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B Nadel

Publications and source records attributed to B Nadel.

15 recordsLinked to original sources
PubMed1998

Decreased frequency of rearrangement due to the synergistic effect of nucleotide changes in the heptamer and nonamer of the recombination signal sequence of the V kappa gene A2b, which is associated with increased susceptibility of Navajos to Haemophilus influenzae type b disease.

Navajos and genetically related populations have a 10-fold increased incidence of Haemophilus influenzae type b (Hib) disease compared with control populations. The Vkappa gene A2 is used to encode the majority of anti-Hib Abs, and these are the highest affinity anti-Hib Abs. Navajos carry a different allele of the A2 gene segment (A2b) that is defective in its ability to undergo V-J recombination. The A2b allele has only three nucleotide changes from the commonly occurring A2a allele, two of which could potentially affect its ability to recombine. In this study we used two independent in vitro assays to test whether the nucleotide change found in the A2b promoter and/or in the A2b recombination signal sequence (RSS) might be responsible for the decrease in recombination frequency observed in vivo. Using a luciferase reporter gene assay, we found no significant difference between A2a and A2b promoter activities. However, the competition recombination substrate assay showed a 4.5-fold reduction in the relative frequency of recombination of the A2b RSS compared with A2a. We show that this decreased frequency is due to a synergistic effect of the unique nucleotide change present in the heptamer of the A2b RSS and the shared nucleotide change present in the nonamer of both A2b and A2a. This in vitro relative frequency of rearrangement is not significantly different from that observed in vivo; therefore, the A2b RSS is probably the factor associated with the increased susceptibility to Hib disease among individuals carrying the A2b allele.

Alleles↗
PubMed1998

Sequence of the spacer in the recombination signal sequence affects V(D)J rearrangement frequency and correlates with nonrandom Vkappa usage in vivo.

Functional variable (V), diversity (D), and joining (J) gene segments contribute unequally to the primary repertoire. One factor contributing to this nonrandom usage is the relative frequency with which the different gene segments rearrange. Variation from the consensus sequence in the heptamer and nonamer of the recombination signal sequence (RSS) is therefore considered a major factor affecting the relative representation of gene segments in the primary repertoire. In this study, we show that the sequence of the spacer is also a determinant factor contributing to the frequency of rearrangement. Moreover, the effect of the spacer on recombination rates of various human Vkappa gene segments in vitro correlates with their frequency of rearrangement in vivo in pre-B cells and with their representation in the peripheral repertoire.

B-Lymphocytes↗
PubMed1998

V(H) replacement is unlikely to contribute significantly to receptor editing due to an ineffectual embedded recombination signal sequence.

Receptor editing is a process consisting of replacement of pre-existing H or L chain rearrangements by secondary rearrangements. This process could serve to remove autoreactive specificities, or to rescue loci with non-functional rearrangements. At the H chain locus, functional replacement of a V(H)DJ(H) rearrangement by an upstream V(H) requires the presence of an embedded RSS located in reverse orientation near the 3' end of the V(H) segment. Although most V(H) genes contain a fairly consensus embedded heptamer, the nonamer sequence bears little resemblance to the consensus RSS nonamer. Therefore, the physiologic rate of H chain editing by V(H) replacement is yet unknown. In this study, we used both conventional and sensitive competition recombination substrate assays to determine the recombination frequency of the V(H)1X embedded RSS relative to consensus and non-consensus RSS's. Results show no detectable recombination of the 81X embedded RSS in a recombination substrate, and the competition substrate allows us to estimate that the 81X embedded RSS recombines at least 1300 fold less often than a consensus RSS. This suggests that V(H) gene replacement is not responsible for the decrease in representation of the 81X gene during differentiation. Furthermore, since the sequence of the embedded RSS is very similar for many V(H) genes, our results suggest that receptor editing of the H chain will be an infrequent event, leaving L chain editing as the main mode of avoiding autoreactive specificities in vivo.

Gene Rearrangement, B-Lymphocyte, Heavy Chain↗
PubMed1997

Nucleotide deletion and P addition in V(D)J recombination: a determinant role of the coding-end sequence.

