ABSTRACT
This chapter demonstrates that the relevance of Cap Analysis of Gene Expression (CAGE) data to studying promoter biology in depth. Understanding transcriptional regulation and gene regulatory networks underlying basic biological mechanisms in the cells is key to understanding their physiological and pathological roles. The chapter outlines the knowledge and methodological approaches to understanding macrophage biology that can be applied to cells and tissues in diverse biological systems. The challenge in modulating macrophage action for therapeutic purposes is to balance these diverse macrophage functions; this requires a detailed understanding of gene regulation by factors that regulate macrophage differentiation and acquisition of effector functions. The development of an approach for simultaneous sequencing of CAGE tags from multiple libraries in a single reaction, allied to high-throughput sequencing means that CAGE can be viewed as a unique form of expression profiling. Macrophages are part of the mononuclear phagocyte system, a cell lineage that includes precursors in bone marrow and circulating monocytes.
