Mathematical models can integrate different types of experimental datasets, reconstitute biological systems in silico, and identify previously unknown molecular mechanisms. Over the past decade, mathematical models have been developed based on quantitative observations, such as live-cell imaging and biochemical assays. However, it is difficult to directly integrate next-generation sequencing (NGS) data. Although highly dimensional, NGS data mostly only provides a "snapshot" of cellular states. Nevertheless, the development of various methods for NGS analysis has led to much more accurate predictions of transcription factor activity and has revealed various concepts regarding transcriptional regulation. Therefore, fluorescence live-cell imaging of transcription factors can help alleviate the limitations in NGS data by supplementing temporal information, linking NGS to mathematical modeling. This chapter introduces an analytical method for quantifying dynamics of nuclear factor kappaB (NF-κB) which forms aggregates in the nucleus. The method may also be applicable to other transcription factors regulated in a similar fashion.
Keywords: DT40; Fluorescence microscopy; Image analysis; NF-κB; Transcription factor; Transcriptional regulation.
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