Differences in the nuclease sensitivity between the two alleles of the immunoglobulin kappa light chain genes in mouse liver and myeloma nuclei

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

As a first step toward defining the elements necessary for lambda immunoglobulin gene regulation, DNase I hypersensitive sites were mapped in the mouse lambda locus. A hypersensitive site found 15.5 kb downstream of C lambda 4 was present in all the B-cell but not in the T-cell lines tested. This site coincided with a strong B-cell-specific transcriptional enhancer (E lambda 2-4). This novel enhancer is active in myeloma cells, regardless of the status of endogenous lambda genes, but is inactive in a T-cell line and in fibroblasts. The enhancer E lambda 2-4 functions in the absence of the transcription factor NF kappa B, which is necessary for kappa enhancer function. No evidence could be found for NF kappa B binding by this element. Rearrangement of V lambda 2 to JC lambda 3 or JC lambda genes deletes E lambda 2-4; however, a second strong enhancer was found 35 kb downstream of C lambda 1, which cannot be eliminated by lambda gene rearrangements. The second lambda enhancer (E lambda 3-1) is 90% homologous to the E lambda 2-4 sequence in the region determined to comprise the active enhancer and likewise lacks the consensus binding site for NF kappa B. The data support a model for the independent activation of kappa and lambda gene expression based on locus-specific regulation at the enhancer level.

DNA superhelicity enhances the assembly of transcriptionally active chromatin in vitro

Using an in vitro chromatin assembly system, we analyzed the influence of DNA superhelicity on the development of transcriptionally active minichromosomes. Plasmid DNA molecules containing either a Xenopus borealis 5S RNA gene or an X. laevis methionine tRNA gene were utilized as templates for the assembly of chromatin. Both plasmids were processed into active minichromosomes if introduced as supercoiled molecules into the extract (S-150). The degree of superhelicity is a determining factor in the assembly of active chromatin. Molecules containing varying superhelical densities were processed into minichromosomes with different transcriptional activities. The absence of supercoils leads to the assembly of chromatin with substantially lower transcriptional activity. Assembled minichromosomes are stable enough to be isolated by sucrose gradient centrifugation while retaining their transcriptional phenotype. The formation of nucleosomes with a periodic spacing occurred with the same efficiency and to the same degree regardless of the initial DNA topology. Hence, a determining factor in the development of transcriptionally active chromatin may be the initial superhelicity of the DNA molecule to which activator (trans-acting factors) or repressor (histones) proteins bind. Once the chromatin assembly process has begun, the transcriptional activity of the resulting minichromosome may already have been determined.

DNase I sensitivity of immunoglobulin light chain genes in Abelson murine leukemia virus transformed pre-B cell lines

We have used Abelson murine leukemia virus (A-MuLV) transformed pre-B cell lines to test the hypothesis that the rearrangement potential of a developing B-lymphocyte is dependent on an "opening" of the chromatin structure surrounding immunoglobulin (Ig) genes, thus allowing accessibility to an Ig gene recombinase. The chromatin structures surrounding heavy (H), kappa (kappa), and lambda (lambda) chain constant-region genes were assessed by DNase I sensitivity in A-MuLV transformed cell lines capable of H, kappa or lambda gene rearrangement. Our results indicate that DNase I-sensitive chromatin structures of these Ig constant-region genes correlate closely with the ability of the genes to undergo recombination. We also find that the chromatin structure of an Ig constant-region locus becomes DNase I sensitive before any DNA rearrangement events occur.

The effects of transcription on the nucleosome structure of four Dictyostelium genes

Micrococcal nuclease digestion of Dictyostelium discoideum nuclei from various developmental stages was used to investigate transcription-related changes in the chromatin structure of the coding region of four genes. Gene activity was determined by Northern blotting and nuclear run on experiments. During strong transcription of the developmentally regulated cysteine proteinase I gene, a smear superimposed on a nucleosomal ladder was observed, indicating perturbation of nucleosomal structure was occurring. However, two other developmentally regulated genes, discoidin I and pSC253, showed only slight nucleosome disruption during high levels of transcription. The chromatin structure of a fourth gene (pCZ22) was disrupted throughout development, even at those stages where transcription was greatly reduced. We suggest that although nucleosome structure can be transiently perturbed by the passage of the transcription complex in vivo, the degree of perturbation and the speed with which nucleosomes reassemble is also influenced by the DNA sequence.

