Abstract
Introduction Immune repertoire diversity is largely achieved by a process termed V(D)J recombination, during which functional antigen receptor genes are assembled from discrete gene segments through site-specific DNA rearrangements. The V(D)J recombinase includes two lymphocyte specific proteins: recombination activating gene 1 (RAG1) and recombination activating gene 2 (RAG2). They form a protein complex (RAG1/2) that recognizes recombination signal sequences (RSSs) flanking each receptor gene segment and introduces a DNA double-strand break (DSB) at the border between a RSS and a coding gene segment. The RSS contains highly conserved heptamer and nonamer motifs separated by either 12- or 23-base pairs of poorly conserved sequence (12RSS and 23RSS, respectively). Efficient recombination occurs only between a 12RSS and a 23RSS, which is called the 12/23 rule. Illegitimate V(D)J recombination, however, can occur outside of antigen receptor loci to form chromosomal abnormalities, such as translocations and deletions. Some of these breakpoints containing an RSS-like motif are proposed to be mis-targeted by the RAG1/2 proteins to form DSBs. Other breakpoints are believed to undergo RAGmediated structure-specific cleavage.|Specific aims The purpose of my thesis study is to explore the molecular mechanisms underlying RAG1/2-mediated cleavage of breakpoints that cause chromosomal abnormalities in lymphoid malignancies. This study consists of two aims: (1) defining molecular mechanisms for RAG1/2-mediated sequence-specific cleavage of cryptic RSSs (cRSSs); (2) defining molecular mechanisms for RAG1/2-mediated structure-specific illegitimate cleavage of cryptic RSSs.|Background information, results and conclusions for each sub-study are summarized below: (omitted here)