Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq

Chromatin immunoprecipitation (ChIP), using antibody against RNA Pol-II, followed by massive parallel sequencing (ChIP-seq) are invaluable techniques for genome-wide identification of alternative promoters and their patterns of use in different tissues, cell types, and/or developmental stages. However, the identification of promoters cannot be performed solely based on the presence of Pol-II enrichment on a genomic location because of its enrichment throughout the transcribed genomic region and lack of highly specific antibodies that can distinguish promoter-bound Pol-II from elongating Pol-II. In order to overcome this limitation, we developed a combined Pol-II ChIP-seq and bioinformatics promoter prediction approach to identify promoter regions and their activity in different mouse tissues. Here, we describe the integrative approach to identify alternative promoters in the mouse genome.