BACKGROUND
epigenetic regulation acts through heritable changes in genome function that occur without a change in dna sequence.
one well-known epigenetic mechanism is through posttranslational covalent modifications of histones; these modifications include acetylation, methylation, ubiquitylation and others, and form the basis of the 'histone code' for gene regulation  <cit> .
histone lysine methylation plays a pivotal role in a wide range of cellular processes including heterochromatin formation, transcriptional regulation, parental imprinting, and cell fate determination  <cit> .
at least six lysine residues, five on histone h <dig>  and one on h <dig> , are subject to methylation.
each lysine can carry one, two or three methyl residue, known as mono-, di- and tri-methylation, respectively.
in general, di-/tri- methylation of h3k <dig> and h3k <dig> correlates with transcriptional activation, whereas di-methylation of h3k <dig> and trimethylation of h3k <dig> correlates with gene silencing in plants and animals  <cit> .
all known lysine methylation modifications, with the exception of h3k <dig> methylation, are carried out by methyltransferases that contain an evolutionarily conserved set domain, named after three drosophila genes , e, and trithorax)  <cit> .
the set domain encompasses approximately 130- <dig> amino acids that form a knot-like structure and constitute the enzyme catalytic site for lysine methylation  <cit> .
in addition to the set domain, flanking sequences, more distant protein domains, and possibly some cofactors are also important for enzyme activity and specificity.
the genes encoding set-domain proteins are ancient, existing in prokaryotes and eukaryotes, but have proliferated and evolved novel functions connected with the appearance of eukaryotes  <cit> .
the first plant genes encoding set-domain proteins to be genetically characterized were curly leaf  and medea  in arabidopsis thaliana  <cit> .
chromatin-binding properties and histone methylation activity of plant set-domain proteins were first reported for tobacco ntset <dig> and arabidopsis kryptonite   <cit> .
phylogenetic analysis of plant set domain proteins has proven helpful as a guide for genetic and molecular studies of this large family of proteins  <cit> .
to date, some of the arabidopsis set-domain family members have been characterized and shown to play crucial functions in diverse processes including flowering time control, cell fate determination, leaf morphogenesis, floral organogenesis, parental imprinting and seed development  <cit> .
genome sequences of an increasing number of plant species, in addition to the model plants , have also been completed.
other brassica species are of particular interest because of their agro-economical importance and their close relationship with arabidopsis, thus providing insights into recent set-domain gene amplification during evolution of brassica species.
here, we identified and analyzed  <dig> set-domain proteins from the recently completed brassica rapa whole genome sequence  <cit> .
our data provide a platform for future functional characterization of these important epigenetic regulatory genes in brassica species.
RESULTS
identification of set-domain proteins from the b. rapa genome
using blastp and tblastn with the full complement of known arabidopsis and rice set-domain proteins as queries, we identified  <dig> genes encoding different set-domain proteins from the b. rapa genome .
we used the nomenclature recently proposed for lysine methyltransferases  and named the newly identified b. rapa genes based on our phylogenetic analysis of their corresponding protein sequences .
apart from brkmt1b;1a and brkmt1b;2b genes, whose chromosomal locations are yet unknown, the other  <dig> genes are distributed on the ten b. rapa chromosomes, with 1- <dig> kmt genes per chromosome .
*ud, undetermined
b. rapa set-domain proteins can be grouped into six classes
to analyze the b. rapa set-domain protein sequences, we extracted set-domain proteins from several other green lineage species, including  <dig> proteins from a. thaliana,  <dig> proteins from o. sativa,  <dig> proteins from b. distachyon, and  <dig> proteins from ostreococcus tauri .
we also included the saccharomyces cerevisiae sckmt2/set <dig> and sckmt3/set <dig> proteins, which are h3k4- and h3k36-specific kmts, respectively  <cit> , and can be used to represent ancient eukaryotic set-domain proteins from an evolutionary point of view.
phylogenetic analysis of the aforementioned  <dig> set-domain proteins revealed that they could be grouped into  <dig> distinct classes, namely kmt <dig>  kmt <dig>  kmt <dig>  kmt <dig>  kmt <dig> and s-et class .
the first four class numbers used here are consistent with the nomenclature previously proposed for yeast and animal kmts  <cit> .
furthermore, two plant-specific subclasses  were identified for kmt <dig> and kmt <dig>  representative members of each class/subclass are found in a. thaliana, b. rapa, o. sativa and b. distachyon.
the s-et class members contain an interrupted set domain and are likely involved in methylation of nonhistone proteins, e.g.
rubisco subunits; however, their biological functions remain largely unknown.
hereafter, we focused on the kmt classes/subclasses that are involved in histone methylation.
