Immunoglobulin heavy chain genes: demethylation accompanies class switching

Developmental regulation of DNA cytosine methylation at the immunoglobulin heavy chain constant locus

DNA cytosine methylation is involved in the regulation of gene expression during development and its deregulation is often associated with disease. Mammalian genomes are predominantly methylated at CpG dinucleotides. Unmethylated CpGs are often associated with active regulatory sequences while methylated CpGs are often linked to transcriptional silencing. Previous studies on CpG methylation led to the notion that transcription initiation is more sensitive to CpG methylation than transcriptional elongation. The immunoglobulin heavy chain (IgH) constant locus comprises multiple inducible constant genes and is expressed exclusively in B lymphocytes. The developmental B cell stage at which methylation patterns of the IgH constant genes are established, and the role of CpG methylation in their expression, are unknown. Here, we find that methylation patterns at most cis-acting elements of the IgH constant genes are established and maintained independently of B cell activation or promoter activity. Moreover, one of the promoters, but not the enhancers, is hypomethylated in sperm and early embryonic cells, and is targeted by different demethylation pathways, including AID, UNG, and ATM pathways. Combined, the data suggest that, rather than being prominently involved in the regulation of the IgH constant locus expression, DNA methylation may primarily contribute to its epigenetic pre-marking.

Somatic hypermutation of immunoglobulin kappa transgenes: association of mutability with demethylation

Following antigen encounter, immunoglobulin genes are diversified by somatic hypermutation. The mechanism by which this mutational process preferentially targets immunoglobulin genes is not known, but is likely linked to transcription. However, transcription is not sufficient to ensure mutability. Here, by polymerase chain reaction amplification of bisulfite-modified DNA, the pattern of demethylation within the Igkappa mutation domain is analysed and transgenes are used to identify an association between demethylation and mutability. In mice carrying an Igkappa transgene that is well transcribed but only poorly targeted for hypermutation, the mutated transgene copies have been demethylated within the mutation domain, whereas the methylated copies remain unmutated. Thus, the hypermutation mechanism only acts on immunoglobulin gene targets that are demethylated as well as transcribed, although transcription and demethylation do not themselves guarantee mutability.

A submicroscopic interstitial deletion of chromosome 14 frequently occurs adjacent to the t(14;18) translocation breakpoint in human follicular lymphoma

The t(14;18) chromosomal translocation characteristic of follicular lymphoma (FL) juxtaposes the immunoglobulin heavy chain locus (IGH) and the BCL2 proto-oncogene. The translocation can be readily detected as a non-germline Notl fragment resolved by pulsed-field gel electrophoresis. A benefit of this approach is that it enables examination of the structure of a large region (+/- 300 kb) surrounding the chromosomal breakpoint. In 40/46 cases the observed translocated Notl fragment was smaller than the 680-690 kb expected from published restriction maps of the involved loci suggesting a deletion in the region of the breakpoint. Analysis of the der(14) allele by molecular hybridization demonstrated that in 35/46 cases the mu constant region (C mu) was deleted. Further molecular dissection of the IGH locus demonstrated that this resulted from an interstitial deletion of the der(14) chromosome within the region defined by the mu switch region (S mu) on the 5' side and the epsilon constant region (C epsilon) on the 3' end. Thus, the deletion resembled a class switch (CS) recombination event. Surprisingly, the CS deletion was as common in FL which was sIGM positive (24/33, 72.7%) as in cases where the productive allele had already undergone CS deletion (11/13, 84.6%) suggesting that the observed non-physiologic CS deletion resulted from a cis effect of the chromosomal translocation. Similar interstitial deletions of the non-productive IGH allele were not seen in B cell lymphocytic lymphomas which do not have the t(14;18) translocation. Mapping of the 3' extent of the deletion by an isotype PCR assay demonstrated frequent involvement (11/12 cases) of the gamma 1 constant region (C gamma 1). Analysis of cases in which the deletion was not evident by Southern blotting but detectable by PCR suggested that the CS deletion had occurred in a small subpopulation of FL cells subsequent to the t(14;18) translocation. The biological role of frequent interstitial deletions of the der(14) chromosome in t(14;18)-carrying lymphomas remains to be elucidated.

