Finding and characterizing mRNAs, their transcription start sites (TSS), and 
their associated promoters is a major focus in post-genome biology. Mammalian 
cells have at least 5-10 magnitudes more TSS than previously believed, and 
deeper sequencing is necessary to detect all active promoters in a given tissue. 
Here, we present a new method for high-throughput sequencing of 5' cDNA 
tags-DeepCAGE: merging the Cap Analysis of Gene Expression method with 
ultra-high-throughput sequence technology. We apply DeepCAGE to characterize 1.4 
million sequenced TSS from mouse hippocampus and reveal a wealth of novel core 
promoters that are preferentially used in hippocampus: This is the most 
comprehensive promoter data set for any tissue to date. Using these data, we 
present evidence indicating a key role for the Arnt2 transcription factor in 
hippocampus gene regulation. DeepCAGE can also detect promoters used only in a 
small subset of cells within the complex tissue.