scid cells efficiently integrate hairpin and linear DNA substrates

Illegitimate DNA integration in mammalian cells

Foreign DNA integration is one of the most widely exploited cellular processes in molecular biology. Its technical use permits us to alter a cellular genome by incorporating a fragment of foreign DNA into the chromosomal DNA. This process employs the cell's own endogenous DNA modification and repair machinery. Two main classes of integration mechanisms exist: those that draw on sequence similarity between the foreign and genomic sequences to carry out homology-directed modifications, and the nonhomologous or 'illegitimate' insertion of foreign DNA into the genome. Gene therapy procedures can result in illegitimate integration of introduced sequences and thus pose a risk of unforeseeable genomic alterations. The choice of insertion site, the degree to which the foreign DNA and endogenous locus are modified before or during integration, and the resulting impact on structure, expression, and stability of the genome are all factors of illegitimate DNA integration that must be considered, in particular when designing genetic therapies.

The RAG proteins and V(D)J recombination: complexes, ends, and transposition

V(D)J recombination proceeds through a series of protein:DNA complexes mediated in part by the RAG1 and RAG2 proteins. These proteins are responsible for sequence-specific DNA recognition and DNA cleavage, and they appear to perform multiple postcleavage roles in the reaction as well. Here we review the interaction of the RAG proteins with DNA, the chemistry of the cleavage reaction, and the higher order complexes in which these events take place. We also discuss postcleavage functions of the RAG proteins, including recent evidence indicating that they initiate the process of coding end processing by nicking hairpin DNA termini. Finally, we discuss the evolutionary and functional implications of the finding that RAG1 and RAG2 constitute a transposase, and we consider RAG protein biochemistry in the context of several bacterial transposition systems. This suggests a model of the RAG protein active site in which two divalent metal ions serve alternating and opposite roles as activators of attacking hydroxyl groups and stabilizers of oxyanion leaving groups.

Ku86-deficient mice exhibit severe combined immunodeficiency and defective processing of V(D)J recombination intermediates

Ku is a heterodimeric DNA end binding complex composed of 70 and 86 kDa subunits. Here, we show that Ku86 is essential for normal V(D)J recombination in vivo, as Ku86-deficient mice are severely defective for formation of coding joints. Unlike severe combined immunodeficient (scid) mice, Ku86-deficient mice are also defective for signal joint formation. Both hairpin coding ends and blunt full-length signal ends accumulate. Contrary to expectation, Ku86 is evidently not required for protection of either type of V(D)J recombination intermediate. Instead, V(D)J recombination appears to be arrested after the cleavage step in Ku86-deficient mice. We suggest that Ku86 may be required to remodel or disassemble DNA-protein complexes containing broken ends, making them available for further processing and joining.

Mechanism of V(D)J recombination

V(D)J recombination can be separated into two basic operations: DNA cleavage and joining of broken ends. Our understanding of both reactions has increased substantially in the past year. Major advances include the development of a cell-free system capable of cleavage and the identification of several proteins involved in both V(D)J recombination and double-strand break repair.

Efficient nonhomologous and homologous recombination in scid cells

The severe combined immunodeficiency (scid) mutation affects both coding joint formation during immunoglobulin and T-cell receptor V(D)J recombination and double-strand break repair. We analyzed scid cells for their ability to undergo other types of DNA end joining: nonhomologous and homologous recombination. Using plasmid constructs carrying antibiotic resistance genes, we observed that the efficiency of nonhomologous integration in scid cells was equal to that in wildtype cell lines. In addition, there was no obvious difference in the fidelity of the integration and in the expression of the resistance genes. Moreover, scid cells were able to carry out homologous recombination of extrachromosomal substrates just as well as wildtype cells. These results suggest a mechanistic difference between nonhomologous integration and homologous recombination on the one hand and V(D)J recombination and double-strand break repair on the other.

Stimulation of defective DNA transfer activity in recombination deficient SCID cell extracts by a 72-kDa protein from wild-type thymocytes

The SCID (Severe Combined Immune Deficiency) mutation causes two DNA recombination deficiencies: an aberrant joining of V(D)J immunoglobulin gene elements and a failure to perform efficient repair of DNA double-strand breaks. A recently established cell-free assay for DNA transfer (DTA) was applied to study nuclear extracts from normal and SCID-derived cells. The recombination deficiency was reflected in the cell-free system: SCID lymphocyte and fibroblast extracts showed reduced levels of DTA activity on a variety of DNA substrates. Analysis of nuclear extracts prepared from wild-type thymocytes and B cells representing different stages in lymphocyte ontogeny revealed the highest activities at the most immature stages. With progression of development, DTA activity decreased. Corresponding to their early developmental arrest, V(D)J rearrangement-incompetent RAG-2-/- lymphocyte extracts show high DTA activity. In contrast, extracts from SCID early lymphocytes express very low DNA transfer activity. Induction of V(D)J rearrangement in vivo in a normal preB cell line lead to a co-induction of the cell-free recombination activity. This indicates a development stage specificity of cell-free DNA recombination, which temporally parallels V(D)J recombination. A protein could be purified to near-homogeneity from wild-type thymocytes which stimulates the recombination activity specifically in SCID thymocyte and proB cell extracts. This protein, SRSP (SCID Recombination Stimulatory Protein), migrates as a single band of approximately 72 kDa in SDS-polyacrylamide gel electrophoresis.

Characterization of coding ends in thymocytes of scid mice: implications for the mechanism of V(D)J recombination

We previously identified possible intermediates in V(D)J recombination at the TCR delta locus and characterized molecules with signal ends and with covalently sealed (hairpin) coding ends in thymocytes of scid mice by Southern blotting. Here, we use a sensitive ligation-mediated PCR assay to demonstrate that all coding ends detected in scid thymocytes are covalently sealed. Neither coding nor signal ends exhibit loss or addition of nucleotides. These data imply that hairpin formation is coupled to the initial cleavage at the signal/coding border, and that the cleavage step in V(D)J recombination is conservative. In scid/+ or wild-type thymocytes, hairpin coding ends are at least 1000-fold less abundant than signal ends. These results provide insight into the mechanism of V(D)J recombination.