Protective methylation of immunoglobulin and T cell receptor (TcR) gene loci prior to induction of class switch and TcR recombination

Methylation of the S gamma 1 switch region and C gamma 1 constant region gene from the immunoglobulin heavy chain locus and of the J beta 2 and C beta regions from the T cell receptor beta chain (TcR beta) locus is compared here in murine germ-line cells, nonlymphoid cells and lymphocytes. In germ-line cells and in lymphocytes prior to recombination all four regions show strong methylation, i.e. most Msp I sites are methylated. After activation of lymphocytes, demethylation is observed for those regions which are activated for recombination, at specific sites 5' of S gamma 1 in B cells activated with bacterial lipopolysaccharide and interleukin 4, and for J beta 2 in thymocytes. In nonlymphoid cells, where these regions cannot be used for recombination, considerable demethylation is observed for all four regions analyzed as compared to lymphocytes. The result implies an important role for methylation of recombinatorial regions. Methylation may be involved in protecting them from uninduced recombination, thus allowing regulated expression of distinct genes in lymphocyte ontogeny.

Strong transcriptional activation of translocated c-myc genes occurs without a strong nearby enhancer or promoter

We have studied the transcriptional activation of translocated c-myc genes in murine plasmacytomas in which the translocation juncture occurs within the first intron of c-myc and juxtaposes c-myc with the immunoglobulin C alpha gene segment. It has been widely suggested that a novel transcriptional enhancer element located near the C alpha gene segment might activate the translocated c-myc gene. We have carried out an extensive search for such an element and find no significant transcriptional enhancer activity in a 22 kb region encompassing the translocation junction, C alpha gene segment and regions 3' of C alpha. We also find that the cryptic promoter region of the translocated c-myc gene is a very weak promoter of transcription. Despite this evidence against the presence of strong transcriptional regulatory elements, the translocated c-myc gene locus is transcribed at high rates that are 25-greater than 100% of that measured for the highly active immunoglobulin genes in murine plasmacytomas. These data suggest the presence of a novel type of strong activator of transcription in the murine heavy chain locus.

Specificity of immunoglobulin heavy chain switch correlates with activity of germline heavy chain genes prior to switching

IgM+ cells cultured from the I.29 B cell lymphoma can be induced with lipopolysaccharide (LPS) or, to a greater extent, with LPS plus anti-idiotype antibody to switch to IgG2a, IgE or IgA expression. The isotype switch is accompanied by rearrangement of immunoglobulin (Ig) heavy (H) chain genes. Here we demonstrate that the commitment of the I.29 IgM+ cells to switch to IgA appears to be manifested by hypomethylation of the alpha constant region genes in IgM+ cells, and by the presence of small amounts of RNAs transcribed from non-rearranged alpha gene(s) in IgM+ cells. The commitment to switch to IgE or IgG2a is also in accord with the presence of small amounts of RNA transcripts from the non-rearranged epsilon and gamma 2a genes, although the hypomethylation of the epsilon and gamma 2a genes is not as dramatic as that of the alpha genes. These results suggest that I.29 cells switch specifically to IgA, IgE or IgG2a due to the activation of the corresponding H chain constant region genes in IgM+ cells prior to the actual switch recombination event.

Specific 5' and 3' regions of the mu-chain gene are undermethylated at distinct stages of B-cell differentiation

The mu-chain gene is expressed differently in successive stages of B-lymphocyte development. The heavy chain product appears as a cytoplasmic constituent in pre-B-cells, as part of the IgM receptor in maturing B cells, and as a component in the pentamer IgM antibody synthesized and secreted by the antigen-stimulated cell. We have used the methylation of CpG sequences as an assay system to define the chromatin changes associated with different expression of the mu-chain. The methylation status of eight index sites was followed by restriction enzyme analysis of murine cell lines representing the major stages in the developmental pathway. The analyses showed that a single Msp I/Hpa II site 5' to the immunoglobulin enhancer becomes undermethylated with the onset of mu-chain gene transcription. Four midgene Msp I/Hpa II sites exhibit a progressive loss of methyl groups unrelated to changes in mu-chain gene expression, whereas a Msp I/Hpa II site and two Hha I sites surrounding the exon encoding the carboxyl terminus of the secreted form of mu chain (mus) become undermethylated during the transition to IgM secretion. These results indicate that structural changes in local regions of the mu-chain gene correlate with specific developmental events.

