The 3 ′ part of the immunoglobulin κ locus of the mouse

Kirschbaum, Thomas; Pourrajabi, Soheil; Zocher, Ines; Schwendinger, Jürgen; Heim, Verena; Röschenthaler, Franz; Kirschbaum, Verena; Zachau, Hans G.

doi:10.1002/(sici)1521-4141(199805)28:05<1458::aid-immu1458>3.0.co;2-5

Cited by 32 publications

(36 citation statements)

References 37 publications

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“…By definition, the IS represents a boundary within the locus, separating the array of upstream V gene segments from the downstream J regions. The IS either becomes deleted or translocated far upstream after V-J joining at least 260 kb, based on distance of the closest V gene with a reverse orientation (26). This region, therefore, is a likely candidate to contain an element(s) that specifies regulation by its physical location or relocation relative to other important components within the Ig gene locus.…”

Section: Resultsmentioning

confidence: 99%

“…The V family residing closest to J1 is V21 (24,26,69,70). Previously we performed chromosome fragmentation of V21 gene segments within the recombinant YAC clone FAW.A3 and found that the length of the IS is about 20 kb and that the closest V21 family member to J1 is V21G (24).…”

Section: Resultsmentioning

confidence: 99%

“…The mouse locus is the largest multi-gene family locus thus far identified with respect to genomic length, spanning more than 3.5 megabases (25)(26)(27)(28)(29)(30). The locus contains 96 potentially functional V genes that have been grouped into 18 families based on sequence homologies (29,31,32), 4 functional and 1 non-functional J regions, and a single C exon.…”

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confidence: 99%

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Chromatin Structural Analyses of the Mouse Igκ Gene Locus Reveal New Hypersensitive Sites Specifying a Transcriptional Silencer and Enhancer

Liu

George-Raizen

et al. 2002

Journal of Biological Chemistry

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To identify new regulatory elements within the mouse Ig locus, we have mapped DNase I hypersensitive sites (HSs) in the chromatin of B cell lines arrested at different stages of differentiation. We have focused on two regions encompassing 50 kilobases suspected to contain new regulatory elements based on our previous high level expression results with yeast artificial chromosome-based mouse Ig transgenes. This approach has revealed a cluster of HSs within the 18-kilobase intervening sequence, which we cloned and sequenced in its entirety, between the V gene closest to the J region. These HSs exhibit pro/pre-B cell-specific transcriptional silencing of a V gene promoter in transient transfection assays. We also identified a plasmacytoma cell-specific HS in the far downstream region of the locus, which in analogous transient transfection assays proved to be a powerful transcriptional enhancer. Deletional analyses reveal that for each element multiple DNA segments cooperate to achieve either silencing or enhancement. The enhancer sequence is conserved in the human Ig gene locus, including NF-B and E-box sites that are important for the activity. In summary, our results pinpoint the locations of presumptive regulatory elements for future knockout studies to define their functional roles in the native locus.The mouse immunoglobulin (Ig) gene locus has provided a paradigm to investigate many challenging and biologically relevant problems, including site-specific recombination (1-5), tissue-specific transcriptional regulation (1, 6, 7), somatic hypermutation (8 -11), DNA methylation (12-14), the relationship between chromatin structure and function (15-23), and the evolution of DNA sequence organization (24).The mouse locus is the largest multi-gene family locus thus far identified with respect to genomic length, spanning more than 3.5 megabases (25-30). The locus contains 96 potentially functional V genes that have been grouped into 18 families based on sequence homologies (29, 31, 32), 4 functional and 1 non-functional J regions, and a single C exon. The V families are semi-clustered but partially interspersed with other V families (25,29). The most 5Ј V gene is a member of the V24 family, some 3.5-megabases away from the J-C region (29). The most 3Ј V gene is V21G (29), 18 kb 1 away from J1 gene segment (this work).Previous studies have identified several cis-acting regulatory elements in the mouse Ig locus. All of these elements except for V gene promoter elements reside in a 16-kb segment near or within the J-C region toward the 3Ј end of the locus. These include two germ line promoter elements (33, 34), KI-KII sequences (35), two non-B cell-specific silencers (36, 37), a nuclear matrix association region (MAR) (38), an intronic enhancer (Ei) (39), and a 3Ј enhancer (E3Ј) (40). In some instances targeted deletions of these elements have been performed in cell lines or mice, permitting their functional significance to be addressed in the native locus. Deletion of a germ line promoter or KI-KII sequences or both res...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Chromatin Structural Analyses of the Mouse Igκ Gene Locus Reveal New Hypersensitive Sites Specifying a Transcriptional Silencer and Enhancer

Liu

George-Raizen

et al. 2002

Journal of Biological Chemistry

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“…gov). Comparisons with germ-line genes followed the nomenclature of H. G. Zachau (27)(28)(29). Analysis of V-J junctions provided the ratio of nonfunctional͞functional sequences (NF͞F ratio).…”

