The chromo shadow domain,
a second chromo domain in Heterchromatin-binding protein 1, HP1.

by Rein Aasland(1) and A. Francis Stewart

Gene Expression Programme, EMBL, Meyerhofstrasse 1,
D-69117 Heidelberg. Germany

Published in: Nucleic Acids Research 23(16): 3168-3173 (1995)

Abstract

The chromo domain was originally identified as a protein sequence motif common to the Drosophila chromatin proteins, Polycomb (Pc) and Heterochromatin protein 1 (HP1). Here we describe a second chromo domain-like motif in HP1. Subsequent refined searches identified further examples of this chromo domain variant which all occur in proteins that also have an N-terminally located chromo domain. Due to its relatedness to the chromo domain, and its occurrence in proteins that also have a classical chromo domai n, we call the variant the "chromo shadow domain". Chromo domain-containing proteins can therefore be divided into two classes depending on the presence, for example in HP1, or absence, for example in Pc, of the chromo shadow domain. We have also found ex amples of proteins which have two classical chromo domains. The S. pombe SWI6 protein, involved in repression of the silent mating-type loci, is a member of the chromo shadow group. The similar modular architecture of SpSWI6, HP1 and HP1-like proteins sup ports the model that the specificity of action of chromatin proteins is generated by combinations of protein modules.

• a hyperlinked table of chromo domain proteins,
• an alignment and
• a tree describing the relationship between the different subsets of chromo domains.
• We also use Georg Casari's Sequence Space analysis to divide the chromo domains into subfamilies.
• The profiles used to search for chromo domains and chromo shadow domains are also available.

• A cartoon showing the Chromo domain structure [PDB:1AP0] (Ball et al. 1997)
• Our original alignment with the structure-derived secondary structure elements indicated
• Pfam entry for the chromo domain (including multiple alignments)
  [NB! you can USE Pfam and HMMer to check if your protein has chromo domains]
• The Prosite entry for the chromo domain.
• Use these two searches to find chromo domain references in PubMed.
• Chromo domains (and/or chromo domain protein) have been reported to interact with several other proteins including TIF1, lamins, ORC and it self check it out with PubMed.

Phone: +47-5558-4531
Fax: +47-5558-9683
E-mail: aasland@bio.uib.no and E-mail: stewart@embl-heidelberg.de

This work was carried out at the EMBL and partly at the University of Bergen.
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