Bioinformatic identification of novel putative photoreceptor specific cis-elements

Background: Cell specific gene expression is largely regulated by different combinations of transcription factors that bind cis-elements in the upstream promoter sequence. However, experimental detection of cis-elements is difficult, expensive, and time-consuming. This provides a motivation for developing bioinformatic methods to identify cis-elements that could prioritize future experimental studies. Here, we use motif discovery algorithms to predict transcription factor binding sites involved in regulating the differences between murine rod and cone photoreceptor populations. Results: To identify highly conserved motifs enriched in promoters that drive expression in either rod or cone photoreceptors, we assembled a set of murine rod-specific, cone-specific, and nonphotoreceptor background promoter sequences. These sets were used as input to a newly devised motif discovery algorithm called Iterative Alignment/Modular Motif Selection (IAMMS). Using IAMMS, we predicted 34 motifs that m...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Charles G. Danko, Vera A. McIlvain, Maochun Qin, Barry E. Knox, Arkady M. Pertsov
• Keywords: BMCBI 2007, Motif Discovery Algorithm, Promoters, Transcription Factor