Genome-wide Analysis of Core Promoter Regions in Emiliania Huxleyi

Emiliania huxleyi (E. huxleyi), the most abundant coccolithophorid, has served as a model system for environmental studies pertaining to global carbon cycling, oceanic sulfur bio-transformations, and paleoclimatology. It has also potential applications in material sciences and biomedical studies. E. huxleyi was selected by the Department of Energy in 1999 for genome sequencing, which was recently completed in 2006. To date, little is known about the transcription regulatory elements of E. huxleyi and other coccolithophorids. Because of its exceptionally high GC content (~66%), the E. huxleyi genome may contain unique and novel regulatory elements that have not yet been identified in other organisms. Genome-wide analysis of core promoter regions in E. huxleyi represents an initial and important step towards understanding the transcriptional regulation mechanism in this important organism. Using a collection of 190 full-length complementary DNAs (cDNAs) and 84,385 expressed sequence tags (ESTs) , we first extracted a robust dataset of 3,132 potential core promoter regions of from the first assembly the E. huxleyi genome (released November 3, 2006). These promoter regions were then scanned for both known and novel sequence motifs. The E. huxleyi core-promoters lack the TATA motif but contain overrepresented novel motifs. In addition we computed for these regions dinstictive physical and structural properties that may be related to the transcriptional regulation process. Twelve out of fourteen properties analyzed showed significant distinction between the promoter regions and other background coding and non-coding regions. The core-promoter profile consisting of regulatory motifs, sequence characteristics, and structural and physical features will be used to develop computational models to predict core promoters across the entire E. huxleyi genome.