the kmt1a subclass proteins
the kmt1a subclass is the largest class and can be further divided into 4distinct groups .
in each group, proteins from dicots  and monocots  clearly fall into separate branches, indicating that they are derived from a common ancestral gene but diverged before the monocot/dicot separation.
the first three groups have a relatively simple relationship and small number of genes, but group- <dig> is more complex: each plant species has 4- <dig> members that diverged at various times during evolution.
in the case of b. rapa, among the  <dig> members belonging to group- <dig>  brkmt1a;4a, brkmt1a;4c, brkmt1a;4d, and brkmt1a;4f are clustered with the arabidopsis atkmt1a;4a/sdg32/suvh1; brkmt1a;4b with atkmt1a;4b/sdg19/suvh3; and brkmt1a;4e, brkmt1a; <dig> g and brkmt1a; <dig> h with atkmt1a;4e/sdg11/suvh <dig> .
examination of synteny between b. rapa and a. thaliana  revealed that brkmt1a;4a, brkmt1a;4c and brkmt1a;4d but not brkmt1a;4f are syntenic with atkmt1a;4a/sdg32/suvh <dig>  and brkmt1a; <dig> h but not brkmt1a;4e nor brkmt1a; <dig> g is syntenic with atkmt1a;4e/sdg11/suvh <dig>  it thus appears that multiple duplication events occurred, in either a chromosome segment or single gene scale, resulting in more recent amplification of group- <dig> genes in b. rapa after separation from a. thaliana during evolution.
in agreement with previous studies in arabidopsis, rice and maize  <cit> , few introns are present in brkmt1a genes .
most brkmt1a genes are represented by ests, but some do not have any ests in current databases .
our rt-pcr analysis revealed that indeed two genes that lack ests, brkmt1a;2a and brkmt1a;2c, are very weakly expressed.
strong expression was detected for brkmt1a;4a, but relatively weak expression was detected for brkmy1a;4d and expression was undetectable for brkmt1a;4c .
together, these data indicate that expression levels of different brkmt1a genes varied considerably and thus these genes may regulate genome function to different degrees.
the plant kmt1a subclass proteins show high sequence similarity to the animal kmt <dig> proteins both within the set domain and in the surrounding regions known as the pre-set and post-set domains.
additionally, most of the plant proteins contain a specific domain named sra .
similar to previously studied arabidopsis proteins  <cit> , most of the brkmt1a proteins also contain sra, pre-set, set and post-set domains .
these domains are missing in some of the group- <dig> proteins; for example, brkmt1a.4e, brkmt1a;4f and brkmt1a; <dig> g lack a post-set domain, and brkmt1a.
<dig> h lacks sra, pre-set and post-set domains .
several functions have been reported for sra domains, including binding with the n-terminal tail of histone h <dig> and with dna cytosine methylation  <cit> .
the crystal structure of atkmt1a;3a/sdg9/suvh <dig> revealed that sra recognizes the methylation status of cg and chh sequences  <cit> .
the pre-set domain contains  <dig> conserved cysteines.
the post-set domain is a small cysteine-rich region often found at the c-terminal side of set domains.
both pre-set and post-set domains have been shown to affect histone methyltransferase activity of the set domain  <cit> .
members of the plant kmt1a subclass, like animal kmt <dig> proteins, are likely to be responsible for h3k <dig> methylation, an epigenetic mark involved in heterochromatin formation and gene silencing.
consistent with this, analysis of atkmt1a;1/sdg33/suvh4/kyp, atkmt1a;2a/sdg3/suvh <dig>  atkmt1a;3a/sdg9/suvh <dig> and atkmt1a;3b/sdg23/suvh <dig> has revealed their important roles in h3k <dig> methylation, in heterochromatic gene silencing and in cross-talk between h3k <dig> and dna methylation  <cit> .
work in rice also confirmed that several members of this subclass are involved in h3k <dig> methylation and in transposon silencing  <cit> .
some of the brkmt1a genes might also have similar functions.
the kmt1b subclass proteins
six b. rapa proteins belong to the kmt1b subclass, which can be further divided into  <dig> groups .
group- <dig> contains two b. rapa proteins  whose genes show synteny with atkmt1b;1/sdg31/suvr <dig>  moreover, sequence analysis showed that brkmt1b;1b and atkmt1b;1/sdg31/suvr <dig> have highly similar protein domain organization, indicating that brkmt1b;1b is more conserved and brkmt1b;1a diverged relatively late during evolution after the b. rapa/a.
thaliana separation.
group- <dig> has two b. rapa, two a. thaliana proteins, one o. sativa protein, and three b. distachyon proteins.
both brkmt1b;2a and brkmt1b;2b show synteny with atkmt1b;2b/sdg18/suvr <dig>  group- <dig> and  <dig> each have one representative member in each of the four examined higher plant species.
