Causes and Consequences of Programmed DNA Breaks and Translocations in B Cell Nuclei

Mammalian cells are regularly subjected to DNA damaging agents that create DNA double strand breaks (DSBs) within the genome which must be managed and repaired to avoid cancerous outcomes. In certain cell types, in particular B cells of the immune system, developmentally programmed DNA damage also occurs and must be correctly repaired. In this body of work, I investigated some of the causes and consequences of DNA repair failure as a result of programmed DSBs in B cell nuclei. The results of this research indicate that two proteins, recombination activating gene (RAG) and activation-induced cytidine deaminase (AID), which both mediate programmed DNA breaks in the immunoglobulin loci, have non-canonical activities. The novel non-canonical activities described in this work relate to both the timing of DNA cleavage and repair as well as the influence of the DNA target sequences in this process. An important consequence of genome instability created by RAG and AID is the formation of chromosomal translocations that lead to cancer development. However, the impact of translocation formation on the structure and function of affected chromosomes in the nucleus is not well understood. Here I used the translocations generated by unrepaired DNA breaks in progenitor B cells to examine the 3D relationships of translocated chromosomes in lymphoma nuclei and the effect of translocation on gene expression. My research demonstrated that despite gross changes in DNA sequence organization attributable to the translocation, there were minimal affects on the organization or expression of genes near the breakpoint. Taken together these studies reveal unappreciated non-canonical aspects of programmed DNA breakage and repair that occurs in B lymphocytes which influences both normal B cell development and cancer progression. In addition, these studies add a critical component to our understanding of the functional organization of the genome in the cell nucleus. Combined, these data can aid in both the identification of critical factors that may influence human lymphomagenesis and the development of potential therapeutics