Cloning and characterization of cDNAs coding for the heavy and light chains of a monoclonal antibody specific for Pseudomonas aeruginosa outer membrane protein I

A set of seven monoclonal antibodies (MAb) directed against outer membrane proteins of Pseudomonas aeruginosa has been examined by Western blot analysis, indirect immunofluorescence tests and subclass typing. The hybridoma cell line secreting MAb 6A4, which reacts with outer membrane protein I, belongs to the IgG2a subclass and crossreacts with the 17 P. aeruginosa serotypes as listed in the International Antigenic Typing System, was selected as source for the preparation of poly(A)+RNA which in turn was used as template for cDNA synthesis and cloning. Full length cDNA clones of the gamma heavy chain as well as the kappa light chain were obtained and characterized by nucleotide sequence analysis. The complete cDNA sequences coding for the heavy and light chains will be the prerequisite for the construction and heterologous expression of a chimeric human-mouse monoclonal antibody which might be used in therapy of P. aeruginosa infections.

DNase I- and micrococcal nuclease-hypersensitive sites in the human apolipoprotein B gene are tissue specific

We have mapped the DNase I- and micrococcal nuclease-hypersensitive sites present in the 5' end of the human apolipoprotein B (apo-B) gene in nuclei from cells expressing or not expressing the gene. Four DNase I-hypersensitive sites were found in nuclei from liver-derived HepG2 cells and intestine-derived CaCo-2 cells, which express the apo-B gene, but not in HeLa cells, which do not. These sites are located near positions -120, -440, -700, and +760 base pairs relative to the transcriptional start site. Undifferentiated CaCo-2 cells exhibited another site, near position -540. Six micrococcal nuclease-hypersensitive sites were found in nuclei from HepG2 and CaCo-2 cells, but not in HeLa cells or free DNA. These sites are located near positions -120, -390, -530, -700, -850, and +210. HepG2 cells exhibited another site, near position +460. Comparison of the DNA sequence of the 5' flanking regions of the human and mouse apo-B genes revealed a high degree of evolutionary conservation of short stretches of sequences in the immediate vicinity of each of the DNase I- and most of the micrococcal nuclease-hypersensitive sites.

DNase I- and micrococcal nuclease-hypersensitive sites in the human apolipoprotein B gene are tissue specific

We have mapped the DNase I- and micrococcal nuclease-hypersensitive sites present in the 5' end of the human apolipoprotein B (apo-B) gene in nuclei from cells expressing or not expressing the gene. Four DNase I-hypersensitive sites were found in nuclei from liver-derived HepG2 cells and intestine-derived CaCo-2 cells, which express the apo-B gene, but not in HeLa cells, which do not. These sites are located near positions -120, -440, -700, and +760 base pairs relative to the transcriptional start site. Undifferentiated CaCo-2 cells exhibited another site, near position -540. Six micrococcal nuclease-hypersensitive sites were found in nuclei from HepG2 and CaCo-2 cells, but not in HeLa cells or free DNA. These sites are located near positions -120, -390, -530, -700, -850, and +210. HepG2 cells exhibited another site, near position +460. Comparison of the DNA sequence of the 5' flanking regions of the human and mouse apo-B genes revealed a high degree of evolutionary conservation of short stretches of sequences in the immediate vicinity of each of the DNase I- and most of the micrococcal nuclease-hypersensitive sites.

The role of the kappa enhancer and its binding factor NF-kappa B in the developmental regulation of kappa gene transcription

We report here on a comparison of plasmacytoma cell lines that differ markedly in their ability to express kappa immunoglobulin genes introduced by transfection, but nevertheless express their endogenous kappa genes at comparable levels. The cell line that fails to express exogenous kappa genes is nonpermissive for kappa enhancer function, apparently because it lacks a specific kappa enhancer-binding nuclear factor (NF-kappa B). We show that this same nuclear factor is also lacking in pre-B cells and that treatment of these cells with bacterial lipopolysaccharide induces the appearance of NF-kappa B in nuclear extracts and concomitantly activates the kappa enhancer. These findings indicate that factor NF-kappa B controls kappa enhancer activity, and that this activity is only transiently required during B cell maturation.

