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

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 exp...

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Autores principales: Diella, Francesca, Chabanis, Sophie, Luck, Katja, Chica, Claudia, Ramu, Chenna, Nerlov, Claus, Gibson, Toby J.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638927/
https://www.ncbi.nlm.nih.gov/pubmed/19033273
http://dx.doi.org/10.1093/bioinformatics/btn594
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author Diella, Francesca
Chabanis, Sophie
Luck, Katja
Chica, Claudia
Ramu, Chenna
Nerlov, Claus
Gibson, Toby J.
author_facet Diella, Francesca
Chabanis, Sophie
Luck, Katja
Chica, Claudia
Ramu, Chenna
Nerlov, Claus
Gibson, Toby J.
author_sort Diella, Francesca
collection PubMed
description 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.
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spelling pubmed-26389272009-02-25 KEPE—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors Diella, Francesca Chabanis, Sophie Luck, Katja Chica, Claudia Ramu, Chenna Nerlov, Claus Gibson, Toby J. Bioinformatics Discovery Note 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. Oxford University Press 2009-01-01 2008-11-24 /pmc/articles/PMC2638927/ /pubmed/19033273 http://dx.doi.org/10.1093/bioinformatics/btn594 Text en © The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Discovery Note
Diella, Francesca
Chabanis, Sophie
Luck, Katja
Chica, Claudia
Ramu, Chenna
Nerlov, Claus
Gibson, Toby J.
KEPE—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
title KEPE—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
title_full KEPE—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
title_fullStr KEPE—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
title_full_unstemmed KEPE—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
title_short KEPE—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
title_sort kepe—a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
topic Discovery Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638927/
https://www.ncbi.nlm.nih.gov/pubmed/19033273
http://dx.doi.org/10.1093/bioinformatics/btn594
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