Analysis of genomic Regions of IncreaseD Gene Expression (RIDGE)s in immune activation

Abstract

A RIDGE (Region of IncreaseD Gene Expression), as defined by previous studies, is a consecutive set of active genes on a chromosome that span a region around 110 kbp long. This study investigated RIDGE formation by focusing on the well-defined, immunological important MHC locus. Macrophages were assayed for gene expression levels using the Affymetrix MG-U74Av2 chip are were either 1) uninfected, 2) primed with IFN-g, 3) viral activated with mCMV, or 4) both primed and viral activated. Gene expression data from these conditions was studied using data structures and new software developed for the visualisation and handling of structured functional genomic data. Specifically, the data was used to study RIDGE structures and investigate whether physically linked genes were also functionally related, and exhibited co-expression and potentially co-regulation. A greater number of RIDGEs with a greater number of members than expected by chance were found. Observed RIDGEs featured functional associations between RIDGE members (mainly explored via GO, UniProt, and Ingenuity), shared upstream control elements (via PROMO, TRANSFAC, and ClustalW), and similar gene expression profiles. Furthermore RIDGE formation cannot be explained by sequence duplication events alone. When the analysis was extended to the entire mouse genome, it became apparent that known genomic loci (for example the protocadherin loci) were more likely to contain more and longer RIDGEs. RIDGEs outside such loci tended towards single-gene RIDGEs unaffected by the conditions of study. New RIDGEs were also uncovered in the cascading response to IFNg priming and mCMV infection, as found by investigating an extensive time series during the first 12 hours after treatment. Existing RIDGEs were found to be elongated having more members the further the cascade progress.