Long-distance DNA interactions are critically involved in developmental regulation of gene expression, stem cell biology, and immune functions. The immunoglobulin (Ig) genes best exemplify the importance of long- distance DNA interactions as somatic rearrangement of these genes requires linkage of DNA sequences separated by as much as 3 megabases. Similarly, Ig class switch recombination (CSR) requires formation of both constitutive and cytokine-inducible loops within switch region DNA sequences, and interactions between enhancer sequences (E? and 3'RR enhancers) that are separated by 200 kb. Although many long-distance loops have been identified at the Ig loci, the molecular mechanisms that control their formation remain unclear. We recently published the novel observation that the transcription factor YY1 controls antibody repertoires at the Ig? locus and physically interacts with condensin, cohesin, and Polycomb Group (PcG) proteins, all of which are involved in long-distance DNA loop formation. Moreover, co-localization of YY1 with these proteins within the Ig? locus suggests that YY1 controls long-distance DNA interactions. In further support, recent evidence shows that YY1 plays critical roles in long-distance DNA interactions at the IgH, Ig?, and the Th2 cytokine loci. Notably, our preliminary data demonstrate that YY1 conditional knock-out reduces CSR and dramatically ablates long-distance DNA loops required for CSR. Based on our combined data, we hypothesize that YY1 developmentally regulates CSR by both constitutive and cytokine inducible binding to DNA, and subsequent recruitment of proteins (condensin, cohesin, PcG proteins, etc.) required for long-distance DNA loop formation. We are uniquely poised to test this hypothesis in our recently developed powerful and innovative YY1 conditional knockout/reconstitution primary ex vivo splenoctye system. As YY1 is a ubiquitous protein, its role in DNA loop formation must be regulated tissue-specifically and B cell stage-specifically by either post-translational modification, or by developmentally regulated protein-protein interactions. Therefore, in addition to determining how YY1 contributes to long-distance DNA loop formation, we will identify the YY1- interacting proteins required for loop formation, and characterize the developmental and inducible mechanisms governing this process. Defining the role of YY1 in CSR will provide foundational insights into humoral immune mechanisms, and may lead to new paradigms of long-distance DNA interactions, and the translocations that drive lymphomagenesis. We have over two decades experience with YY1 function and have developed numerous unique molecular clones and genetically modified mouse lines to address YY1 function in DNA loop formation.
Our studies will determine how YY1 controls long-distance DNA interactions needed of immunoglobulin class switch recombination. Defects in this process causes immune deficiency and to translocations involved in lymphomagenesis. These studies may define new mechanisms for regulating DNA interactions applicable to other systems, and will be relevant to disease formation.