The main goal of this work is to understand the basic mechanisms underlying the developmental regulation of V(D)J recombination. Developmental regulation is thought to depend in part on regulated expression of the RAG1/RAG2 recombinase, and in part on changes in T cell receptor (TCR) locus chromatin structure and organization that allow access to and synapsis of recombination signal sequences. The specific focus of this project is the murine TCRalpha/delta locus, which undergoes recombination according to distinct developmental programs during the double negative (DN) and double positive (DP) stages of thymocyte development.
One aim will be to more fully characterize how local changes in chromatin structure are established and how such changes contribute to the recombination of Vdelta gene segments in DN thymocytes and Jalpha gene segments in DP thymocytes. This will be accomplished through detailed mapping of chromatin disruption, RAG protein binding and V(D)J recombination on genetically manipulated alleles.
A second aim will be to evaluate the hypothesis that developmentally regulated changes in locus conformation are essential to support the developmental program. Developmental changes in locus conformation will be mapped by three-dimensional fluorescence in situ hybridization (3D-FISH) and chromosome conformation capture (3C). Genetically manipulated strains of mice will be used to test the roles of TCR locus enhancers and the roles of proteins CTCF and cohesin in defining locus conformational states. To formally test the significance of locus conformation, the TCRalpha/delta locus will genetically modified to permit trapping of a contracted conformation.
A third aim will be to elucidate the mechanism by which the architectural protein SATB1 regulates recombinase expression in DP thymocytes. The hypothesis to be tested is that SATB1 is required for long distance interactions in the RAG locus that are critical for transcription of the RAG genes.

Public Health Relevance

V(D)J recombination is essential for the development of a functional immune system. Failure of V(D)J recombination can cause immunodeficiency and errors in V(D)J recombination can result in chromosomal translocations that contribute to tumorigenesis. These studies will elucidate basic mechanisms that contribute to normal immune system development and pathologies such as immunodeficiency and cancer.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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No Study Section (in-house review) (NSS)
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Marino, Pamela
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Duke University
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Rupp, Levi J; Chen, Liang; Krangel, Michael S et al. (2016) Molecular Analysis of Mouse T Cell Receptor α and β Gene Rearrangements. Methods Mol Biol 1323:179-202
Zhao, Lijuan; Frock, Richard L; Du, Zhou et al. (2016) Orientation-specific RAG activity in chromosomal loop domains contributes to Tcrd V(D)J recombination during T cell development. J Exp Med 213:1921-36
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