Journal Article

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

Francesca Diella, Sophie Chabanis, Katja Luck, Claudia Chica, Chenna Ramu, Claus Nerlov and Toby J. Gibson

in Bioinformatics

Volume 25, issue 1, pages 1-5
Published in print January 2009 | ISSN: 1367-4803
Published online November 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn594

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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-1α, 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@embl.de

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  3926 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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