Ab initio identification of putative human transcription factor binding sites by comparative genomics

Background: Understanding transcriptional regulation of gene expression is one of the greatest challenges of modern molecular biology. A central role in this mechanism is played by transcription factors, which typically bind to specific, short DNA sequence motifs usually located in the upstream region of the regulated genes. We discuss here a simple and powerful approach for the ab initio identification of these cis-regulatory motifs. The method we present integrates several elements: human-mouse comparison, statistical analysis of genomic sequences and the concept of coregulation. We apply it to a complete scan of the human genome. Results: By using the catalogue of conserved upstream sequences collected in the CORG database we construct sets of genes sharing the same overrepresented motif (short DNA sequence) in their upstream regions both in human and in mouse. We perform this construction for all possible motifs from 5 to 8 nucleotides in length and then filter the resulting sets ...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Davide Corà, Carl Herrmann, Christoph Dieterich, Ferdinando Di Cunto, Paolo Provero, Michele Caselle
• Keywords: BMCBI 2005, DNA Sequence, Human Genome, Upstream Regions