the kmt1b subclass differs from the kmt1a subclass in protein domain organization; specifically, these proteins lack the sra domain .
a recent study demonstrated that atkmt1b;1/sdg31/suvr <dig> possesses h3k9-methyltransferase activities and its binding with ubiquitin converts h3k9me <dig> to h3k9me <dig> deposition on transposon chromatin  <cit> .
notably, the wiyld domain, which binds ubiquitin, is conserved in brkmt1b;1a, brkmt1b;1b, brkmt1b;2a and brkmt1b;2b .
it was reported that atkmt1b;3/sdg6/suvr5/atczs is involved in regulation of flowering time, possibly through deposition of h3k <dig> methylation at the flowering time repressor flc  <cit> .
the functions of other members of the kmt1b subclass remain uncharacterized so far.
the kmt <dig> class proteins
the kmt <dig> class includes six b. rapa and six a. thaliana proteins in  <dig> groups .
this class features highly conserved set and post-set domains with the yeast h3k4-methyltransferase sckmt2/set <dig>  nevertheless, some plant proteins have acquired specific domains during evolution, namely pwwp, phd, fyr and/or gyf.
the pwwp domain is also found in eukaryotic proteins involved in dna methylation, dna repair, and regulation of transcription  <cit> , and regulates cell growth and differentiation by mediating protein-protein interactions  <cit> .
the phd domain is found in a number of chromatin-associated proteins and is thought to be involved in protein-protein interactions important for the assembly of multiprotein complexes  <cit> .
the pwwp domain of the animal brpf <dig> protein binds h3k36me <dig>  <cit> , and the phd domain is also an important module in proteins that read histone modifications  <cit> .
the fyr domain is composed of fyr-c and fyr-n terminal portions, which are often located close to each other but can also be separated  <cit> .
the gyf domain is proposed to be involved in recognition of proline-rich sequences in protein-protein interactions  <cit> .
kmt <dig> group- <dig> members contain one pwwp, one fyr and two phd domains.
only one member belonging to group- <dig> is found in o. sativa or b. distachyon, but two members are found in b. rapa and a. thaliana.
our examination revealed that brkmt2;1a has synteny with atkmt2;1a/sdg27/atx <dig>  and brkmt2;1b with atkmt2;1b/sdg30/atx <dig>  suggesting that they are derived from two different ancestral copies before the b. rapa/a.
thaliana separation.
consistent with this, the atx <dig> mutant plants exhibit strong and pleiotropic defects  <cit> , but the atx <dig> mutant plants have a normal phenotype  <cit> .
the atx <dig> mutation can enhance atx <dig> in reduction of expression of the flowering repressor gene flc through reduced levels of h3k4me <dig> at the flc locus  <cit> .
the pwwp and fyr domains are absent from the group- <dig> members and the phd domain is found only in some monocot proteins .
only one group- <dig> representative member is found in the dicot species b. rapa or a. thaliana, but the monocot o. sativa has two members and b. distachyon has three members.
the b. rapa and a. thaliana proteins, as well as one member each from o. sativa and b. distachyon, contain a gyf domain in the n-terminal part of the protein .
the fact that this domain is conserved in kmt2; <dig> proteins from all four higher plant species suggests that the acquisition of the gyf domain occurred before the monocot/dicot separation and may have a conserved function in higher plants.
genetic analysis demonstrated that atkmt2;2/sdg25/atxr <dig> is necessary in preventing early flowering  <cit> .
the recombinant atkmt2;2/sdg25/atxr <dig> protein was shown to methylate histone h <dig> in vitro and the depletion of atkmt2;2/sdg25/atxr <dig> in planta slightly reduced h3k <dig> and h3k <dig> methylation at flc chromatin  <cit> .
oskmt2;2b/sdg <dig> and bdkmt2;2c contain two phd domains, but bdkmt2;2b, like the yeast protein sckmt2/set <dig>  does not contain a recognizable phd domain.
future study of these monocot proteins will likely provide a deeper understanding of the domain evolution of kmt <dig> proteins.
the group- <dig> kmt <dig> proteins have a domain organization more similar to group- <dig> except that they lack the fyr domain .
b. rapa and a. thaliana both have three group- <dig> members, but each of the other two higher plant species has only two group- <dig> members.
synteny was observed for brkmt2;3c with atkmt2;3c/sdg29/atx <dig> but not with atkmt2;3b/sdg16/atx <dig>  suggesting that atkmt2;3b/sdg16/atx <dig> was derived from a relatively recent duplication event.
this is in agreement with a previous study revealing that atkmt2;3b/sdg16/atx <dig> and atkmt2;3c/sdg29/atx <dig> are collinearly duplicated with atkmt2;1a/sdg27/atx <dig> and atkmt2;1b/sdg30/atx <dig>  <cit> .