Hypersensitive sites in the 5' and 3' flanking regions of the cysteine proteinase I gene of Dictyostelium discoideum

The cysteine proteinase I gene of Dictyostelium discoideum is a developmentally regulated single copy gene. Specific sites in the 5' and the 3' flanking regions of the gene were cleaved by an endogenous nuclease when the gene was being transcribed. The majority of these sites were not cut when the gene was inactive. A dramatic change in the pattern of micrococcal nuclease and DNase I hypersensitive sites occurred in the 5' flanking region when transcription commenced at the 8 h stage of development. The major sites, doublets at -220/-300 bp and -670/-770 bp upstream of the transcription start site, corresponded to those cut by the endogenous nuclease. When transcription subsequently ceased the hypersensitive sites did not significantly change, indicating the gene remained in an activated state. The micrococcal nuclease hypersensitive sites in the 3' flanking region did not change significantly during development.

Cell-type-specific transcription of an immunoglobulin kappa light chain gene in vitro

We have established a cell-free system, derived from a human B-cell lymphoma, in which immunoglobulin kappa light chain gene promoters are both accurately transcribed and regulated in a cell-type-specific manner. Thus, accurate transcription from the T1 kappa light chain gene promoter was much more efficient in B-cell extracts than in HeLa cell extracts, whereas control promoters (adenovirus major late and histone H2B) were transcribed equally well in either extract. More important, the increased kappa light chain gene transcription in B-cell extracts was dependent upon upstream sequences (containing the conserved decanucleotide element) previously shown to be necessary for B-cell-specific transcription in vivo; in contrast, removal of these sequences had no effect on the low level of kappa transcription in HeLa extracts. The maximal level of upstream sequence-mediated transcription was dependent upon template topology. These studies show that there is at least one B-cell-specific factor that stimulates transcription from purified DNA templates, and they further suggest that the in vivo action of the factor(s) on other components of the transcription machinery is direct rather than indirect (e.g., via the maintenance of an open chromatin structure). The cell-free system described here should facilitate both purification and functional studies of the B-cell-specific factor(s).

Chromosomal position and specific demethylation in enhancer sequences of germ line-transmitted retroviral genomes during mouse development

The methylation pattern of the germ line-transmitted Moloney leukemia proviral genome was analyzed in DNA of sperm, of day-12 and day-17 embryos, and of adult mice from six different Mov substrains. At day 12 of gestation, all 50 testable CpG sites in the individual viral genomes as well as sites in flanking host sequences were highly methylated. Some sites were unmethylated in sperm, indicating de novo methylation of unique DNA sequences during normal mouse development. At subsequent stages of development, specific CpG sites which were localized exclusively in the 5' and 3' enhancer regions of the long terminal repeat became progressively demethylated in all six proviruses. The extent of enhancer demethylation, however, was tissue specific and strongly affected by the chromosomal position of the respective proviral genome. This position-dependent demethylation of enhancer sequences was not accompanied by a similar change within the flanking host sequences, which remained virtually unchanged. Our results indicate that viral enhancer sequences, but not other sequences in the M-MuLV genome, may have an intrinsic ability to interact with cellular proteins, which can perturb the interaction of the methylase with DNA. Demethylation of enhancer sequences is not sufficient for gene expression but may be a necessary event which enables the enhancer to respond to developmental signals which ultimately lead to gene activation.

Tandem kappa immunoglobulin promoters are equally active in the presence of the kappa enhancer: implications for models of enhancer function

Transcription of immunoglobulin kappa genes is regulated by enhancer and promoter elements, both of which function in a tissue-specific fashion. We have studied the interaction of these elements by transfecting plasmacytoma cells with genes that have tandem kappa promoters located next to a single kappa enhancer and assaying these genes for transient or stable transcription. We find that the promoters located proximal and distal to the enhancer function identically whether they are separated by 440 bp or by 2.7 kb or whether they are located 1.7 or 7.7 kb away from the enhancer. Our results indicate that the immunoglobulin kappa enhancer does not operate as a bidirectional entry site for RNA polymerase or for other factors associated with the transcription complex. Rather, they suggest that the enhancer exerts its influence uniformly over large distances and independently of the presence of intervening promoters.