During V(D)J recombination, the coding ends to be joined are extensively modified. Those modifications, termed coding-end processing, consist of removal and addition of various numbers of nucleotides. We previously showed in vivo that coding-end processing is specific for each coding end, suggesting that specific motifs in a coding-end sequence influence nucleotide deletion and P-region formation. In this study, we created a panel of recombination substrates containing actual immunoglobulin and T-cell receptor coding-end sequences and dissected the role of each motif by comparing its processing pattern with those of variants containing minimal nucleotide changes from the original sequence. Our results demonstrate the determinant role of specific sequence motifs on coding-end processing and also the importance of the context in which they are found. We show that minimal nucleotide changes in key positions of a coding-end sequence can result in dramatic changes in the processing pattern. We propose that each coding-end sequence dictates a unique hairpin structure, the result of a particular energy conformation between nucleotides organizing the loop and the stem, and that the interplay between this structure and specific sequence motifs influences the frequency and location of nicks which open the coding-end hairpin. These findings indicate that the sequences of the coding ends determine their own processing and have a profound impact on the development of the primary B- and T-cell repertoires.

Animals↗
PubMed1995

Influence of coding-end sequence on coding-end processing in V(D)J recombination.

The large diversity of the Ig and TCR repertoires is accounted for by combinatorial assembly of the germ-line-encoded V, D, and J gene segments, as well as extensive modification at the junctions during the recombination process. Those modifications, termed coding-end processing, consist of removal and addition of an apparently random number of nucleotides. To obtain further insights into the mechanism of the coding-end processing, we constructed a large data base of several Ig and TCR coding ends obtained in vivo, using conditions that avoid potential bias by cellular selection events. We show that the processing patterns are not random, but rather specific for each coding end, suggesting that specific motifs in the coding-end sequence influence the processing. We found a good correlation between the presence of internal stretches of at least three A.T nucleotides, absence of stretches of G.C nucleotides, and high average nucleotide deletion. Based on a detailed analysis of the processing patterns, we propose that nicks of the hairpin intermediate take place preferentially in potential open structures formed by weaker pairings of A.T stretches. Together, these findings indicate that the sequence of the coding end plays an important role in nonrandom aspects of the recombination mechanism. This suggests that coding-end sequences might have been selected throughout evolution to participate in an early control of the development of the primary repertoire.

Animals↗
PubMed1995

Coding end processing is similar throughout ontogeny.

During the recombination process, extensive processing of the coding ends provides tremendous potential diversity to the joint of any two gene segments. However, the diversity of the newborn B and T cell repertoires is greatly reduced compared with that of the adult. At the mechanistic level, this difference is primarily due to the absence of terminal deoxynucleotidyltransferase expression until the first week after birth. Additionally, one direct consequence of the lack of N regions early in ontogeny is the more frequent occurrence of homology-directed recombination, reducing even further the potential of diversity. Other enzymatic factors could also contribute to this ontogenic difference. However, the use of the homology-directed recombination pathway early in life obscures the analysis of the coding end processing. In this study we compared the coding end processing throughout ontogeny, in normal and terminal deoxynucleotidyltransferase -/- mice in the presence of minimal homology-directed recombination. The analysis of partial D-J joints allowed us to avoid potential bias by early selection events. Our results show that the extent of nucleotide deletion of a given end is consistent throughout ontogeny in the presence or absence of terminal deoxynucleotidyltransferase. However, a distinctive processing pattern is observed for each coding end.

Age Factors↗
PubMed1995

Analysis of homology-directed recombination in VDJ junctions from cytoplasmic Ig- pre-B cells of newborn mice.

