Title: Role of secondary IgH rearrangements in B cell Ab repertoire
Description: In mammals, antibody diversity is generated by the RAG mediated recombination of V, D and J elements into V(D)J joints encoding variable regions of immunoglobulins. The imprecise nature of the joining process leads to a significant number of non-functional rearrangements with approximately two thirds of the joints being out of frame. To rescue the cells that have acquired non-productive rearrangements or cells with rearrangements that result in self-reactive specificities, B cells often utilize secondary rearrangements. While the extent of secondary recombination has been well characterized for V L J L joints of antibody light chains, where further rearrangement of upstream un-rearranged V L to downstream J L elements can take place, the physiological role of heavy chain secondary rearrangements has not been established. RAG mediated V(D)J recombination can modify pre-existing V H D H J H joints by a process called V H replacement. During this process an upstream non-rearranged V H element invades a pre-existing V H D H J H joint at a conserved cryptic heptamer which is located close to the 3' end of most V H genes.

In order to study the mechanism and diversifying power of V H replacement we generated a mouse model in which the entire antibody repertoire depends upon the replacement of a single non-productive V H D H J H joint inserted into its physiological location in the IgH locus. These mice produced a large compartment of B lymphocytes, which expressed a highly diverse antibody repertoire generated by V H replacement and a second process of non-canonical V(D)J recombination, direct V H to J H joining. We found V H to J H joining to be three fold less efficient than V H replacement. V H replacement rarely generated detectable sequence duplications at the sites of V H invasion and often proceeded through conserved microhomology sequences at the 3' end of V H genes. Because V H replacement frequently did not leave diagnostic molecular footprints of the reaction, previous assessments of frequency of V H replacement that relied on footprint analysis likely underestimated the role of this mechanism in IgH repertoire generation. Direct V H to J H joining is also described in this dissertation in the context of another mouse where the entire IgH repertoire is generated from a D H -less allele by this process. We show that while this process, which violates the 12/23, rule is inefficient, it can nevertheless support B cell development.

In order to study the contribution of V H replacement to B cell development beyond the rescue of progenitor B cells with two non-functional IgH rearrangements, we also generated and studied a mouse model in which a productive V H D H J H joint is positioned in its physiological context in the IgH locus.We show that despite the presence of the productive IgH rearrangement, a significant number of cells acquire a new V H D H J H joint by either an in frame V H replacement of the original V H D H J H rearrangement or by inactivation of the knock-in allele and subsequent rearrangement of the WT IgH allele. Surprisingly, majority of the replacement events in this mouse utilize the most proximal V H element. The difference in V H usage between the mouse models with productive and non-productive insertions is discussed in the context of IgH locus accessibility and allelic exclusion.