Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkit.
BACKGROUND
Polycomb group (PcG) proteins maintain expression pattern of genes set early during development. Although originally isolated as regulators of homeotic genes, PcG members play a key role in epigenetic mechanism that maintains the expression state of a large number of genes. Polycomb (PC) is conserved during evolution and while invertebrates have one PC gene, vertebrates have five or more homologues. It remains unclear if different vertebrate PC homologues have distinct or overlapping functions. We have identified and compared the sequence of PC homologues in various organisms to analyze similarities and differences that shaped the evolutionary history of this key regulatory protein.


RESULTS
All PC homologues have an N-terminal chromodomain and a C-terminal Polycomb Repressor box. We searched the protein and genome sequence database of various organisms for these signatures and identified approximately 100 PC homologues. Comparative analysis of these sequences led to the identification of a novel insect specific motif and several novel and signature motifs in the vertebrate homologue: two in CBX2 (Cx2.1 and Cx2.2), four in CBX4 (Cx4.1, Cx4.2, Cx4.3 and Cx4.4), three in CBX6 (Cx6.1, Cx6.2 and Cx6.3) and one in CBX8 (Cx8.1). Additionally, adjacent to the chromodomain, all the vertebrate homologues have a DNA binding motif - AT-Hook in case of CBX2, which was known earlier, and 'AT-Hook Like' motif, from this study, in other PC homologues.


CONCLUSIONS
Our analysis shows that PC is an ancient gene dating back to pre bilaterian origin that has not only been conserved but has also expanded during the evolution of complexity. Unique motifs acquired by each homologue have been maintained for more than 500 millions years indicating their functional relevance in boosting the epigenetic 'tool kit'. We report the presence of a DNA interaction motif adjacent to chromodomain in all vertebrate PC homologues and suggest a three-way 'PC-histoneH3-DNA' interaction that can restrict nucleosome dynamics. The signature motifs of PC homologues and insect specific motif identified in this study pave the way to understand the molecular basis of epigenetic mechanisms.
Senthilkumar
Ramamoorthy
R
Centre for Cellular and Molecular Biology, Hyderabad 500007, India. rsenthil@ccmb.res.in
Mishra
Rakesh K
RK
D024761:AT-Hook Motifs; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D006801:Humans; D007313:Insecta / Q000235:genetics; D008025:Ligases; D051379:Mice; D033681:Mitochondrial Membrane Transport Proteins; D008969:Molecular Sequence Data; D010802:Phylogeny; D063150:Polycomb Repressive Complex 1; D063146:Polycomb-Group Proteins; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D013329:Structure-Activity Relationship; D044767:Ubiquitin-Protein Ligases
C570428:CBX8 protein, human; C570426:Cbx2 protein, mouse; D033681:Mitochondrial Membrane Transport Proteins; D063146:Polycomb-Group Proteins; D012097:Repressor Proteins; C570429:Cbx8 protein, mouse; D063150:Polycomb Repressive Complex 1; D044767:Ubiquitin-Protein Ligases; D008025:Ligases; C570427:CBX4 protein, human