The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes

Abstract

SET domains are conserved amino acid motifs present in chromosomal proteins that function in epigenetic control of gene expression. These proteins can be divided into four classes as typified by their Drosophila members E(Z), TRX, ASH1 and SU(VAR)3-9. Homologs of all four classes have been identified in yeast and mammals, but not in plants. A BLASTP screening of the Arabidopsis genome identified 37 genes: three E(z) homologs, five trx homologs, four ash1 homologs and 15 genes similar to Su(var)3-9. Seven genes were assigned as trx-related and three as ash1-related. Only four genes have been described previously. Our classification is based on the characteristics of the SET domains, cysteine-rich regions and additional conserved domains, including a novel YGD domain. RT-PCR analysis, cDNA cloning and matching ESTs show that at least 29 of the genes are active in diverse tissues. The high number of SET domain genes, possibly involved in epigenetic control of gene activity during plant development, can partly be explained by extensive genome duplication in Arabidopsis. Additionally, the lack of introns in the coding region of eight SU(VAR)3-9 class genes indicates evolution of new genes by retrotransposition. The identification of putative nuclear localization signals and AT-hooks in many of the proteins supports an anticipated nuclear localization, which was demonstrated for selected proteins.

Plant SET domain-containing proteins: Structure, function and regulation

“…In plants, Arabidopsis SET (AtSET) proteins are the best annotated and characterized. Baumbusch et al [44] were the first to classify 37 putative Arabidopsis SET genes into four distinct classes: 1) Enhancer of zeste [E(z)] homologs; 2) Ash1 homologs and related; 3) trithorax (trx) homologs and related; and 4) Suppressor of variegation [Su(var)] homologs and related. Subsequently, Springer et al [22] classified 32 Arabidopsis and 22 maize SET proteins into 19 orthology groups distributed among five classes according to their phylogenetic relationships and domain organization.…”

“…ASHH1 is the Arabidopsis homolog of yeast Set2 [44] which has been shown to exhibit H3K36 methyltransferase activity [64]. In addition, genetic studies revealed that ashh2 mutants show an early flowering phenotype that is accompanied by a decrease in H3K36 methylation at the FLOWERING LOCUS C (FLC) [65].…”

“…Here, we summarize current knowledge concerning plant SET proteins and compare the known functions of orthologous SET proteins of plants and other organisms. In addition to the existing classification of SET proteins in Arabidopsis and maize [22,44], we have included 9 additional Arabidopsis SET proteins and 34 rice SET proteins from Plant Chromatin Database (ChromDB; http://www.chromdb.org). We also comment on recent evidence that alternative splicing may be relatively common for plant SET genes and consider the possibility that it has a functional role in regulating histone methylation.…”

Structural dynamics of protein lysine methylation and demethylation

“…The SET domain is found in a large number of eukaryotic proteins (see pfam database) as well as in a few bacterial proteins [23] and is not limited to HKMTs. HKMTs can be classified according to the presence or absence and the nature of sequences surrounding the SET domain that are conserved within families [24,25]. Representatives of the major families include SUV, SET1, SET2, EZ, and RIZ (for example, see [26]).…”

Epigenetics: heterochromatin meets RNAi

“…These factors are, in many cases, remarkably well conserved in distantly related species [4][5][6][7][8][9][10]. Histone Lysine Methyl Transferases (KMTs), enzymes that add one, two or three methyl groups to lysine residues within the tails of histones, as well as proteins with chromodomains that bind specifically to motifs generated by KMTs, are the best characterized factors required for setting up heterochromatin.…”