We previously showed that most VD and DJ gene combinations from newborn surface Ig- pre-B cells had one to three predominant junctions, all of which occurred at the sites of short sequence homologies between the two coding ends. Because the majority of sequences that are present in pre-B cells are in-frame, however, the possibility existed that the frequency of occurrence of predominant IgH junctions was skewed by proliferation of pre-B cells with productive rearrangements. In this study, we analyzed cytoplasmic Ig- pre-B cells, because these cells should not yet be subject to such selection. Two-thirds of the rearrangements from this population in the adult were out-of-frame, suggesting that these rearrangements are unbiased. In newborn cIg- pre-B cells, DJ junctions still showed the same predominant sequences as sIg- pre-B cells, but there was less use of predominant junctions in VD junctions for three of four different VH genes analyzed. For those three VH genes, an average of 30% of the sequences were in-frame. When only the in-frame rearrangements from these cIg- newborn cells were analyzed, frequencies of predominant VD junctions were comparable to those in sIg- pre-B cells. For sequences using the VHS107/V11 gene, however, 67% of the junctions were created at the site of the same dinucleotide in the V gene, and as a result, 73% of the sequences were in-frame. Thus homology-directed recombination does not initially produce as much junctional homogeneity as anticipated in all VD combinations, although it is a frequently used mechanism in the early fetal/neonatal gene rearrangements.

Animals↗
PubMed1995

Cell-specific organization of the 5S ribosomal RNA gene cluster DNA loop domains in spermatozoa and somatic cells.

DNA in eucaryotic cells is organized into loop domains, ranging in size from 25 to 100 kb, that are attached at their bases to the structural component of the nucleus termed the nuclear matrix. These DNA loop domains have been shown to be important in the regulation of both DNA replication and RNA transcription. In this study we have compared the structural organization of the DNA loop domains of the 5S rRNA gene cluster in sperm, liver, and brain nuclei in the Syrian golden hamster. The individual loop domains were visualized by fluorescent in situ hybridization to protamine (sperm)- and histone (somatic)-depleted nuclei, termed nuclear matrix halo preparations. We found that in sperm nuclei, the 5S rRNA gene cluster was organized into three small loop domains that were approximately 48 kb each. In both types of somatic cell nuclei examined, the 5S rRNA gene cluster was organized into a single, much larger loop domain that was up to 480 kb in length. The data suggest that at least some of the compaction that sperm DNA undergoes during spermiogenesis is mediated by the nuclear matrix independent of protamine binding. Additionally, this sperm-specific DNA organization may be involved in the specific patterns of DNA replication and transcription of the paternal genome in the embryo.

Animals↗
PubMed1994

Influence of the V(D)J recombination mechanism on the formation of the primary T and B cell repertoires.

T and B cells exploit the mechanism of V(D)J recombination to make diverse or very restricted repertoires at varying times during ontogeny. Fetal repertoires are limited since there are no N nucleotides. Also, if short sequence homologies are present near the coding ends, junctions are preferentially made at that site. For gamma delta TCR, and to a lesser extent for Ig, this results in a very homogeneous population of junctions early in ontogeny. alpha beta TCR, however, have a paucity of homologous stretches, and maintain junctional diversity in the newborn. In both newborns and adults, some coding ends show very restricted nucleotide deletion, while others show heterogeneous and extensive deletion. It appears that the sequences of the coding ends have been selected through evolution as a mechanism to control repertoire formation.

Animals↗
PubMed1993

Available lambda B cell repertoire in the mouse: evidence of positive selection by environmental factors.

We have recently shown that, from two BALB/c mice treated with rabbit anti-C lambda 2/C lambda 3 antibodies coupled to lipopolysaccharide, variable heavy chain (VH) family repertoires associated with lambda 2 or lambda 3 light chains can differ from one lambda subtype to another and from one individual mouse to another. Indeed, 4 out of 6 lambda 2 (VxJ2) hybridomas from one mouse preferentially expressed the VH10 family while 3 out of 8 lambda 2 (V2J2) and 5 out of 8 lambda 2 (VxJ2) hybridomas from a second mouse preferentially expressed the S107 and VGAM3.8 VH families, respectively. In this report, we describe the structural basis of such preferential pairings by sequence analysis of the 12 lambda 2 hybridomas. The sequence comparison of their VH regions show that each preferential association of a VH family to one V lambda region is restricted to the use of a single member or very closely related members inside a VH family and that a great variability of CDR3 of heavy chain is observed. We, therefore, suggest that environmental factors can modify the available lambda B cell repertoire through a positive selection of particular VH/V lambda pairings. Moreover, our data support that this selection does not require clonal expansion and punctual somatic mutation.

Amino Acid Sequence↗
PubMed1992

Preferential VH/V lambda pairings occur in the available B cell repertoire of adult BALB/c mice.