Growth conditions of F9 embryonal carcinoma cells affect the degree of DNA methylation

We have investigated differences in C pG methylation between F9 embryonal carcinoma cells in vitro and as tumor cells grown in vivo using Msp I and Hpa II restriction isoschizomers. Southerns were hybridized with two low copy number probes, mouse major beta-globin (f7) and a class I, histocompatibility-2 cDNA clone (pH-2d-4). In each case, the tumor-DNA was hypomethylated while the DNA from F9 cells grown in vitro was moderately methylated. We conclude that growth conditions or cell-cell interactions can greatly affect methylation of C pG sites.

The methylation state of 2 muscle-specific genes: restriction enzyme analysis did not detect a correlation with expression

To examine the possible role of DNA methylation in the modulation of expression of genes involved in the differentiation of muscle cells, we compared the methylation state of a number of CpG sites in the rat skeletal muscle actin and myosin light chain 2 genes, in muscle and nonmuscle cells, and in proliferating myoblasts and differentiated myotubes of the myogenic cell line L8. No correlation was detected between the state of methylation of these sites and the expression of the two genes. Essentially the same pattern of DNA methylation was observed, in the sites examined, in DNA from muscle, kidney and stomach. In DNA extracted from cultures of proliferating mononucleated myoblasts, as well as from differentiated multinucleated fibers of the myogenic cell line L8, the two genes were more methylated than in other tissues.

Is there a higher level genetic code that directs evolution?

Because the genetic code is redundant for most amino acids, different codons can be used in a given position without altering the structure of the protein for which the gene codes. This flexibility permits information encoding structural, and therefore functional, properties of RNA and DNA to be transmitted simultaneously by a protein-coding sequence of DNA. Among the other messages that might be transmitted, it is proposed, is one modulating the evolution of the DNA itself.

Genomic sequencing

Unique DNA sequences can be determined directly from mouse genomic DNA. A denaturing gel separates by size mixtures of unlabeled DNA fragments from complete restriction and partial chemical cleavages of the entire genome. These lanes of DNA are transferred and UV-crosslinked to nylon membranes. Hybridization with a short 32P-labeled single-stranded probe produces the image of a DNA sequence "ladder" extending from the 3' or 5' end of one restriction site in the genome. Numerous different sequences can be obtained from a single membrane by reprobing. Each band in these sequences represents 3 fg of DNA complementary to the probe. Sequence data from mouse immunoglobulin heavy chain genes from several cell types are presented. The genomic sequencing procedures are applicable to the analysis of genetic polymorphisms, DNA methylation at deoxycytidines, and nucleic acid-protein interactions at single nucleotide resolution.

Albumin extinction without methylation of its gene

In earlier work we identified at the 5' end of the rat albumin gene an Msp I site whose undermethylation appears to be necessary but not sufficient for stable expression of the gene in rat hepatoma cells. Here, we ask whether the block to expression of albumin production, which occurs when rat hepatoma cells are hybridized with cells that do not produce the protein, could be the result of de novo methylation of this site. In two types of somatic hybrids, rat hepatoma-mouse L cell fibroblasts, and rat hepatoma-dedifferentiated variant rat hepatoma cells, extinction occurs and is maintained during the first 5-15 generations after fusion. During this time the Msp I site of the now inactive rat albumin gene remained unmethylated.

