HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing

Background: Correct temporal and spatial gene expression during metazoan development relies on combinatorial interactions between different transcription factors. As a consequence, cisregulatory elements often colocalize in clusters termed cis-regulatory modules. These may have requirements on organizational features such as spacing, order and helical phasing (periodic spacing) between binding sites. Due to the turning of the DNA helix, a small modification of the distance between a pair of sites may sometimes drastically disrupt function, while insertion of a full helical turn of DNA (10–11 bp) between cis elements may cause functionality to be restored. Recently, de novo motif discovery methods which incorporate organizational properties such as colocalization and order preferences have been developed, but there are no tools which incorporate periodic spacing into the model. Results: We have developed a web based motif discovery tool, HeliCis, which features a flexible model which...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Erik Larsson, Per Lindahl, Petter Mostad
• Keywords: Binding Sites, BMCBI 2007, Periodic Spacing, Spatial Gene Expression