RT Journal
A1 Scherf, Matthias
A1 Klingenhoff, Andreas
A1 Frech, Kornelie
A1 Quandt, Kerstin
A1 Schneider, Ralf
A1 Grote, Korbinian
A1 Frisch, Matthias
A1 Gailus-Durner, Valérie
A1 Seidel, Alexander
A1 Brack-Werner, Ruth
A1 Werner, Thomas
T1 First Pass Annotation of Promoters on Human Chromosome 22
JF Genome Research 
JO Genome Research 
YR 2001 
FD March 01 
VO 11 
IS 3 
SP 333 
OP 340 
DO 10.1101/gr.154601 
UL http://genome.cshlp.org/content/11/3/333.abstract 
AB 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 will serve as an information resource for numerous future projects. We noted that the annotation did not cover regulatory regions; in particular, no promoter annotation has been provided. Here we present an analysis of the complete 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 sequence databases revealed only 20 experimentally verified promoters, of which 10 were correctly predicted by our approach. Nearly 40% of our 465 predicted promoter regions are supported by the currently available gene annotation. Promoter finding also provides a biologically meaningful method for “chromosomal scaffolding”, by which long genomic sequences can be divided into segments starting with a gene. As one example, the combination of promoter region prediction with exon/intron structure predictions greatly enhances the specificity of de novo gene finding. The present study demonstrates that 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 current large-scale (megabase) sequencing projects. Results are available on-line at http://genomatix.gsf.de/chr22/.