to date, none of the group- <dig> proteins has been functionally characterized.
the kmt <dig> class proteins
the kmt <dig> class contains  <dig> members in a. thaliana but  <dig> members in b. rapa, and these can be further divided into four groups .
the other groups contain a single member per plant species, but group- <dig> contains  <dig> members in a. thaliana and  <dig> members in b. rapa.
our examination indicates that brkmt3;4a and brkmt3;4c are syntenic with atkmt3;4a/sdg7/ashh <dig>  and brkmt3;4b and brkmt3;4d with atkmt3;4b/sdg24/ashh <dig>  the ests found in the current databases match all four brkmt3; <dig> genes , and thus do not allow us to distinguish expression of each gene.
our rt-pcr analysis indicated that brkmt3;4a and brkmt3;4c are expressed at higher levels and more broadly in different examined organs/tissues, whereas only weak expression was detected for brkmt3;4b and brkmt3;4d in some organs/tissues .
the kmt <dig> class plant proteins share high sequence similarity and share the aws , set and post-set domain organization with the yeast h3k36-methyltransferase sckmt3/set <dig> .
the group- <dig> proteins have a long sequence and contain an additional cw domain specific to this group.
the cw domain of atkmt3;1/sdg8/ashh2/efs/ccr <dig> was recently shown to bind h3k4me1/me <dig>  <cit> , suggesting a novel link between h3k <dig> and h3k <dig> methylation in plants.
atkmt3;1/sdg8/ashh2/efs/ccr <dig> is the major h3k36-methyltransferase specifically required for h3k36me <dig> and h3k36me <dig> deposition, and activates expression of hundreds of genes including flc and mafs  <cit> .
depletion of atkmt3;1/sdg8/ashh2/efs/ccr <dig> causes pleiotropic phenotypes, including early flowering, reduced organ size, increased shoot branching, perturbed fertility and carotenoid composition, and impaired plant defenses against pathogens  <cit> .
the other group of kmt <dig> plant proteins have a shorter sequence and do not contain the cw domain; interestingly the depletion of atkmt3;2/sdg26/ashh <dig> resulted in a late-flowering phenotype associated with elevated levels of flc expression  <cit> .
the group- <dig> kmt <dig> proteins, with the exception of bdkmt3;3b and oskmt3;3b/sdg <dig>  contain a phd domain; and atkmt3;3/sdg4/ashr <dig> was reported to be involved in pollen and stamen development possibly through mediating h3k4me <dig> and h3k36me <dig> deposition  <cit> .
the functions of the group- <dig> proteins remain unexamined so far.
examination of this group in b. rapa could be a challenge because of gene multiplication and more diverged sequences .
the kmt6a subclass proteins
the kmt6a subclass includes  <dig> members in b. rapa and  <dig> well-characterized members in a. thaliana, atkmt6a;1/sdg1/clf, atkmt6a;2/sdg10/eza1/swn and atkmt6a;3/sdg5/mea, which represent three distinct groups .
atkmt6a;1/sdg1/clf and atkmt6a;2/sdg10/eza1/swn are broadly expressed and partially redundant in regulation of vegetative and reproductive development, whereas atkmt6a;3/sdg5/mea appears to function specifically in gametophyte and seed development  <cit> .
the three arabidopsis proteins can act as a key component of the evolutionarily conserved polycomb repressive complex  <dig> , which trimethylates h3k <dig> involved in transcriptional repression  <cit> .
atkmt6a;1/sdg1/clf and atkmt6a;2/sdg10/eza1/swn represent group- <dig> and group- <dig>  respectively, and each has an orthologue in different higher plant species.
atkmt6a;3/sdg5/mea, which belongs to group- <dig>  has no orthologue in monocots but has two orthologues in b. rapa.
both brkmt6a;3a and brkmt6a;3b are syntenic with atkmt6a;3/sdg5/mea, and brkmt6a;3a has a more similar protein domain organization to atkmt6a;3/sdg5/mea than does brkmt6a;3b, suggesting that brkmt6a;3b may have diverged after the a. thaliana/b.
rapa separation during evolution.
the sant  domain is found in most of the plant kmt6a subclass proteins.
this domain is also found in a number of other chromatin remodeling proteins with multiple activities such as dna-binding, histone tail binding, and protein-protein interactions  <cit> .
nevertheless, the precise role of the sant domain in kmt6a proteins is currently unknown.
notably, brkmt6a;3b does not contain a sant domain.
as expected from restricted atkmt6a;3/sdg5/mea expression in only a small number of cells during reproduction, expression of both brkmt6a;3a and brkmt6a;3b is barely detectable in the examined tissues .
