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Bioinformatics Advance Access originally published online on November 24, 2008
Bioinformatics 2009 25(1):1-5; doi:10.1093/bioinformatics/btn594
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© 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, 2European School Karlsruhe, 3Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany and 4Mouse Biology Unit, European Molecular Biology Laboratory, Monterotondo, Italy

*To whom correspondence should be addressed.


  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 Gene Ontology 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 localization 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 KEPEmotif 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: Alex Bateman

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

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