The genome is organized not merely as strings of nucleotides but as intricate folded structures that permit long-range interactions between genetic segments. Enhancers in particular have emerged as critical cis-regulatory elements that control gene transcription even at large distances from target promoters. These 3D structures are organized in the nucleus within transcriptionally permissive and repressive compartments, reflecting a previously unappreciated layer of regulation. In this regard, our laboratory has recently used high- throughput chromosome capture (Hi-C) to identify global changes in both the nuclear location of genes and the genomic interactions between distant promoters and enhancers during the developmental progression from the pre-pro-B to pro-B cell stage. Germinal centers are distinct anatomical structures that arise in peripheral lymphoid tissues in response to invading pathogens. During consecutive rounds of proliferation and affinity- based selection, via mechanisms that remain unclear, two effector B cell types emerge: memory B cells and antibody-secreting plasma cells. Plasma cells constitutively secrete antibody, sustaining serum antibody titers for months to years in mice and decades in people. In contrast, memory B cells remain quiescent but poised, ready to generate antibody-secreting cells upon antigen re-exposure. Our laboratory has found that E- and Id-proteins modulate germinal center B cell, plasma cell, and memory B cell differentiation. How these factors activate distinct patterns of gene expression in plasma cells versus memory B cells, how they act in concert with other factors, and how they are regulated themselves remains largely unknown. In this proposal, I hypothesize that germinal center B cells sequester lineage-specific transcription factors within nuclear compartments, and that tightly regulated mechanisms control their differential release in memory B cells and plasma cells. Here, we will characterize the binding sites of E-proteins in germinal center B cells, memory B cells, and plasma cells, describe their epigenomes, and determine which genes are recruited to the nuclear lamina. Overall, the experiments within this proposal will serve to better define the requirements for serum antibody maintenance and may suggest new ways to optimize these titers.
The proposed studies will define global regulatory networks for germinal center B cells, memory B cells, and plasma cells. We will define the role of E-proteins and identify cis-regulatory regions critical for antibody secretion;these findings will advance approaches to manipulate memory B cell and antibody responses.