Expression of an immunoglobulin heavy chain gene transfected into lymphocytes

We determined that mouse lymphoid cell lines can be transfected at high efficiencies (10-70%) by a polyoma virus shuttle vector. With this vector, we obtained expression of a cloned mouse alpha heavy chain gene transfected into cell lines representative of all stages in B-lymphocyte development, a T-cell lymphoma line, and 3T3 fibroblasts. Heavy chain gene expression in transfected light chain-producing myeloma cells occurred at levels comparable to those in IgA-secreting myeloma cells. Heavy chains produced in transfected myeloma cells were associated with light chains in membrane-bound IgA. While T-lymphoma cells and fibroblasts were transfected at similar efficiencies to B cells, significantly lower levels of alpha heavy chains were produced. This immunoglobulin gene transfection system provides a powerful approach for defining important regulatory regions in immunoglobulin genes and for identifying lymphoid cell factors involved in immunoglobulin gene expression in B-lymphocyte development.

Differential expression of porcine major histocompatibility DNA sequences introduced into mouse L cells

The expression of a porcine genomic DNA segment containing a major histocompatibility gene and its chromatin structure in mouse L cells have been investigated. The transformed cells, which contain about two copies of the 17.8-kilobase pig DNA insert per haploid genome, stably and uniformly express major histocompatibility antigen on their surfaces. This expression is the result of differential transcription of the 3-kilobase major histocompatibility gene; the other 14 kilobases of pig sequences flanking the coding sequence are not transcribed. Although the entire pig DNA segment is packaged into nucleosomes, only the transcriptionally active DNA sequences are packaged in a DNase I-sensitive conformation. These results suggest that the expression of this foreign DNA is actively regulated in L cells.

The molecular biology of immunoglobulin D

Immunoglobulin D (IgD) is co-expressed with immunoglobulin M (IgM) on the membranes of most B cells, yet its biological function has remained a mystery. Recent detailed information on the structure and transcription of the unusual IgD heavy chain (delta) gene in mouse suggests a complex genetic control. A model is presented for the developmental regulation of IgM and IgD and roles suggested for the membrane and secreted forms of IgD in the immune network.

Unusual sequences in the murine immunoglobulin mu-delta heavy-chain region

The delta heavy (H) chain of mouse immunoglobulin D (IgD) is unusual both in its structure and in its differential expression relative to immunoglobulin M (IgM; reviewed in ref. 1). The region of DNA between IgM and IgD H-chain constant-region genes is probably implicated in this control. So far only fragments of the area have been sequenced. Now, however, we present the complete sequence as well as the sequence of the introns of the C delta gene. We have found several interesting features (Fig. 1), including an open reading frame (ORF) between Cmu and C delta which encodes 146 amino acids that might represent a previously unsuspected domain-like protein; three blocks of simple repetitive sequences; a 162-base pair (bp) unique-sequence inverted repeat; and a domain-like pseudogene in the large intron of C delta. We have not found, however, any sequence 5' of C delta resembling the switch (S) recombination sequences associated with class switching in other heavy chains. Moreover, we have determined the 3' deletion end point of an IgD-producing myeloma and find no sequences reminiscent of switch sites nearby.

Methylation of unique sequence DNA during spermatogenesis in mice

In order to study whether changes in methylation of unique sequence DNA were related to meiosis, DNA was purified from F9 embryonal carcinoma (a "primordial germ cell" equivalent), germ cells from immature testes (containing germ cells up to early spermatocytes), sperm, and appropriate somatic tissues. Restriction was performed with the isoschizomers Msp I and Hpa II, and Eco RI as a control. Electrophoresis and Southern transfers were followed by hybridization to a mouse major beta-globin clone (f7), a mouse pancreatic amylase clone (pMPa21), a type I, histocompatibility-2 clone (pH-2D-4), and a spermatid cDNA clone (pPM 459). The variably methylated sites were all hypomethylated in the embryonal carcinoma DNA and hypermethylated in DNA from immature testes and sperm, irrespective of the transcription state of the gene. The pattern in control tissues generally conformed to an inverse correlation of methylation with transcription. These results suggest that hypermethylation of sperm DNA persists from hypermethylation of these sequences early in testicular development, independent of gene expression.

