/ Independent Study Abstract: Recombination Signal Sequences
The diversity of the antigen receptor repertoire in mammals and other jawed vertebrates is made possible primarily by V(D)J recombination, a genetic mechanism that rearranges V, D, and J gene segments to form antigen receptor genes encoding unique antigen binding regions. V(D)J recombination is mediated by regions flanking the V, D, and J segments called recombination signal sequences (RSS), which include relatively well conserved 7- and 9-bp regions and a highly variable region of either 12- or 23-bp. Dr. Cowell et al. have developed a statistical method for detecting and predicting patterns of correlation between any number of nucleotides at any position in RSS, and have applied this method to a library of mouse RSS. Using this statistical method as a starting point, I will write a computer program to efficiently analyze RSS. I will then attempt to improve the model selection method used by Cowell et al., and test my new methods on the mouse RSS library and simulated data. I will then apply this method to analyze human RSS, and potentially RSS from other species as well, with the end goal of successful identification of RSS, prediction of their recombinogenic potential, and insight into their binding interactions with the V(D)J recombinase.