Target Specificity of Immunoglobulin Class Switch Recombination Is Not Determined by Nucleotide Sequences of S Regions

Kinoshita, Kazuo; Tashiro, Junko; Tomita, Shuhei; Lee, Chung-Gi; Honjo, Tasuku

doi:10.1016/s1074-7613(00)80650-0

Cited by 76 publications

(57 citation statements)

References 51 publications

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“…Previously, we described an artificial CSR substrate in which each of two S regions was directed by a different constitutive promoter, and transcripts were spliced (22). This study demonstrated that the isotype specificity of CSR was not determined by the nucleotide sequences of S regions.…”

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confidence: 82%

“…This plasmid was digested with restriction enzymes to generate a fragment containing the whole transcription unit as SR␣-TM-GFP. The BOS-EC-SS fragment and the SR␣-TM-GFP were connected on a plasmid with the neomycin-resistance gene cassette pSMC-11 (22), which is derived from pMC1neopolyA (Stratagene). The recombinants with the two transcription units in the opposite directions were designated as pSCR(0,0).…”

Section: Construction Of Inversion-type Class-switch Substrates Andmentioning

confidence: 99%

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Variable deletion and duplication at recombination junction ends: Implication for staggered double-strand cleavage in class-switch recombination

Chen

Kinoshita²,

Honjo³

2001

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

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Immunoglobulin class-switch recombination (CSR) gives rise to looped-out circular DNA of a cleaved S segment, which is lost eventually after cell divisions. To understand the molecular mechanism of S region cleavage during CSR, we constructed artificial CSR substrates in which inversion-type CSR takes place to retain the cleaved S segment. Sequencing analyses of recombinant clones of these substrates revealed that varying degrees of deletions and duplications exist at CSR breakpoints, suggesting the involvement of staggered cleavage of the S region in CSR. In addition, mutations frequently found near junctions showed a similar profile of base replacement to Ig somatic hypermutation. These findings suggest that single-strand tails of staggered cleavage may be repaired by error-prone DNA synthesis. N ewly generated B cells expressing IgM and IgD migrate to peripheral lymphoid organs where they are activated by encounters with antigens, resulting in the clonal expansion of antigenspecific B cells. Activated B cell clones secrete not only IgM but also other isotypes of Ig molecules without altering the antigen specificity. This phenomenon, termed class switching, is mediated by DNA recombination in the Ig heavy (H) chain constant (C) region locus, which results in expression of a new transcription unit containing the same productively rearranged variable region (V H ) gene with a downstream C H gene other than C .Class-switch recombination (CSR) from IgM to another isotype takes place anywhere in several-kilobase G-rich regions, termed switch (S) regions, which are located 5Ј to each set of C H exons and consist of tandemly repetitive short sequences with many palindromes (1-9). CSR is accompanied by a looping-out deletion of intervening DNA sequences (10-12). Only limited sequence homology is found near the site of recombination between S and other S sequences (13-15). Because the junctions of CSR are scattered over the S regions and in some instances in proximity to but outside the S regions, CSR is a region-specific recombination event.It has been well established that the ability of a given cytokine to determine the target specificity of CSR is correlated with transcription induction (germline transcription) from a specific intron promoter located immediately upstream of each S region (16). The germline transcription is believed to regulate chromatin opening (accessibility) of the target S region to determine the isotype specificity of CSR (17, 18). Efficiency of CSR seems to be correlated quantitatively with the activity of germline transcription (19). In addition, subsequent splicing of the CSR germline transcripts seems important for CSR (20,21), but the exact role of germline transcripts per se in CSR remains to be elucidated.Previously, we described an artificial CSR substrate in which each of two S regions was directed by a different constitutive promoter, and transcripts were spliced (22). This study demonstrated that the isotype specificity of CSR was not determined by the nucleotide sequences of S regio...

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confidence: 82%

Section: Construction Of Inversion-type Class-switch Substrates Andmentioning

confidence: 99%

Variable deletion and duplication at recombination junction ends: Implication for staggered double-strand cleavage in class-switch recombination

Chen

Kinoshita²,

Honjo³

2001

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

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“…Genomic DNA was purified from the same source after separation of RNA from TRIzol lysate. cDNA was synthesized with Superscript II (GIBCO) by using 2 g of total RNA and 1 g of poly d(T) [12][13][14][15][16][17][18] (Amersham Pharmacia) in a 20-l reaction volume, one twentieth of which was used as a template for reverse transcription (RT)-PCR in a 25-l reaction volume. Amplification of AID transcripts was done by an initial denaturing step of 94°C for 5 min followed by 22 cycles of PCR (94°C for 20 s, 58°C for 30 s, 72°C for 1 min) by using recombinant Taq polymerase (Takara) with a 119-and 118-primer pair (11).…”

Section: Methodsmentioning

confidence: 99%

A hallmark of active class switch recombination: Transcripts directed by I promoters on looped-out circular DNAs

Kinoshita

Harigai

Fagarasan

et al. 2001

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

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To specify when and where Ig class switch recombination (CSR) takes place, a good molecular marker closely associated with active CSR is required. CSR is accompanied by deletion of circular DNA from the Ig heavy chain locus. The circular DNA contains a DNA segment between S and a target S region including its I promoter, which is driven by specific cytokine stimulation before CSR. We found that the specific I promoter is still active in looped-out circular DNA and directs production of I-C transcripts termed "circle transcripts.

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“…Isotype class switching in activated B cells illustrates this capability. The location of class switch recombination (CSR) is determined by lymphokine signals that control the transcription of "switch" regions where the necessary double-stranded breaks occur [190,191]. In other words, the immune system instructs the activated B cells which class of antibody to produce in response to a particular infection by targeting a specific DNA breakage-and-joining process.…”

Section: Targeting Of Nge and Mobile Elementsmentioning

confidence: 99%

How life changes itself: The Read–Write (RW) genome

Shapiro

2013

Physics of Life Reviews

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The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

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Target Specificity of Immunoglobulin Class Switch Recombination Is Not Determined by Nucleotide Sequences of S Regions

Cited by 76 publications

References 51 publications

Variable deletion and duplication at recombination junction ends: Implication for staggered double-strand cleavage in class-switch recombination

Variable deletion and duplication at recombination junction ends: Implication for staggered double-strand cleavage in class-switch recombination

A hallmark of active class switch recombination: Transcripts directed by I promoters on looped-out circular DNAs

How life changes itself: The Read–Write (RW) genome

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