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

Abstract

Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/ interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein-protein interactions through both intra-and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread. An exciting and tantalizing question is whether, or how, this alternative splicing affects gene function. For example, it is conceivable that one isoform may debilitate methyltransferase function whereas the other may enhance it, providing an opportunity for differential regulation. The review concludes with the speculation that modulation of SET protein function is mediated by antisense or sense-antisense RNA.

Impact of nucleosome dynamics and histone modifications on cell proliferation during Arabidopsis development

“…H3K36me: On the basis of the homology to the yeast Set2 protein, it is likely that ASHH1, also named SDG8, is Nucleosome dynamics and histone modifications in Arabidopsis B Desvoyes et al the KMTase that methylates H3K36 (Ng et al, 2007). Further support comes from the finding of a decreased level of H3K36 methylation at the FLC gene in sdg8 mutant plants (Zhao et al, 2005).…”

“…In Arabidopsis, 39 SET domain-containing genes have been identified and classified into six different families, a classification that most likely reflects their substrate specificity (Ng et al, 2007). Unlike histone acetylation that is usually associated with gene activation, histone methylation can either repress or activate gene transcription.…”

“…H3K9me: The KMTase responsible for H3K9me belong to the SUVH family, of which several members have been characterized (Ng et al, 2007). SUVH4, also named KRYPTONITE (KYP), SUVH5 and SUVH6 mediate mono-and dimethylation of H3K9 and are required for the nonCG DNA methylation by CMT3 to silence heterochromatic loci and transposons (Jackson et al, 2002;Ebbs and Bender, 2006).…”

A Functional Component of the Transcriptionally Active Chromosome Complex, Arabidopsis pTAC14, Interacts with pTAC12/HEMERA and Regulates Plastid Gene Expression

“…Enzymes that catalyze histone Lys methylation contain an evolutionarily conserved SET domain (Tschiersch et al, 1994). There are at least 47 SET proteins present in Arabidopsis, which can be classified into seven distinct phylogenetic groups: class I, E(z) class; class II, ASH1 class; class III, Trithorax class; class IV, proteins with a SET domain and a PHD domain; class V, Su (var) class; class VI, proteins with an interrupted SET domain; and class VII, nonhistone methyltransferases and related proteins (Ng et al, 2007). So far, studies indicate that SET domain proteins are involved in chromatin structure, gene silencing, transcriptional activation, plant metabolism, and other processes (Trievel et al, 2002;Yu et al, 2009b;Liu et al, 2010).…”

EMBRYONIC FLOWER1 and ULTRAPETALA1 Act Antagonistically on Arabidopsis Development and Stress Response

“…The Arabidopsis genome encodes nine proteins related to the D. melanogaster TRITHORAX proteins (AlvarezVenegas and Avramova, 2001;Baumbusch et al, 2001;Ng et al, 2007). Among these, the Arabidopsis homolog of trxG, ARABIDOPSIS TRITHORAX1 (ATX1), harbors a SET domain with weak methylating activity in vitro (Alvarez-Venegas et al, 2003).…”