Nuclear factors bind to regulatory regions of the mouse kappa immunoglobulin gene

At least two regions of the mouse kappa immunoglobulin gene are necessary for appropriate transcription. One is located within the J-C intron; another is located 5' of the transcription start site in all variable region gene segments and contains a highly conserved octanucleotide sequence, ATTTGCAT. Trans-acting nuclear factors have been thought to interact with these regions on the basis of studies with transient transfection of modified immunoglobulin genes into lymphoid and fibroblast cell lines. Using a sensitive gel electrophoresis DNA binding assay, we have found nuclear factors that bind to these two regulatory regions of the kappa gene. Two patterns of specific binding of nuclear factors to DNA sequences containing the J-C intron enhancer were observed. One pattern was seen in cell lines which do not express immunoglobulin, while a different pattern was observed in cell lines which actively transcribe light chain genes. We also find factors which bind to the octanucleotide containing 5' sequence which are distinct from those which bind the J-C enhancer region.

Structure of transcriptionally active chromatin

Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.

Chromosomal position and specific demethylation in enhancer sequences of germ line-transmitted retroviral genomes during mouse development

The methylation pattern of the germ line-transmitted Moloney leukemia proviral genome was analyzed in DNA of sperm, of day-12 and day-17 embryos, and of adult mice from six different Mov substrains. At day 12 of gestation, all 50 testable CpG sites in the individual viral genomes as well as sites in flanking host sequences were highly methylated. Some sites were unmethylated in sperm, indicating de novo methylation of unique DNA sequences during normal mouse development. At subsequent stages of development, specific CpG sites which were localized exclusively in the 5' and 3' enhancer regions of the long terminal repeat became progressively demethylated in all six proviruses. The extent of enhancer demethylation, however, was tissue specific and strongly affected by the chromosomal position of the respective proviral genome. This position-dependent demethylation of enhancer sequences was not accompanied by a similar change within the flanking host sequences, which remained virtually unchanged. Our results indicate that viral enhancer sequences, but not other sequences in the M-MuLV genome, may have an intrinsic ability to interact with cellular proteins, which can perturb the interaction of the methylase with DNA. Demethylation of enhancer sequences is not sufficient for gene expression but may be a necessary event which enables the enhancer to respond to developmental signals which ultimately lead to gene activation.

Active T-cell receptor genes have intron deoxyribonuclease hypersensitive sites

The T-cell receptor beta-chain gene has a nuclease hypersensitive site in several kinds of T cells, which does not appear in B cells expressing immunoglobulins. Conversely, the kappa immunoglobulin gene shows a known hypersensitive site at its enhancer element in B cells, as expected, but this site is absent in T cells. As is the case with immunoglobulin genes, the T-cell receptor site lies within the gene, in the intron separating joining and constant region segments. These nuclease hypersensitive DNA configurations in the introns of active T-cell receptor and immunoglobulin genes may arise from control elements that share ancestry but have diverged to the extent that each normally acts only in lymphoid cells which use the proximal gene product.

Transposition of the immunoglobulin heavy chain enhancer to the myc oncogene in a murine plasmacytoma

A novel mechanism of oncogene activation by transposition of a tissue-specific cellular enhancer is described. A rearranged c-myc oncogene was cloned from murine plasmacytoma ABPC17 in the expectation that it would reflect the t(6;15) chromosome translocation carried by this tumor. The rearrangement instead reflects an insertion 361 bp 5' to the c-myc gene on chromosome 15. The insert conveys a 2.3 kb segment of the immunoglobulin heavy (H) chain locus from chromosome 12. Since the insertion introduces the lymphoid-specific enhancer from the JH-Smu region and also disrupts a region implicated in normal c-myc control, it may account for the c-myc transcription observed in ABPC17. The structure of the transposed segment and a corresponding deletion in the JH-Smu region suggests that the transposition reflects a complex recombination between chromosomes 15 and 12. Since the t(6;15) breakpoint is not near c-myc, chromosome 15 must have undergone an independent exchange with chromosome 6.

Variant (6 ; 15) translocation in a murine plasmacytoma occurs near an immunoglobulin kappa gene but far from the myc oncogene