it will be interesting to investigate brkmt6a;3a and brkmt6a;3b expression during reproduction and to examine whether both genes are functionally important.
the kmt6b subclass proteins
the kmt6b subclass includes two members each in a. thaliana, b. distachyon and o. sativa, and four members in b. rapa, which together can be divided into two distinct groups .
the two members from a. thaliana, atkmt6b;1/sdg15/atxr <dig> and atkmt6b;2/sdg34/atxr <dig>  were classified as trithorax-related in the first genome analysis of arabidopsis set-domain proteins  <cit> .
however, our study as well as two previous studies that included a more complete set of plant set-domain proteins clearly show that atkmt6b;1/sdg15/atxr <dig> and atkmt6b;2/sdg34/atxr <dig> belong to the kmt6b subclass   <cit> .
consistent with this, functional analysis revealed that atkmt6b;1/sdg15/atxr <dig> and atkmt6b;2/sdg34/atxr <dig> are involved in monomethylation of h3k <dig>  <cit> .
they appear to act redundantly, because depletion of h3k <dig> monomethylation is only detectable in the atxr <dig> atxr <dig> double mutant  <cit> .
kmt6a-mediated h3k27me <dig> is mainly present in euchromatic regions and is important for gene silencing  <cit> , but kmt6b-mediated h3k27me <dig> is found in heterochromatic chromocenters and is important for heterochromatin condensation and replication in arabidopsis  <cit> .
distinct from kmt6a proteins containing a sant domain, many plant kmt6b subclass proteins contain a phd domain .
the phd domain of both atkmt6b;1/sdg15/atxr <dig> and atkmt6b;2/sdg34/atxr <dig> strongly bind unmethylated h <dig> tail peptides , and this binding is negatively affected by methylation on h3k <dig>  <cit> .
this binding preference may help to assure that these kmt6b proteins are not targeted to euchromatin and active genes enriched in h3k <dig> methylation.
remarkably, both group- <dig> and group- <dig> members are duplicated in b. rapa.
both brkmt6b;1a and brkmt6b;1b are syntenic with atkmt6b;1/sdg15/atxr <dig>  and both brkmt6b;2a and brkmt6b;2b with atkmt6b;2/sdg34/atxr <dig>  expression of brkmt6b;1a, brkmt6b;2a and brkmt6b;2b was detected in different tissues, but we failed to detect brkmt6b;1b expression .
it is reasonable to speculate that brkmt6b;1a, brkmt6b;2a and brkmt6b;2b might have redundant functions.
the kmt <dig> class proteins
the kmt <dig> class contains a single member each in a. thaliana, o. sativa and b. distachyon, but three members in b. rapa .
although the arabidopsis protein atkmt7;1/sdg2/atxr <dig> was considered to be related to members of the kmt <dig> class in some previous studies  <cit> , it was located outside of any classes in the phylogenetic tree analysis by springer and colleagues  <cit> , and our analysis here revealed that it is grouped together with some other green lineage proteins, forming the plant kmt <dig> class .
unlike the classes described above, the plant and animal kmt <dig> classes do not cluster although they are predicted to have similar functions in h3k <dig> methylation.
representatives of the animal kmt <dig> class are only found in mammals and include the human set7/ <dig>  which monomethylates h3k <dig> and also methylates a number of nonhistone proteins  <cit> .
the plant kmt <dig> proteins did not show the highest sequence similarities with the human set7/ <dig>  and depletion of atkmt7;1/sdg2/atxr <dig> resulted in a global reduction of h3k4me <dig> and caused pleiotropic defects in both sporophyte and gametophyte development  <cit> .
both brkmt7;1a and brkmt7;1b but not brkmt7;1c have synteny with atkmt7;1/sdg2/atxr <dig>  and phylogenetic analysis showed that brkmt7;1a is more closely related to atkmt7;1/sdg2/atxr <dig>  rt-pcr analysis revealed that brkmt7;1b is expressed at a higher level than brkmt7;1a .
in view of the important function of atkmt7;1a/sdg2/atxr <dig>  it will be interesting to investigate roles of brkmt7;1a and brkmt7;1b in histone methylation and plant development in b. rapa.
discussion
over last  <dig> years, a number of set-domain genes in arabidopsis and in rice have been characterized and shown to exert crucial chromatin-based functions via histone methylation during plant growth and development  <cit> .
however, the nomenclature of plant set-domain proteins remains complex, and multiple synonyms exist for many arabidopsis proteins , which could cause considerable confusion in this important field.
nomenclature based on sequence similarity has several advantages, informing the prediction of kmt enzyme substrate specificity for its histone lysine residue and providing a global view of kmt types in an organism once its whole genome sequence becomes available.
