First pass annotation of promoters on human chromosome 22

The publication of the first almost complete sequence of a human chromosome (chromosome 22) is a major milestone in human genomics. Together with the sequence, an excellent annotation of genes was published which certainly wi ll serve as an information resource for numerous future projects. We noted that the annotation did not cover regulatory regions; in particular, no pro moter annotation has been provided. Here we present an analysis of the comp lete published chromosome 22 sequence for promoters. A recent breakthrough in specific in silico prediction of promoter regions enabled us to attempt large-scale prediction of promoter regions on chromosome 22. Scanning of se quence databases revealed only 20 experimentally verified promoters, of whi ch 10 were correctly predicted by our approach. Nearly 40% of our 465 predi cted promoter regions are supported by the currently available gene annotat ion. Promoter finding also provides a biologically meaningful method for "c hromosomal scaffolding", by which long genomic sequences can be divided int o segments starting with a gene. As one example, the combination of promote r region prediction with exon/intron structure predictions greatly enhances the specificity of de novo gene finding. The present study demonstrates th at it is possible to identify promoters in silico on the chromosomal level with sufficient reliability for experimental planning and indicates that a wealth of information about regulatory regions can be extracted from curren t large-scale (megabase) sequencing projects. Results are available on-line at http://genomatix.gsf.de/chr22/.