Chromosome translocations in B-lymphoid tumours are providing intriguing insights and puzzles regarding the role of immunoglobulin genes in the activation of the myc oncogene (reviewed in refs 1, 2). The 15 ; 12 translocations found in most murine plasmacytomas and the analogous 8 ; 14 translocation in human Burkitt's lymphomas involve scissions of murine chromosome 15 (human chromosome 8) near the 5' end of the c-myc gene and subsequent fusion near an immunoglobulin heavy-chain gene. The less well characterized 'variant' translocations found in about 15% of such tumours also involve the myc-bearing chromosome band, but exchange occurs with a chromosome bearing an immunoglobulin light-chain locus--in mice, the kappa-chain locus bearing chromosome 6 (refs 3-5) and, in man, chromosome 2 (or 22), at the same band at which the kappa (or lambda) locus lies (reviewed in ref. 1). The Burkitt variant translocations involve scissions 3' of c-myc; one 8 ; 22 translocation placed the C lambda locus just 3' of c-myc, but usually the chromosome 8 breakpoint is a greater, but unknown, distance away from c-myc, more than 20 kilobases (kb) in one 8 ; 2 translocation involving the C kappa gene. Little is known about the murine 6 ; 15 translocations, although a C kappa gene cloned from one plasmacytoma (PC7183) is linked, via chromosome 12 sequences, to an unidentified region of chromosome 15 (ref. 11). We describe here the chromosome fusion region from plasmacytoma ABPC4, which displays the typical reciprocal 6;15 translocations. We find that the chromosome 6 breakpoint is near C kappa but, unlike those in the heavy-chain locus, not at a position where immunoglobulin genes normally recombine. Moreover, the chromosome 15 sequences involved in the ABPC4 translocation are not derived from the vicinity of c-myc.

Correlation between DNase I hypersensitive sites and putative regulatory sequences in human immunoglobulin genes of the kappa light chain type

The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hypersensitive site was mapped 0.13 kb upstream of the leader segment of the rearranged VK genes; it comprises a region in which promoter-like regulatory elements were discovered recently. Additional hypersensitive sites are located further upstream. A hypersensitive site in the JK-CK intron coincides with a putative tissue specific enhancer element. A hypersensitive region down-stream of CK overlaps with the cleavage/polyadenylation recognition signal which is flanked by sequences related to the above mentioned putative regulatory sequences. The coincidence between DNAase I hypersensitive sites and those sequences may be functionally significant.

Immunoglobulin genes of the kappa light chain type from two human lymphoid cell lines are closely related

As a first step in our studies of functionally rearranged K genes of man we cloned the germline JK-CK region from placenta DNA employing a mouse JK clone as hybridization probe. Subclones of the human JK-CK region were then used to characterize and clone the rearranged K genes of the lymphoid cell lines Walker and Daudi. The Walker cell line contains one rearranged and one germline K allele (K+,KO; ref. 1). Only one K gene was found in Daudi cells (K+). Restriction mapping and DNA sequencing showed, that the rearranged K genes from both cell lines are closely related. These features make the two cell lines particularly suitable for studies on the chromatin structure of K light chain genes. The 5' flanks of the two genes (388 bp) are identical while there is a 12% divergence between the VK gene segments themselves. This situation may reflect somatic mutation processes and/or gene conversion like events.

Fine mapping of an immunoglobulin gene activator

It has recently been shown that the promoter of a kappa immunoglobulin gene is activated for transcription by a downstream sequence element. Here we mapped the activating element to a resolution of about 20 base pairs by constructing a series of deletions in the cloned kappa gene. After transfection of each deleted gene into myeloma cells, a transient expression assay was used to measure the level of transcription from the kappa promoter. We found that the activating element extends through about 200 base pairs and encompasses a region of sequence that is conserved between mouse and human genes. As successively deeper deletions were made into the conserved region from either the 5' or 3' side, the activating ability was lost gradually rather than abruptly. Although several short segments in this region are homologous to sequences in viral enhancers, they did not seem to play a dominant role in the activating effect. We also found that the activating element remained functional when reversed in orientation or when moved upstream of the kappa gene.

Reversible and persistent changes in chromatin structure accompany activation of a glucocorticoid-dependent enhancer element

A derivative of mouse mammary tumor virus (MTV) DNA, LTL, was constructed in vitro and introduced into the genome of mouse L cells. Transcription of LTL was stimulated by dexamethasone, a glucocorticoid hormone. Two features of LTL chromatin structure are altered upon hormone treatment. First, "moderate" DNAase I sensitivity of the entire LTL element increases following addition of dexamethasone; this alteration persists after hormone withdrawal, when LTL transcription is shut off. Second, a discrete DNAase I-hypersensitive region is induced with a time course that closely parallels the rate of increasing transcription from the MTV promoter; this structure disappears upon hormone removal. The induced hypersensitive region coincides with a segment of the MTV long terminal repeat sequence that specifically binds purified glucocorticoid receptor in vitro and functions as a hormone-dependent enhancer element in vivo. We suggest that specific glucocorticoid receptor-DNA interactions may alter the configuration of DNA or chromatin in the vicinity of the binding sites, thereby creating an active transcriptional enhancer.