however, the sdg nomenclature failed to provide information concerning enzyme substrate specificity and the number following "sdg" could be long and difficult to remember  <cit> , e.g., the first sdg from b. rapa  would have been named sdg <dig>  while the nomenclature by baumbusch and colleagues provided information about homology to animal proteins, an incomplete list of arabidopsis set-domain proteins and the limitation  of having only one plant species with a genome-wide analysis restricted the precision and correctness of phylogenetic grouping in this study  <cit> .
in addition, animal kmt nomenclature had also been noncoherent; a rational nomenclature was proposed only recently  <cit> .
therefore, the nomenclature we propose here is in line with the latest advances in the field.
in accordance with the guidelines of the commission on plant gene nomenclature  <cit> , the nomenclature of plant kmts is defined by species initials  before kmt, which is followed by the class number .
the class number is based on the yeast and animal systems indicating the enzyme substrate specificity, i.e.
kmt <dig> for h3k <dig>  kmt <dig> for h3k <dig>  kmt <dig> for h3k <dig>  kmt <dig> for h3k <dig>  and kmt <dig> also for h3k <dig>  <cit> .
multiple subclasses are indicated by upper-case letters , and distinct groups within the class/subclass are indicated by an arabic numeral suffix .
members within the group are indicated by lower-case letters .
subgroups are not currently defined but may be designated in the future as functional analysis and an increasing number of sequenced genomes demonstrate sequence conservation between species or distinct functions for several members of a defined kmt group.
the use of a given subgroup suffix should indicate highly similar sequences or equivalent functional roles between several species.
the new nomenclature may be difficult to adopt in arabidopsis because the original names for a number of set-domain proteins are familiar to researchers, but a coherent and rational nomenclature for different species is important and useful because of the enormous interest in kmts.
the guidelines proposed here will be particularly useful for nomenclature of newly identified set-domain proteins, which are being discovered at an exponentially increasing rate as genome sequences become available for additional plant species.
we identified  <dig> set-domain proteins from the recently completed whole genome sequence of b. rapa.
among them,  <dig> proteins belong to the s-et class likely involved in nonhistone protein methylation,  <dig> proteins belong to the kmt <dig> class potentially involved in h3k <dig> methylation,  <dig> proteins belong to the kmt <dig> class potentially involved in h3k <dig> methylation,  <dig> proteins belong to the kmt <dig> class potentially involved in h3k <dig> methylation,  <dig> proteins belong to the kmt <dig> class potentially involved in h3k <dig> methylation, and  <dig> belong to the kmt <dig> class also potentially involved in h3k <dig> methylation.
this in silico survey is useful for future functional analysis of this important family of epigenetic regulators in brassica.
h4k <dig> methylation was detected in arabidopsis using antibodies  <cit> , but the catalyzing enzyme involved is not yet known and the current phylogenetic analysis did not allow prediction of a specific kmt class involved in h4k <dig> methylation.
it is possible that some members of the aforementioned kmt classes catalyze h4k <dig> methylation.
the total number of kmts in b. rapa  is slightly higher than that identified in a. thaliana , o. sativa  and b. distachyon .
nevertheless, we could not exclude the possibility that a few more kmts may be missing from the currently available genome sequence of b. rapa.
gene duplication is one of the primary driving forces in the evolution of genomes and genetic systems, and is considered to be a major mechanism for the establishment of new gene functions and the generation of evolutionary novelty  <cit> .
contrary to what would be expected from the chromosome number duplication in b. rapa compared to a. thaliana, the number of kmt genes in b. rapa  is much less than double the number of a. thaliana kmts .
many duplicated genes show synteny with their a. thaliana homologues, suggesting that they are derived from chromosome/genome segment duplications.
three alternative outcomes can occur in the evolution of duplicated genes:  one copy may simply become silenced by degenerative mutations ;  one copy may acquire a novel, beneficial function and become preserved by natural selection ;  both copies may become partially compromised by mutation so that their total capacity adds up to the capacity of the single-copy ancestral gene   <cit> .
these different outcomes likely apply to different duplicated kmt genes, judging from their expression patterns .
expression of brkmt1a;4c and brkmt6b;1b was undetectable, suggesting that they might have been nonfunctionalized.
the duplicated pairs brkmt1b;2a and brkmt1b;2b, brkmt3;4b and brkmt3;4d, or brkmt7;1a and brkmt7;1b are differentially expressed in plant organs, suggesting that they might have acquired distinct tissue-specific functions.
finally, expression of some duplicated genes, e.g.
brkmt1a;2a and brkmt1a;2c, brkmt1b;1a and brkmt1b;1b, or brkmt6a;3a and brkmt6a;3b showed similar patterns, suggesting that they might be subfunctionalized and/or have redundant functions.
among the groups showing gene duplications in b. rapa, it is worth to note that in arabidopsis, atkmt6a;3/sdg5/mea is critical for parental gene imprinting and seed development  <cit> , atkmt6b;1/sdg15/atx <dig> and atkmt6b;2/sdg34/atx <dig> are important for heterochromatin condensation and replication in arabidopsis  <cit> , and atkmt7;1/sdg2/atxr <dig> is essential for both sporophyte and gametophyte development  <cit> .
it will be of great interest to investigate these groups of genes for their regulation and function in chromatin organization, plant growth and development in b. rapa.