To gain insights into the composition of the B cell repertoire, we have investigated VH gene family expression associated with individual light chains. For this purpose, we have examined the use of 12 VH gene families in a large collection of hybridomas expressing one of the four lambda light chains [lambda 1 (V1J1), lambda 2 (V2J2 and V x J2) and lambda 3 (V1J3)]. Our results show that the distribution of the VH families is very different from one lambda subtype to another. This suggests that a few substitutions between VL regions are sufficient to generate very different associated repertoires by strong selection mechanisms. Moreover, we assume that the global VH expression pattern is not random but rather composed of many preferential VH/VL associations.

Animals↗
PubMed1991

V lambda-J lambda rearrangements are restricted within a V-J-C recombination unit in the mouse.

The murine lambda gene locus is organized as follows: V lambda 2-V lambda x-J lambda 2C lambda 2-psi J lambda 4C lambda 4-V lambda 1-J lambda 3C lambda 3-J lambda 1C lambda 1 where all segments have the same transcriptional orientation. The combinatorial process of gene recombination should allow the generation of eight distinct immunoglobulin light chains. We have therefore investigated the probability of obtaining such chains among the mature lambda B cell repertoire. We analyze serum lambda immunoglobulins and lambda B cell clones induced by treatment with rabbit anti-lambda antibodies coupled to LPS. Confirming previous data obtained by others, our results indicate that the rearrangements of lambda segments take place within each V lambda-J lambda-C lambda cluster, thereby defining a unit of recombination. Our results also provide no evidence for the use of undescribed segments as has been recently suggested by the finding of the V lambda x segment.

Animals↗
PubMed1990

Murine lambda gene rearrangements: the stochastic model prevails over the ordered model.

The ontogeny of the immunoglobulin (Ig) gene rearrangement in mammalian B cells seems to be ordered. Heavy chain gene segments rearrange first, followed by light chain gene segments, kappa before lambda. The genomic organization of murine lambda locus does not preclude the simultaneous expression of two subtypes from the same chromosome. In order to distinguish between an ordered and a stochastic model of rearrangement, a panel of 67 B cell hybridomas secreting either lambda 1, lambda 2, lambda 3 or lambda x (recently described) were analysed for V lambda J lambda rearrangements. The results show that in 97% of cases, a single rearrangement occurred, favouring the stochastic model over the ordered one. Strikingly, the possibility of having a productive rearrangement if the first try results in an aberrant one is rare. We propose therefore, that the lambda Ig is not necessarily required to ensure allelic and subtypic exclusion mechanisms. Moreover, in 97% of the cases, at least one kappa allele is rearranged. Furthermore, the RS recombination has been detected in 77% of the cases. This suggests that, although the stimulation of kappa precedes that of lambda locus, the RS recombination acts as a transacting albeit dispensable lambda activator.

Animals↗
PubMedDate not supplied

Structure of the rRNA genes in the hamster sperm nucleus.

We have examined the structure of the major ribosomal RNA (rRNA) genes in the hamster sperm nucleus, using fluorescent in situ hybridization (FISH). The rRNA genes are present as tandemly repeated clusters located at the telomeric ends of the short arms of five pairs of acrocentric chromosomes in the Syrian golden hamster (as they are in humans). In somatic cells, these five chromosome pairs come together to form the nucleolus, the site of rRNA synthesis. The nucleolus remains intact through S phase of the cell cycle, breaking apart only during late G2 and mitosis when the chromosomes condense. Mammalian sperm nuclei are the final products of meiotic division and morphological differentiation that includes a dramatic chromatin condensation. Consequently, it was not immediately obvious whether the rRNA genes would be condensed into a nucleolus-like structure in the mature spermatozoa, or separated, as they are in mitotic chromosomes. We found that of 117 sperm nuclei examined, 91.5% contained between two and five FISH signals for the rRNA gene clusters, and 64.0% contained four (29%) or five (35%) signals. In decondensed hamster sperm nuclei, the rRNA hybridized signals were separated into independent strands. These data collectively indicate that the chromosomes containing the rRNA genes are not bound together into a pre-nucleolar structure in fully condensed mammalian sperm nuclei.

Animals↗