha transcripts. Spleen cells of the partially immunodeficient mice CBA/N and C3H/HeJ, which do not express IgG3 could be induced, however, by polyclonal activators to express germ-line gamma 3 and gamma 2b transcripts. The data indicate that the capacity of a ligand to induce/suppress transcription of a particular unrearranged heavy chain gene is a good indicator of its capacity to induce switching to the corresponding Ig isotype. However, it is also clear that control of switching can be carried out at other levels.