1 General introduction and outline of the thesis | 11 At the same time, this system poses a serious threat to genome stability if not tightly regulated. The V(D)J gene recombination process requires the activity of the recombination-activating gene-1 (RAG1) and recombination-activating gene-2 (RAG2) protein complex. RAG1 and RAG2 form a complex that cuts DNA at specific sites within the immunoglobulin (Ig) and T-cell receptor (Tcr) loci, thereby initiating gene recombination. DNA cleavage in genes outside of the Ig regions could give rise to potentially oncogenic genetic lesions such as chromosomal translocations or deletions. As a matter of fact, there is compelling evidence that some of the genomic lesions identified in subsets of B-cell acute lymphoblastic leukemia (B-ALL) result from aberrant RAG1/2 recombination activity. Though in the last couple of decades the physiological mechanisms of the regulation RAG1/2 regulations have extensively been studied, the mechanisms of pathological regulation of RAG1/2 are less well described. This thesis aims to provide a deeper understanding of the mechanisms that regulate the expression and the activity of RAG1 and RAG2 in response to exogenous DNA damage, but also to DNA damage originating from RAG-dependent V(D)J recombination activity itself. Understanding the intricacies of RAG1/2 regulation is important for our understanding of how the integrity of the genome is maintained in developing B cells that have to deal with DNA damage during the Ig receptor formation. The misregulation of RAG1/2, or the illegitimate targeting of RAG1/2, might also pose a threat to genome integrity, as off-target DNA cleavage (outside the Ig loci), could potentially give rise to genomic lesions that may result in oncogenic mutations. In Chapter 2, the current understanding of B-cell development and the regulation of RAG1 and RAG2 expression and activity is extensively summarized. The responses of pre-B cells to DNA damage, and specifically the regulatory role of the double-stranded DNA breaks (DSBs) are described in detail. This chapter reviews also the evidence for a possible role of RAG1/2 in the etiology of B-cell malignancies, and the targeting properties of RAG1/2 in this context. Aberrant RAG1/2 targeting during B-cell development has been implicated in the development of lymphoid malignancies. In Chapter 3 we developed a method that allows the identification of RAG1/2-induced DSBs on a genome-wide scale in developing pre-B cells. We found that many of the RAG1/2-induced DNA breaks can be detected outside of the Ig loci, providing in vivo evidence for the off-target activity of RAG1/2. Moreover, analysis of the common denominators with regard to the genomic locations and sequence motifs of the RAG1/2-induced DNA breaks revealed an enrichment of simple sequence repeats (SSR) and GC-rich regions in the proximity of the RAG1/2-induced DNA breaks. To gain a further understanding of the implications of programmed DNA damage in developing lymphocytes, it is essential to unravel the intricacies of the regulation of RAG1/2 activity during B-cell development, especially in the context of the DNA damage originating from V(D)J recombination itself. Inappropriate regulation of RAG1/2 expression may result in per-
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