Summary: Identification of highly specific localized sequence motifs in human
ribosomal protein gene promoters
Stefan Roepcke a,, Degui Zhi b
, Martin Vingron a
, Peter F. Arndt a
Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany
Bioinformatics Program, University of California at San Diego, La Jolla, CA 92093-0419, USA
Received 24 March 2005; received in revised form 22 July 2005; accepted 27 September 2005
Available online 15 December 2005
For ribosomal protein (RP) genes the start of transcription is rigidly controlled to maintain the 5-TOP signal on the messenger RNA. The
responsible regulatory mechanism is not yet fully understood. Careful comparative analysis of their proximal promoter sequences reveals common
characteristics and thus provides clues to the underlying mechanism.
We have extracted the proximal promoters of the 80 human cytosolic ribosomal protein genes together with the orthologous mouse sequences.
After annotating the set with transcription factor binding sites based on the available literature, we searched for over-represented sequence motifs.
We uncovered a novel motif that is localized at a fixed distance downstream to the transcription start. 31 out of the 80 promoters contain the motif
in the same orientation around position +62 (standard deviation 6). A second evolutionary conserved and palindromic motif is found 13 times in
the RP promoter set, 9 instances of which are located upstream around position -40. In addition, we see a characteristic profile of the GC-content