Section: Rna Preparation and Rt-pcrmentioning

confidence: 99%

“…1). This pro-B repertoire involved V segments dispersed throughout the locus (including the most upstream hf24) and belonging to the four V contigs (Table 1) (27)(28)(29). No transcript included the J 3 segment known to lack a functional recombination signal (33).…”

Section: Features Of Sequences Expressed In Pro-b Cellsmentioning

confidence: 99%

RNA surveillance down-regulates expression of nonfunctional κ alleles and detects premature termination within the last κ exon

Delpy

Sirac

Magnoux

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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Random V(D)J junctions would generate nonfunctional and͞or out-of-frame sequences in about two-thirds of cases and result in abundant transcripts encoding truncated proteins. Although allelic exclusion at the DNA recombination level ensures that a single allele is functional, the frequent biallelic rearrangements need additional mechanisms to down-regulate aberrant transcripts in those cells with both a functionally and a nonfunctionally rearranged allele. The process of nonsense-mediated decay targets aberrantly rearranged Ig heavy-chain transcripts, but the situation of light-chain mRNAs is more complex, because they do not meet the usual requirements for nonsense-mediated decay and most often lack a spliceable intron downstream of the premature termination. We studied immunoglobulin heavy-chain ؊͞؊ pro-B cells in which light chain genes get rearranged and expressed in the absence of any selection for the assembly of a functional B cell receptor. Using this model, we show that the whole locus is accessible in pro-B cells and allows the assembly of a broad spectrum of V J segments, most of which are out-of-frame. This model provides an evaluation of the in vivo efficiency of RNA surveillance toward aberrant mRNAs produced in pro-B cells. Our data show that nonfunctional transcripts are excluded from the mature mRNA pool not only by detecting termination in an upstream exon but also by detecting changes in the position of termination within the last exon. Similar mechanisms efficiently down-regulate nonfunctional transcripts arising in normal mature B cells due to the biallelic transcription of rearranged genes. R andom deletions or additions at the Ig V(D)J junctions generate two-thirds of nonfunctional out-of-frame rearranged genes in B cell progenitors (1-3). Cell selection further allows the outgrowth of clones, each producing a single Ig selected for functionality and affinity for a non-self antigen determinant (4). Although some of those clones carry both functional and nonfunctional alleles of the immunoglobulin heavy-chain (IgH) and͞or light IgL loci, expression of truncated proteins is not observed in normal B cells, where aberrant transcripts are only present in very low amounts (5). For light chain (LC) genes, although the observed frequency of B cells carrying both a functional and a nonfunctional allele is Ͼ30% (1, 3), out-of-frame mature mRNA sequences were rarely obtained (6). Such an exclusion of nonfunctional Ig mRNA in B cells could involve transcriptional down-regulation and͞or mRNA quality control processes. Allelic asymmetry at the transcriptional level has been demonstrated for several cytokine genes (7,8). Concerning Ig genes, differences in the methylation status of alleles have been reported and correlated with an asymmetry in the replication pattern and the nuclear localization (9-10). However, transcriptional silencing of an excluded Ig gene allele has not been demonstrated, and, on the contrary, detection of rare out-of-frame transcripts in normal B cells indicates that this silencing...

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The central part of the mouse immunoglobulin κ locus

et al. 1999

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At the present state of analysis the central part of the kappa locus comprises four contigs of together 1.2 Mb and contains 55 Vkappa genes. It is flanked by the 3' part of the locus with 22 Vkappa genes in 0.4 Mb (T. Kirschbaum et al., Eur. J. Immunol. 1998. 28: 1458-1466) and the 5' part with 63 Vkappa genes in six contigs of together 1.5 Mb (F. Röschenthaler et al., accompanying report). The 5' and the central regions have one large contig in common. A part of the central region is linked to the 3' region resulting in a 1.1-Mb contig. The structure of the contigs was established mainly by the analysis of overlapping cosmid clones derived from genomic DNA and yeast and bacterial artificial chromosomes (YACs and BACs) and by PCR techniques. Pulsed-field gel electrophoresis of YAC digests indicated that three gaps between the contigs of the central region are 10-40 kb in size, comprising together about 90 kb. Internal duplications in this part of the locus and rearranged YACs were the major problems of the structural work. Structural details are to be found on the Internet at http://www.med.uni-muenchen.de/biochemie/zach au/kappa.htm. In a concluding section of the report the mouse kappa locus is compared to the human one and some aspects of the evolution of the kappa locus are discussed.

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The 3 ′ part of the immunoglobulin κ locus of the mouse

Cited by 32 publications

References 37 publications

Chromatin Structural Analyses of the Mouse Igκ Gene Locus Reveal New Hypersensitive Sites Specifying a Transcriptional Silencer and Enhancer

Chromatin Structural Analyses of the Mouse Igκ Gene Locus Reveal New Hypersensitive Sites Specifying a Transcriptional Silencer and Enhancer

RNA surveillance down-regulates expression of nonfunctional κ alleles and detects premature termination within the last κ exon

The central part of the mouse immunoglobulin κ locus

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