Modeling the regulation of the Il12b locus by NF-κB dimers

Abstract

Abstract The transcription factor NF-κB is composed of a family, which regulates the expression of various genes in immune and inflammatory responses. The NF-κB family consists of five members: RelA/p65, RelB, c-Rel, p50/p105, and p52/p100, which control the transcription of target genes by binding to regulatory κB sites in homo-or heterodimer forms. Unlike the widely known RelA, the mechanisms related to the regulation of target genes by c-Rel is less understood. Interleukin 12b(Il12b), which encodes the p40 subunit of IL12 and IL23, is one example of gene that depend on c-Rel for proper activation in macrophages. The differences in intrinsic binding properties of c-Rel- and RelA-containing dimers at various regulatory sites around Il12b can be a key to understand the mechanism of c-Rel-containing dimers’ role in Il12b regulation. Using c-Rel and Il12b reporter mice with fluorescence live-cell imaging, we observe the single-cell dynamics of nuclear c-Rel and Il12b gene expression in bone marrow-derived macrophages induced by NF-κB activating ligands. We analyze the live-cell imaging data and extract quantitative features of nuclear c-Rel and Il12b expression from the time-series data. For additional mechanistic insights of the Il12b gene regulation by NF-κB dimers, we propose a mathematical model of dynamic gene regulation which includes actions of RelA- and c-Rel-containing dimers at κB sites proximal and distal to the Il12b locus. Our combined experimental and mathematical modeling approach will reveal quantitative insights that may provide a more comprehensive understanding of regulatory mechanisms underlying Il12b gene expression employed by NF-κB dimers.