CONCLUSIONS
our study shows that the plant set-domain kmt proteins can be phylogenetically grouped into distinct classes and that the classes involved in histone methylation can be named in accordance with the nomenclature proposed for animal and yeast set-domain kmts.
such a coherent and rational nomenclature in different organisms will help avoid confusion caused by the existence of multiple names for the same protein or gene.
the information provided on the b. rapa kmts will also be beneficial for future research to unravel the mechanisms of epigenetic regulation in brassica crops.

 epigenetic regulation acts through heritable changes in genome function that occur without a change in dna sequence. one well-known epigenetic mechanism is through posttranslational covalent modifications of histones; these modifications include acetylation, methylation, ubiquitylation and others, and form the basis of the'histone code' for gene regulation. histone lysine methylation plays a pivotal role in a wide range of cellular processes including heterochromatin formation, transcriptional regulation, parental imprinting, and cell fate determination. at least six lysine residues, five on histone h and one on h, are subject to methylation. each lysine can carry one, two or three methyl residue, known as mono-, di- and tri-methylation, respectively. in general, di-/tri- methylation of h3k and h3k correlates with transcriptional activation, whereas di-methylation of h3k and trimethylation of h3k correlates with gene silencing in plants and animals. all known lysine methylation modifications, with the exception of h3k methylation, are carried out by methyltransferases that contain an evolutionarily conserved set domain, named after three drosophila genes, e, and trithorax). the set domain encompasses approximately 130- amino acids that form a knot-like structure and constitute the enzyme catalytic site for lysine methylation. in addition to the set domain, flanking sequences, more distant protein domains, and possibly some cofactors are also important for enzyme activity and specificity. the genes encoding set-domain proteins are ancient, existing in prokaryotes and eukaryotes, but have proliferated and evolved novel functions connected with the appearance of eukaryotes. the first plant genes encoding set-domain proteins to be genetically characterized were curly leaf and medea in arabidopsis thaliana. chromatin-binding properties and histone methylation activity of plant set-domain proteins were first reported for tobacco ntset and arabidopsis kryptonite. phylogenetic analysis of plant set domain proteins has proven helpful as a guide for genetic and molecular studies of this large family of proteins. to date, some of the arabidopsis set-domain family members have been characterized and shown to play crucial functions in diverse processes including flowering time control, cell fate determination, leaf morphogenesis, floral organogenesis, parental imprinting and seed development. genome sequences of an increasing number of plant species, in addition to the model plants, have also been completed. other brassica species are of particular interest because of their agro-economical importance and their close relationship with arabidopsis, thus providing insights into recent set-domain gene amplification during evolution of brassica species. here, we identified and analyzed set-domain proteins from the recently completed brassica rapa whole genome sequence. our data provide a platform for future functional characterization of these important epigenetic regulatory genes in brassica species.  identification of set-domain proteins from the b. rapa genome using blastp and tblastn with the full complement of known arabidopsis and rice set-domain proteins as queries, we identified genes encoding different set-domain proteins from the b. rapa genome. we used the nomenclature recently proposed for lysine methyltransferases and named the newly identified b. rapa genes based on our phylogenetic analysis of their corresponding protein sequences. apart from brkmt1b;1a and brkmt1b;2b genes, whose chromosomal locations are yet unknown, the other genes are distributed on the ten b. rapa chromosomes, with 1- kmt genes per chromosome. *ud, undetermined b. rapa set-domain proteins can be grouped into six classes to analyze the b. rapa set-domain protein sequences, we extracted set-domain proteins from several other green lineage species, including proteins from a. thaliana, proteins from o. sativa, proteins from b. distachyon, and proteins from ostreococcus tauri. we also included the saccharomyces cerevisiae sckmt2/set and sckmt3/set proteins, which are h3k4- and h3k36-specific kmts, respectively, and can be used to represent ancient eukaryotic set-domain proteins from an evolutionary point of view. phylogenetic analysis of the aforementioned set-domain proteins revealed that they could be grouped into distinct classes, namely kmt kmt kmt kmt kmt and s-et class. the first four class numbers