Date on Master's Thesis/Doctoral Dissertation
Biochemistry and Molecular Biology
Biochemistry and Molecular Biology, PhD
Committee Co-Chair (if applicable)
Mitchell, Thomas C.
Mitchell, Thomas C.
genomic; germline diversity; mouse antibody; repertoire developement
Given the diversity and complexity within immunoglobulin (IG) loci, effective mouse models first require characterization of intra-strain differences and construction of high-quality reference assemblies for IG loci in several representative strains. To understand light chain germline diversity across biomedically significant mouse strains, we profiled the expressed IGK and IGL repertoires of 18 commonly used laboratory mouse strains using AIRR-seq. Across strains, we observed germline IGKV sequences shared by three different IGK haplotypes and a more conserved IGLV germline repertoire among common laboratory strains. Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing was used to sequence and assemble bacterial artificial chromosomes (BAC) clones spanning the IGH locus in BALB/cByJ and the IGK locus in NOD/LtJ, which represented divergent IG haplotypes. We assembled the BALB/cByJ-IGH assembly into five independent contigs containing 192 functional and 135 non-functional IGHV genes, 30 IGHD genes, 4 IGHJ genes, and 8 IGHC genes. The NOD/ShiLtJ-IGK assembly was assembled into two independent contigs, which contained 82 functional and 31 non-functional IGKV genes. These data guided construction of congenic strains on a C57BL/6 background that carried divergent BALB/cByJ or NOD/ShiLtJ IGH or IGK loci from, respectively. In addition, bulk AIRR-seq data from the BALB/cByJ-IGH congenic strain showed that divergent IGH haplotype influenced usage frequencies of germline IGKV and IGLV repertoire. Overall, this work revealed significant unexplored IG haplotype diversity through AIRR-seq, generated new IG reference assemblies, identified incomplete germline gene databases that lacked haplotype diversity, and provided evidence that heavy and light chain pairing frequencies are likely influenced by underlying IG haplotype variation.
Kos, Justin T., "Genomic tools and models for investigating the role of germline diversity in mouse antibody repertoire development." (2022). Electronic Theses and Dissertations. Paper 3825.