DESCRIPTION (Provided by the applicant) Abstract: This proposal is directed towards the understanding of various mechanisms by which non-coding RNAs (ncRNA) govern antibody diversification during adaptive immune response. Antibodies are polypeptide complexes produced from B-lymphocytes that are present in the bodily fluids of vertebrates, and are used by the immune system to identify and neutralize foreign antigens, such as bacteria and viruses. Newly generated B cells migrate from bone-marrow to secondary lymphoid organs where they encounter antigens, and are stimulated to further undergo two Immunoglobulin (Ig) gene alterations known as class switch recombination (CSR) and somatic hypermutation (SHM). CSR is a B cell-specific DNA rearrangement reaction that replaces an Ig heavy chain constant region gene (CH) from C¿ with other downstream CH exons so that secondary isotypes (IgG, IgA etc) with different effector functions are generated. SHM, on the other hand, introduces point mutations into V genes at a very high rate, ultimately leading to increased antibody affinity. Though two distinct processes, CSR and SHM absolutely require transcription through the relevant Ig loci and activity of a single- strand DNA deaminase, Activation Induced cytidine Deaminase (AID). Approach: WE have previously observed that component of the ncRNA-processing pathway, the RNA exosome complex, regulate CSR in ex vivo assays. Here, we use a combination of modern computational biology, proteomics, high-throughput genomics and mouse genetics to identify and functionally characterize ncRNA generated in the Ig locus during affinity maturation. In addition, we will study the function of RNA exosome complex in CSR and SHM in vivo by generating various mouse model systems that harbor loss of function alleles of subunits of the RNA exosome complex. Implication: If successful, this study will be the first to demonstrate the role of ncRNA biogenesis pathway in the genetic and epigenetic control of the Ig locus. Understanding the mechanism of CSR and SHM is of paramount importance. Human patients with mutations in CSR/SHM pathway components suffer with severe immune-deficiencies, whereas aberrant chromosomal alterations in the Ig locus lead to various B and T cel malignancies. Understanding the regulation of the Ig locus via ncRNA will allow generation of directed clinical therapies for treatment of patients suffering various lymphocyte based diseases. Public Health Relevance: In this proposal we identify the mechanism by which non-coding RNA biogenesis pathways regulate antibody affinity maturation via class switch recombination and somatic hypermutation, two processes required for bio-defense via adaptive immune response. Antibodies are polypeptide complexes produced from B-lymphocytes that are present in the bodily fluids of vertebrates, and are used by the immune system to identify and neutralize foreign antigens, such as bacteria and viruses.

In this proposal we identify the mechanism by which non-coding RNA biogenesis pathways regulate antibody affinity maturation via class switch recombination and somatic hypermutation, two processes required for bio-defense via adaptive immune response. Antibodies are polypeptide complexes produced from B-lymphocytes that are present in the bodily fluids of vertebrates, and are used by the immune system to identify and neutralize foreign antigens, such as bacteria and viruses.! !