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Bioinformatics Advance Access originally published online on July 28, 2006
Bioinformatics 2006 22(20):2459-2462; doi:10.1093/bioinformatics/btl414
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org

SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation

Dapeng Zhang , Christopher J. Martyniuk and Vance L. Trudeau *

Centre for Advanced Research in Environmental Genomics (CAREG), Department of Biology, University of Ottawa Ottawa, ON K1N 6N5, Canada

*To whom correspondence should be addressed.

Since packaging of DNA in the chromatin structure restricts the accessibility for regulatory factors, chromatin remodeling is required to facilitate nuclear processes such as gene transcription, replication, and genome recombination. Many conserved non-enzymatic protein domains have been identified that contribute to the activities of multiprotein remodeling complexes. Here we identified a novel conserved protein domain in Eukaryota whose putative function may be in regulating chromatin remodeling. Since this domain is associated with a known SANT domain in several vertebrate proteins, we named it the SANTA (SANT Associated) domain. Sequence analysis showed that the SANTA domain is approximately a 90 amino acid module and likely composed of four central ß-sheets and three flanking {alpha}-helices. Many hydrophobic residues exhibited high conservation along the domain, implying a possible function in protein–protein interactions. The SANTA domain was identified in mammals, chicken, frog, fish, sea squirt, sea urchin, worms and plants. Furthermore, a phylogenetic tree of SANTA domains showed that one plant-specific duplication event happened in the Viridiplantae lineage.

Contact: trudeauv{at}uottawa.ca

Supplementary Information: Supplementary Figure S1 for this paper is available at Bioinformatics online.

Received on June 8, 2006; revised on July 21, 2006; accepted on July 25, 2006

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