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Bioinformatics Advance Access published online on November 24, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn594
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors

Francesca Diella 1, Sophie Chabanis 2, Katja Luck 1, Claudia Chica 1, Chenna Ramu 3, Claus Nerlov 4 and Toby J. Gibson 1,*

1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany, 2European School Karlsruhe, Karlsruhe, 3Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany, 4Mouse Biology Unit, European Molecular Biology Laboratory, Monterotondo, Italy.

*To whom correspondence should be addressed. Dr. Toby Gibson, E-mail: toby.gibson{at}embl.de


  Abstract

Motivation: We noted that the sumoylation site in C/EBP homologues is conserved beyond the canonical consensus sequence for sumoylation. Therefore we investigated whether this pattern might define a more general protein motif.

Results: We undertook a survey of the human proteome using a regular expression based on the C/EBP motif. This revealed significant enrichment of the motif using different GO terms (e.g. "transcription") that pertain to the nucleus. When considering requirements for the motif to be functional (evolutionary conservation, structural accessibility of the motif and proper cell localisation of the protein) more than 130 human proteins were retrieved from the UniProt/Swiss-Prot database. These candidates were particularly enriched in transcription factors, including FOS, JUN, Hif-1{alpha}, MLL2 and members of the KLF, MAF and NFATC families; chromatin modifiers like CHD-8, HDAC4, and DNA Top1; and the transcriptional regulatory kinases HIPK1 and HIPK2. The KEPE motif appears to be restricted to the metazoan lineage and has three length variants - short, medium and long - which do not appear to interchange.

Contact: toby.gibson{at}embl.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dr. Alex Bateman

Received on September 4, 2008; revised on November 7, 2008; accepted on November 12, 2008

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