Correct transcription of an immunoglobulin kappa gene requires an upstream fragment containing conserved sequence elements

Transcription of the immunoglobulin kappa light-chain genes depends on the presence of a TATA box upstream of the leader gene segment and is regulated by an enhancer sequence in the large intron. In studying a rearranged mouse kappa light-chain gene we have now found that sequences between--90 and--160 base pairs (bp) upstream of the coding region are essential for correct transcription in gene transfer experiments. This region contains the deca- and pentadecanucleotide sequences TNATTTGCAT and TGCAGCCTGTGNCCAG, which we call dc and pd, respectively. Sequences related to dc and pd were found upstream of all human and mouse kappa-chain variable region (Vk) genes, upstream of lambda-chain variable region (V lambda) genes, and within the mouse heavy-chain enhancer. An inverted and complementary form of the dc element (ATGCAAATNA, called cd) occurs upstream of all heavy-chain variable region (VH) genes. The newly defined sequences may be involved in the control of immunoglobulin gene transcription.

Fine mapping of an immunoglobulin gene activator

It has recently been shown that the promoter of a kappa immunoglobulin gene is activated for transcription by a downstream sequence element. Here we mapped the activating element to a resolution of about 20 base pairs by constructing a series of deletions in the cloned kappa gene. After transfection of each deleted gene into myeloma cells, a transient expression assay was used to measure the level of transcription from the kappa promoter. We found that the activating element extends through about 200 base pairs and encompasses a region of sequence that is conserved between mouse and human genes. As successively deeper deletions were made into the conserved region from either the 5' or 3' side, the activating ability was lost gradually rather than abruptly. Although several short segments in this region are homologous to sequences in viral enhancers, they did not seem to play a dominant role in the activating effect. We also found that the activating element remained functional when reversed in orientation or when moved upstream of the kappa gene.

Structure of the 5' ends of immunoglobulin genes: a novel conserved sequence

Recent investigations have suggested that tissue-specific regulatory factors are required for immunoglobulin gene transcription. Cells of the mouse lymphocytoid pre-B-cell line 70Z/3 contain a constitutively rearranged immunoglobulin kappa light chain gene; the nucleotide sequence of this gene exhibits all the known properties of a functionally competent transcription unit. Nevertheless, transcripts derived from this gene are detectable only after exposure of the cells to bacterial lipopolysaccharide, implying that accurate DNA rearrangement is not sufficient to activate expression of the gene. Comparison of the sequence of the 70Z/3 kappa light chain gene with those encoding other immunoglobulin heavy and light chains has revealed that a distinctive promoter region structure is characteristic of this multigene family. The sequence A-T-T-T-G-C-A-T lies approximately 70 base pairs upstream from the site of transcriptional initiation in every light chain gene examined; in heavy chain genes, the corresponding location is occupied by the precise inverse (A-T-G-C-A-A-A-T) of this sequence. Although adjacent regions of DNA have diverged extensively in evolution, these octanucleotide sequences are stringently conserved at this location among diverse immunoglobulin genes from at least two mammalian species. The proximity of this conserved octanucleotide block to the site of transcriptional initiation suggests that it may serve as a recognition locus for factors regulating immunoglobulin gene expression in a tissue-specific fashion.

Lipopolysaccharide-induced transcription of the kappa immunoglobulin locus occurs on both alleles and is independent of methylation status

The transcriptional activity of the kappa immunoglobulin genes in a B-cell lymphoma line, 7OZ/3 was measured before and after stimulation by lipopolysaccharide (LPS). Analyses of accumulated nuclear RNA components and of nascent transcripts showed that LPS induces transcription of both the productively rearranged (kappa+) and the unrearranged (kappa) allele in these cells. This pattern of transcriptional activation correlates well with the LPS induced appearance of a DNAase I hypersensitive site on both alleles in the vicinity of a putative enhancer element (Parslow and Granner, Nucl. Acids Res. 11, 4775, 1983). However, the transcriptional activation is not accompanied by detectable hypomethylation at Hha I and Hpa II sites which are normally undermethylated when kappa genes are constitutively expressed. These findings have enabled us to evaluate the relative importance of various structural parameters to the transcriptional competence of the kappa locus.