Methylation patterns of immunoglobulin genes in lymphoid cells: correlation of expression and differentiation with undermethylation

Different states of eukaryotic gene expression are often correlated with different levels of methylation of DNA sequences containing structural genes and their flanking regions. To assess the potential role of DNA methylation in the expression of immunoglobulin genes, which require complex rearrangements prior to expression, methylation patterns were examined in cell lines representing different stages of lymphocyte maturation. Methylation of the second cytosine in the sequence 5' C-C-G-G 3' was determined by using Hpa II/Msp I endonuclease digestion. Four CH genes (C mu, C delta, C gamma 2b, and C alpha), C kappa, V kappa, C lambda, and V lambda genes were analyzed. The results lead to the following conclusions: (i) transcribed immunoglobulin genes are undermethylated; (ii) the C gene allelic to an expressed C gene is always also undermethylated; and (iii) all immunoglobulin loci tend to become increasingly undermethylated as B cells mature.

Differential expression of porcine major histocompatibility DNA sequences introduced into mouse L cells

The expression of a porcine genomic DNA segment containing a major histocompatibility gene and its chromatin structure in mouse L cells have been investigated. The transformed cells, which contain about two copies of the 17.8-kilobase pig DNA insert per haploid genome, stably and uniformly express major histocompatibility antigen on their surfaces. This expression is the result of differential transcription of the 3-kilobase major histocompatibility gene; the other 14 kilobases of pig sequences flanking the coding sequence are not transcribed. Although the entire pig DNA segment is packaged into nucleosomes, only the transcriptionally active DNA sequences are packaged in a DNase I-sensitive conformation. These results suggest that the expression of this foreign DNA is actively regulated in L cells.

Methylation status and DNase I sensitivity of immunoglobulin genes: changes associated with rearrangement

Immunoglobulin V kappa genes are transcriptionally silent in their germline context and become transcriptionally active upon fusion to the J kappa-C kappa region (kappa locus). To elucidate the role of chromosomal structure in this regulatory phenomenon we have investigated the DNase I sensitivity and methylation status of the kappa locus and selected V kappa genes in a variety of alleles exhibiting different rearrangement configurations and different levels of transcriptional activity. Our findings indicate that the kappa locus in either germline or rearranged contexts maintains a distinctive DNase I-sensitive, hypomethylated structure in plasmacytomas and hybridomas, irrespective of its level of transcriptional activity. In contrast, the germline V kappa genes are in less accessible regions of chromatin and more highly methylated regions of DNA. Upon fusion to the kappa locus, V kappa genes become DNase I-sensitive and hypomethylated. This effect extends several kilobases upstream of the transcriptional initiation site but does not extend to the adjacent V kappa gene or to the identical V kappa allele on the other chromosome, indicating that the structural alteration is a localized cis-acting phenomenon.

Changes in methylation pattern of albumin and alpha-fetoprotein genes in developing rat liver and neoplasia

To determine whether methylation changes in specific DNA sequences of the albumin and AFP genes are implicated in the modulation of transcriptional activity during rat liver development and neoplasia we have analysed the methylation pattern of C-C-G-G sequences within these genes in DNA isolated from fetal and adult hepatocytes, from adult kidney and from a clonal hepatoma cell line which produces AFP but no albumin. We have assayed for methylation of the internal cytosine of this sequence by using the restriction enzyme isoschizomers HpaII and MspI. 32P-labelled cloned cDNA probes were used to reveal the albumin and AFP gene containing fragments. Genomic subclones of the albumin gene were also utilized as molecular probes to measure quantitatively the level of methylation of 6 specific sites within the albumin gene in the different DNA samples. The results indicate that methylation changes at the sites analysed are not responsible for the changes in gene activity during rat liver development. Further they demonstrate that: 1) extensively methylated genes can be actively transcribed; 2) prominent changes in methylation of specific genes during normal development are not necessarily related to alterations in gene activity.

