title: Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots.
abstract: Histone proteins play a central role in chromatin packaging, and modification of histones is associated with chromatin accessibility. SET domain [Su(var)3-9, Enhancer-of-zeste, Trithorax] proteins are one class of proteins that have been implicated in regulating gene expression through histone methylation. The relationships of 22 SET domain proteins from maize (Zea mays) and 32 SET domain proteins from Arabidopsis were evaluated by phylogenetic analysis and domain organization. Our analysis reveals five classes of SET domain proteins in plants that can be further divided into 19 orthology groups. In some cases, such as the Enhancer of zeste-like and trithorax-like proteins, plants and animals contain homologous proteins with a similar organization of domains outside of the SET domain. However, a majority of plant SET domain proteins do not have an animal homolog with similar domain organization, suggesting that plants have unique mechanisms to establish and maintain chromatin states. Although the domains present in plant and animal SET domain proteins often differ, the domains found in the plant proteins have been generally implicated in protein-protein interactions, indicating that most SET domain proteins operate in complexes. Combined analysis of the maize and Arabidopsis SET domain proteins reveals that duplication of SET domain proteins in plants is extensive and has occurred via multiple mechanisms that preceded the divergence of monocots and dicots.
authors.affiliation: Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison 53706, USA.
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Springer
authors.forename: Carolyn A
authors.initials: CA
authors.lastname: Napoli
authors.forename: David A
authors.initials: DA
authors.lastname: Selinger
authors.forename: Ritu
authors.initials: R
authors.lastname: Pandey
authors.forename: Karen C
authors.initials: KC
authors.lastname: Cone
authors.forename: Vicki L
authors.initials: VL
authors.lastname: Chandler
authors.forename: Heidi F
authors.initials: HF
authors.lastname: Kaeppler
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017360:Arabidopsis / Q000145:classification / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics*; D001483:Base Sequence; D016000:Cluster Analysis; D017931:DNA Primers; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D000076983:Histone Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; D008780:Methyltransferases / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D011496:Protein Methyltransferases; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic; D003313:Zea mays / Q000145:classification / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D017931:DNA Primers; D010940:Plant Proteins; D000076983:Histone Methyltransferases; D008780:Methyltransferases; D011496:Protein Methyltransferases; D011495:Histone-Lysine N-Methyltransferase