SMASHing regulatory sites in DNA by human

Regulatory sequence elements provide important clues to understanding and predicting gene expression. Although the binding sites for hundreds of transcription factors are known, there has been no systematic attempt to incorporate this information in the annotation of the human genome. Cross species sequence comparisons are critical to a meaningful annotation of regulatory elements since they generally reside in conserved non-coding regions. To take advantage of the recently completed drafts of the mouse and human genomes for annotating transcription factor binding sites, we developed SMASH, a computational pipeline that identifies thousands of orthologous human/mouse proteins, maps them to genomic sequences, extracts and compares upstream regions and annotates putative regulatory elements in conserved, non-coding, upstream regions. Our current dataset consists of approximately 2500 human/mouse gene pairs. Transcription start sites were estimated by mapping quasi-full length cDNA sequ...

• Type: Conference
• Year: 2003
• Where: CSB
• Authors: Mihaela Zavolan, Nicholas D. Socci, Nikolaus Rajewsky, Terry Gaasterland
• Keywords: Binding Sites, CSB 2003, Human Genome, Transcription Factors