Direct in vivo VH to JH rearrangement violating the 12/23 rule

Koralov, Sergei B.; Novobrantseva, Tatiana; Hochedlinger, Konrad; Jaenisch, Rudolf; Rajewsky, Klaus

doi:10.1084/jem.20041577

Cited by 31 publications

(26 citation statements)

References 30 publications

(36 reference statements)

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“…However, when the V H segment is joined in the fetal rearrangements, the exonucleolytic activity has already increased to an adult-like level, and therefore both the V H and the D5Ј coding ends present similar excision as the adults. In this study we could confirm previous reports from cultured mouse B cell precursors (37), mouse B cells (51), and human cord blood pre-B cells (36) that the ratio between productive and nonproductive rearrangements increases significantly throughout development. Moreover, if both alleles are rearranged, the ratio between productive and nonproductive rearrangements should be 2.5:1, which in our study is closest to that noted with the fetal repertoire.…”

Section: Discussionsupporting

confidence: 81%

Developmental Changes in the Human Heavy Chain CDR3

Souto-Carneiro

Sims

Girschik

et al. 2005

The Journal of Immunology

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The CDR3 of the Ig H chain (CDR3H) is significantly different in fetal and adult repertoires. To understand the mechanisms involved in the developmental changes in the CDR3H of Ig H chains, sets of nonproductive VHDJH rearrangements obtained from fetal, full-term neonates and adult single B cells were analyzed and compared with the corresponding productive repertoires. Analysis of the nonproductive repertoires was particularly informative in assessing developmental changes in the molecular mechanisms of VHDJH recombination because these rearrangements did not encode a protein and therefore their distribution was not affected by selection. Although a number of differences were noted, the major reasons that fetal B cells expressed Ig H chains with shorter CDR3H were both diminished TdT activity in the DJH junction and the preferential use of the short JH proximal D segment D7–27. The enhanced usage of D7–27 by fetal B cells appeared to relate to its position in the locus rather than its short length. The CDR3H progressively acquired a more adult phenotype during ontogeny. In fetal B cells, there was decreased recurrent DJH rearrangements before VH-DJH rearrangement and increased usage of junctional microhomologies both of which also converted to the adult pattern during ontogeny. Overall, these results indicate that the decreased length and complexity of the CDR3H of fetal B cells primarily reflect limited enzymatic modifications of the joins as well as a tendency to use proximal D and JH segments during DJH rearrangements.

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Section: Discussionsupporting

confidence: 81%

Developmental Changes in the Human Heavy Chain CDR3

Souto-Carneiro

Sims

Girschik

et al. 2005

The Journal of Immunology

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“…V(D)J recombination in vivo is governed by the 12/23 rule, as originally suggested by Early and colleagues (23). However, several exceptions to this rule have been documented: for example, 23/23 recombination detected in a mouse strain with a noncanonical immunoglobulin H locus (38) and the apparent cleavage of isolated 12 RSS sequences (49,63). The 12/23 rule also operates in vitro in reactions using purified components (24,36,60,72,73).…”

Section: Resultsmentioning

confidence: 93%

Base Flipping in V(D)J Recombination: Insights into the Mechanism of Hairpin Formation, the 12/23 Rule, and the Coordination of Double-Strand Breaks

Bischerour

Roth

et al. 2009

Molecular and Cellular Biology

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Tn5 transposase cleaves the transposon end using a hairpin intermediate on the transposon end. This involves a flipped base that is stacked against a tryptophan residue in the protein. However, many other members of the cut-and-paste transposase family, including the RAG1 protein, produce a hairpin on the flanking DNA. We have investigated the reversed polarity of the reaction for RAG recombination. Although the RAG proteins appear to employ a base-flipping mechanism using aromatic residues, the putatively flipped base is not at the expected location and does not appear to stack against any of the said aromatic residues. We propose an alternative model in which a flipped base is accommodated in a nonspecific pocket or cleft within the recombinase. This is consistent with the location of the flipped base at position ؊1 in the coding flank, which can be occupied by purine or pyrimidine bases that would be difficult to stabilize using a single, highly specific, interaction. Finally, during this work we noticed that the putative base-flipping events on either side of the 12/23 recombination signal sequence paired complex are coupled to the nicking steps and serve to coordinate the double-strand breaks on either side of the complex.Antibody and T-cell receptor (TCR) diversity is generated by V(D)J recombination initiated by the RAG proteins, RAG1 and RAG2. The recombination signal sequences (RSSs), where recombination takes place, have a distinctive arrangement resembling transposon ends. The relationship between V(D)J recombination and transposition was established beyond doubt by the discovery of RAG-mediated transposition and by the identification of a triad of conserved active-site residues. This evidence placed RAG1 firmly within the family of transposases and retroviral integrases that have a characteristic DDE triad of amino acid residues that coordinate catalytic metal ions in the active site (1,26,30,35,39,46). Later, the Transib family of transposons was identified as the likely ancestral group of RAG1 (33).In V(D)J recombination, the RAG proteins excise the DNA between a pair of RSSs. This fragment is the equivalent of an excised transposon, and it takes no further part in the canonical V(D)J recombination reaction. Instead, the variable regions of the genes encoding antibodies and TCR are created by the imprecise rejoining of the flanking DNA, referred to as the "coding flank." A key feature of the cleaved coding flanks is that they have covalently closed hairpin ends. The asymmetric resolution of these hairpins contributes to the diversification of the coding sequences during rejoining. The hairpins themselves arise as a consequence of the molecular mechanism RAG-mediated RSS cleavage.The crystal structure for the catalytic core of the human immunodeficiency virus type 1 integrase protein revealed a structural fold shared in common with RNase H and the Holliday junction resolving enzyme RuvC (22). RNase H and RuvC monomers each perform a simple nicking reaction that requires a single phosphoryl transfer ...

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“…It thus constitutes a powerful tool for dissecting genetic and epigenetic regulatory mechanisms within the genome. The cloning of mice from lymphocytes, for example, made it possible to study the process of allelic regulation (Gerdes and Wabl, 2004) and secondary Ig rearrangements (Koralov et al, 2005) in monoclonal mice. Similarly, nuclear transfer has been used to determine whether the variety of olfactory receptors is created by gene rearrangements similar to the generation of antibody diversity in the immune system.…”

Section: Epigenetic Versus Genetic Alterationsmentioning

confidence: 99%

Mammalian nuclear transfer

Meissner

Jaenisch

2006

Developmental Dynamics

Self Cite

112

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During development, the genetic content of each cell remains, with a few exceptions, identical to that of the zygote. Differentiated cells, therefore, retain all the genetic information necessary to generate an entire organism (nuclear totipotency). Nuclear transfer (NT) was initially developed to test experimentally this concept by cloning animals from differentiated cells. It has, since then, been used to study the role of genetic and epigenetic alterations during development and disease. In this review, we highlight some of the milestones in mammalian NT reached in the 50 years after the first nuclear transplantations in frogs. We also address problems associated with mammalian nuclear transfer and provide a survey on current NT and stem cell technology. In the long term, nuclear transfer or alternative strategies aim to generate customized pluripotent cells, which would be invaluable to medical research and therapy. Developmental Dynamics 235: 2460 -2469, 2006.

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Direct in vivo VH to JH rearrangement violating the 12/23 rule

Cited by 31 publications

References 30 publications

Developmental Changes in the Human Heavy Chain CDR3

Developmental Changes in the Human Heavy Chain CDR3

Base Flipping in V(D)J Recombination: Insights into the Mechanism of Hairpin Formation, the 12/23 Rule, and the Coordination of Double-Strand Breaks

Mammalian nuclear transfer

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