A novel 6:10 chromosomal translocation in the murine plasmacytoma NS-1

Specific chromosomal abnormalities are regularly associated with many murine and human malignancies. In particular, the majority of murine plasmacytomas and human Burkitt's lymphomas contain a characteristic translocation which results in the juxtaposition of a cellular oncogene, c-myc, with the immunoglobulin heavy-chain gene locus, and this rearranged c-myc directs the synthesis of qualitatively and quantitatively abnormal transcripts which may have an aetiological role in the development of the transformed state in lymphoid malignancies. Similarly, rearrangement and abnormal expression of c-myb (ref. 10) and c-mos (ref. 11) has been reported in other murine lymphoid tumours. Here we describe a novel 6:10 chromosomal translocation in the murine plasmacytoma cell line NS-1 which juxtaposes the immunoglobulin Ck gene with a single-copy sequence of unknown function. The NS-1 plasmacytoma is a frequently used fusion partner in hybridoma production and is known to contain a rearranged c-myc gene and a genetic element which transforms normal mouse fibroblasts in DNA-mediated transfection assays. We conclude that individual B-cell tumours may contain multiple chromosomal translocations perhaps relevant to oncogenesis.

DNase I hypersensitive sites in the chromatin of human mu immunoglobulin heavy-chain genes

An immunoglobulin polypeptide chain is encoded by multiple gene segments that lie far apart in germ-line DNA and must be brought together to allow expression of an immunoglobulin gene active in B lymphocytes. For the immunoglobulin heavy chain genes, one of many variable (V) region genes becomes joined to one of several diversity (D) segments which are fused to one of several joining (J) segments lying 5' of the constant region (C) genes. Here we show that the rearranged mu genes of an IgM-producing human B-lymphocyte cell line exhibit pancreatic deoxyribonuclease (DNase I) hypersensitive sites in the JH-C mu intron that are absent in naked DNA or the chromatin of other differentiated cell types. DNA sequence analysis reveals that the major hypersensitive site maps to a conserved region of the JH-C mu intron recently shown to function as a tissue-specific enhancer of heavy-chain gene expression. A similar association of an enhancer-like element with a DNase I hypersensitive site has been reported for the mouse immunoglobulin light-chain J kappa-C kappa intron. These results implicate disruption of local chromatin structure in the mechanism of immunoglobulin enhancer function.

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.

Structure of a nuclease-sensitive region inside the immunoglobin kappa gene: evidence for a role in gene regulation

A discrete chromatin region inside the active immunoglobulin kappa gene is preferentially accessible to cleavage by nucleolytic enzymes. This region comprises 200-250 bp of DNA, and is situated within the large intron of the gene, approximately 600 bp upstream from the constant region coding sequence. The local chromatin structure of this region correlates with tissue-specific kappa gene expression: it is resistant to nucleolytic digestion in the inactive kappa genes of murine brain and liver nuclei, but becomes uniquely sensitive to cleavage by deoxyribonuclease I or by a variety of restriction endonucleases in the chromatin of kappa-producing cells. Nuclease sensitivity at this site occurs in both rearranged and unrearranged kappa alleles, and can be maintained in the absence of ongoing kappa transcription. The nucleotide sequence of the hypersensitive region has been selectively conserved in evolution, and includes both a 7 bp inverted repeat sequence and a short segment homologous to the transcriptional enhancer elements of certain eukaryotic viruses. Molecular events occurring at this locus may play a role in the regulation of kappa gene expression, perhaps by influencing the activity of promoter sequences several kilobases upstream.

Nuclease-hypersensitive sites in the chromatin domain of the chicken lysozyme gene

We have examined the chromatin structure of a 22 kilobase-pair chromosomal region containing the lysozyme gene in laying hen. Nuclease-hypersensitive sites were probed with DNAase I by using an indirect end-labeling technique. Eight DNAase I-hypersensitive sites could be mapped in the flanking regions of the gene in oviduct cells, in which the gene is expressed. The same sensitive sites were detected by utilization of an endogenous nuclease activity present in oviduct nuclei. Only one hypersensitive site was detected in the chromatin from erythrocytes, in which the gene is not expressed. The 3'-terminus of the lysozyme gene is highly exposed in nuclei from both tissues. Of special interest is the hypersensitive site at the 5'-terminus of the actively transcribed gene since it maps at the region of multiple initiation sites of transcription and the putative control regions of steroid hormones. DNAase I-hypersensitive chromatin structures also at a greater distance from the gene may take part in the control of gene expression.