Role of de novo DNA methylation in the glucocorticoid resistance of a T-lymphoid cell line

A correlation has been shown between changes in the methylation pattern of cytosine residues in DNA and the expression of specific genes in differentiated tissues. The pattern of DNA methylation is conserved, through cell division, by a maintenance methylase but the mechanism by which a given pattern of methylation is established is unknown. De novo methylation of foreign DNA molecules has been shown to occur in several systems, and may serve as a signal to arrest gene expression. Conversely, treatment of cultured cell lines with 5-azacytidine results in DNA hypomethylation and leads to transcriptional activation of previously unexpressed genes. The results described here demonstrate spontaneous de novo methylation of DNA in a T-lymphoid cell line previously treated with 5-azacytidine to generate glucocorticoid sensitivity. This de novo methylation is accompanied by the acquisition of the glucocorticoid-resistant phenotype.

Production of RNA for secreted immunoglobulin mu chains does not require transcriptional termination 5' to the microM exons

The mouse immunoglobulin mu gene encodes both secreted and surface-bound mu heavy chains produced by cells of the B lymphoid series. Transcripts of the mu gene are processed into mu mRNA species which differ at their 3' termini, bearing either 'microsecond' or 'microM' segments, distinguishing secreted and cell-membrane-bound mu polypeptides. During maturation of surface IgM-bearing B cells to IgM-secreting plasma cells, both the total amount of mu mRNA and the ratio of microsecond- to microM-terminated mRNA increase greatly. Two possible mechanisms for the developmental regulation of 3' RNA processing cannot yet be distinguished. One mechanism would yield the microsecond terminus by specific cleavage of a common presursor transcript encompassing both microsecond and the microM exons (Fig. 1), the other by regulated termination of transcription upstream from the microM exons. While the first mechanism would produce, as a by-product, RNA fragments containing microM exons, the second would not. We report here the detection of such microM fragments in cells producing predominantly microsecond-terminated RNA species.

An immunoglobulin promoter region is unaltered by DNA rearrangement and somatic mutation during B-cell development

The V1 gene encodes the heavy chain variable region of antibodies that bind to phosphorylcholine in the Balb/c mouse. V1 genes have been cloned from mouse sperm DNA, an IgM-producing tumor HPCM2 and an IgA-producing tumor M167. The transcription start site of the V1 gene has been mapped 63 +/- 1 base pairs from the coding sequence for both alpha and mu transcripts. Comparison of flanking DNA sequence 574 base pairs 5' to the V1 transcription start site in sperm, HPCM2 and M167 DNA reveals that sperm and HPCM2 sequences are completely identical in this region and the M167 sequence differs from them by a single base change. Although the coding region of the V1 gene has undergone a high (4%) rate of somatic mutation in M167 we demonstrate that the somatic mutation mechanism stops near the transcription start site. These results demonstrate that initiation of V1 gene transcription remains unchanged with respect to location and 5' sequences throughout B-cell development.

Loss of type I procollagen gene expression in SV40-transformed human fibroblasts is accompanied by hypermethylation of these genes

Transformation of human lung fibroblasts (WI-38) by Simian Virus 40 (SV40) resulted in a decline of 25-30% in the amount of secreted collagen. The collagen produced by the transformed fibroblasts contained no type I collagen (i.e. alpha 1(I) and alpha 2 chains), which was the major collagen component produced by untransformed fibroblasts. Measurement of the procollagen mRNA levels by dot hybridization with nick-translated procollagen-cDNA clones showed that the absence of type I collagen was due to the absence of alpha 1(I) and alpha 2 procollagen mRNAs. This result was confirmed by hybridization of cDNA to total RNA with southern blots of the procollagen clones. To clarify the mechanism by which type I procollagen gene transcription is abolished in transformed cells, the methylation patterns of the alpha 1(I) and alpha 2 procollagen genes in normal and SV40-transformed fibroblasts were compared, using the chicken alpha 1(I) and alpha 2 procollagen-cDNA clones as probes. Methylated sites were detected by means of the restriction endonuclease isoschizomers HpaII and MspI. Methylation of the procollagen alpha 1(I) and alpha 2 genes was increased in the SV40-transformed fibroblasts, concurrently with the loss of type I collagen synthesis. DNA methylation may thus contribute to altered regulation of gene expression upon cell transformation.