Prediction and Validation of Transcription Factors Binding Sites in the Il9 Locus

Over the past decade, multiple effector T cell subsets have been identified with varying differentiation conditions in the milieu as well as a broad diversity of cytokine expression. Interleukin-9 (IL-9) secreting T helper 9 (Th9) cells are the newest member of this family. T helper cell differentiation including Th9 cells appears to be an epigenetic phenomenon requiring the coordination of a large variety of transcription factors to reshape the chromatin landscape and generate various T helper phenotypes. This chapter details methods for both predicting and validating potential transcription factor binding sites as well as their downstream epigenetic effect using a variety of in silico and in vitro methods in both primary Th9 cells and IL-9-producing T cell lines.