Nucleotide sequence of a region downstream of the mouse CK immunoglobulin gene

2318 bp downstream of the CK (1) gene segment were sequenced in a clone (L1-D) derived from mouse liver DNA. The 966 bp at the 5' side of this stretch were found to be identical to a sequence which had been determined previously in a myeloma T derived clone, i.e. no somatic mutations had occurred in the transition from the germline to the rearranged configuration. The remaining 1352 bp had not been known and extend the sequenced part of the mouse JK-CK region to about 7.5 kb. Within the newly sequenced area three BspRI sites have been located which were used in chromatin studies (Weischet et al., accompanying publications). In L1-D sequences have been found which are possible targets of aberrant recombination events.

Nucleosome distribution on the Jk and Ck immunoglobulin gene segments of mouse liver chromatin

The chromatin structure of the transcriptionally inactive kappa immunoglobulin gene in mouse liver was investigated by mainly employing indirect endlabeling on Bsp RI restriction nuclease digestions of intact nuclei. The disclosed strong (about 85%) but not uniform protection of the Bsp RI sites by nucleosomes is inconsistent with both a uniquely sequence-oriented localization and a completely random distribution of nucleosomes in this region of the genome. Several possibly applicable models are discussed. A model with multiple phases and non-uniform linker lengths cannot be excluded; however a largely random localization with a weak superimposed organization in two confined areas was tested and found sufficient for explaining the data.

Protection of expressed immunoglobulin genes against nuclease cleavage

Fragmentation of the actively transcribed kappa immunoglobulin gene in mouse myeloma nuclei with micrococcal nuclease and the restriction nuclease Bsp RI reveals a chromatin structure without the regularity of repeating nucleosomes found in bulk chromatin. Such regularity is restored about 2.2 kb 3' of the coding region. An only moderately increased micrococcal nuclease sensitivity and a 65% average protection of the Bsp RI sites indicates a DNA-protein interaction in the transcribed region which is not very different from that of an inactive gene. As determined by indirect endlabeling the frequency of Bsp RI cleavage both, after very mild and exhaustive digestion, varied moderately from site to site along the gene. In addition, it was not in each case the same at analogous sites on both alleles which are both transcribed. Thus, the experiments demonstrate differences between the chromatin structures of the genes which may be related to regulatory phenomena and thereby corroborate earlier findings made with DNAase I.

DNase I-hypersensitive sites in the chromatin of immunoglobulin kappa light chain genes

We have used DNase I as a probe to examine the chromatin structure of mouse immunoglobulin kappa light chain genes in rearranged and unrearranged chromosomes--i.e., in nuclei from myeloma cells and from brain and liver cells. Tissue-specific DNase I-hypersensitive sites are observed 0.7 and 1.7 kilobases upstream from the 5' end of the C kappa gene in the J kappa -C kappa intron region in myeloma nuclei but not in naked DNA or in brain or liver nuclei. In myeloma cells expressing one functional kappa light chain polypeptide, but with more than one rearranged allele, one DNase I-hypersensitive site is found 0.3 kilobases upstream from the start of the coding region of the V kappa sequence in both functionally rearranged and nonfunctionally rearranged alleles but not in cross-hybridizing V kappa genes in the germ line context. Thus, during the development of B lymphocytes, the commitment of immunoglobulin kappa light chain gene expression seems to be associated with the presence of DNase I hypersensitivities that reflect changes of chromosomal structure surrounding the single copy C kappa gene. In contrast, the germ line V kappa multigene family seems to be located in a chromosomal region that does not exhibit change of DNase I hypersensitivity in response to commitment of immunoglobulin expression; a V kappa gene acquires DNase I hypersensitivity only after it is translocated adjacent to the J kappa -C kappa intron region. The DNase I-hypersensitive site 5' to the V kappa sequence is similar in location to hypersensitive sites found for other eukaryotic genes and is probably associated with the promoter region. However, the DNase I-hypersensitive sites in the J kappa -C kappa intron region are not associated with any known promoters. In addition, the DNA sequences surrounding the C kappa-proximal DNase I-hypersensitive site have several stretches of homology with sequences within the 72-base-pair tandem repeat of simian virus 40, which has been shown to modulate the transcriptional activity of neighboring genes. This DNase I-hypersensitive site in the intron region may be significant for the differential expression of the translocated V kappa genes.