used here are consistent with the nomenclature previously proposed for yeast and animal kmts. furthermore, two plant-specific subclasses were identified for kmt and kmt representative members of each class/subclass are found in a. thaliana, b. rapa, o. sativa and b. distachyon. the s-et class members contain an interrupted set domain and are likely involved in methylation of nonhistone proteins, e.g. rubisco subunits; however, their biological functions remain largely unknown. hereafter, we focused on the kmt classes/subclasses that are involved in histone methylation. the kmt1a subclass proteins the kmt1a subclass is the largest class and can be further divided into 4distinct groups. in each group, proteins from dicots and monocots clearly fall into separate branches, indicating that they are derived from a common ancestral gene but diverged before the monocot/dicot separation. the first three groups have a relatively simple relationship and small number of genes, but group- is more complex: each plant species has 4- members that diverged at various times during evolution. in the case of b. rapa, among the members belonging to group- brkmt1a;4a, brkmt1a;4c, brkmt1a;4d, and brkmt1a;4f are clustered with the arabidopsis atkmt1a;4a/sdg32/suvh1; brkmt1a;4b with atkmt1a;4b/sdg19/suvh3; and brkmt1a;4e, brkmt1a; g and brkmt1a; h with atkmt1a;4e/sdg11/suvh. examination of synteny between b. rapa and a. thaliana revealed that brkmt1a;4a, brkmt1a;4c and brkmt1a;4d but not brkmt1a;4f are syntenic with atkmt1a;4a/sdg32/suvh and brkmt1a; h but not brkmt1a;4e nor brkmt1a; g is syntenic with atkmt1a;4e/sdg11/suvh it thus appears that multiple duplication events occurred, in either a chromosome segment or single gene scale, resulting in more recent amplification of group- genes in b. rapa after separation from a. thaliana during evolution. in agreement with previous studies in arabidopsis, rice and maize, few introns are present in brkmt1a genes. most brkmt1a genes are represented by ests, but some do not have any ests in current databases. our rt-pcr analysis revealed that indeed two genes that lack ests, brkmt1a;2a and brkmt1a;2c, are very weakly expressed. strong expression was detected for brkmt1a;4a, but relatively weak expression was detected for brkmy1a;4d and expression was undetectable for brkmt1a;4c. together, these data indicate that expression levels of different brkmt1a genes varied considerably and thus these genes may regulate genome function to different degrees. the plant kmt1a subclass proteins show high sequence similarity to the animal kmt proteins both within the set domain and in the surrounding regions known as the pre-set and post-set domains. additionally, most of the plant proteins contain a specific domain named sra. similar to previously studied arabidopsis proteins, most of the brkmt1a proteins also contain sra, pre-set, set and post-set domains. these domains are missing in some of the group- proteins; for example, brkmt1a.4e, brkmt1a;4f and brkmt1a; g lack a post-set domain, and brkmt1a. h lacks sra, pre-set and post-set domains. several functions have been reported for sra domains, including binding with the n-terminal tail of histone h and with dna cytosine methylation. the crystal structure of atkmt1a;3a/sdg9/suvh revealed that sra recognizes the methylation status of cg and chh sequences. the pre-set domain contains conserved cysteines. the post-set domain is a small cysteine-rich region often found at the c-terminal side of set domains. both pre-set and post-set domains have been shown to affect histone methyltransferase activity of the set domain. members of the plant kmt1a subclass, like animal kmt proteins, are likely to be responsible for h3k methylation, an epigenetic mark involved in heterochromatin formation and gene silencing. consistent with this, analysis of atkmt1a;1/sdg33/suvh4/kyp, atkmt1a;2a/sdg3/suvh atkmt1a;3a/sdg9/suvh and atkmt1a;3b/sdg23/suvh has revealed their important roles in h3k methylation, in heterochromatic gene silencing and in cross-talk between h3k and dna methylation. work in rice also confirmed that several members of this subclass are involved in h3k methylation and in transposon silencing. some of the brkmt1a genes might also have similar functions. the kmt1b subclass proteins six b. rapa proteins belong to the kmt1b subclass, which can be further divided into groups. group- contains two b. rapa proteins whose genes show synteny with atkmt1b;1/sdg31/suvr moreover, sequence analysis showed that brkmt1b;1b and atkmt1b;1/sdg31/suvr have highly similar protein domain organization, indicating that brkmt1b;1b is more conserved and brkmt1b;1a diverged relatively late during evolution after the b. rapa/a. thaliana separation. group- has two b. rapa, two a. thaliana proteins, one o. sativa protein, and three b. distachyon proteins. both brkmt1b;2a and brkmt1b;2b show synteny with atkmt1b;2b/sdg18/suvr group- and each have one representative member in each of the four examined higher plant species. the kmt1b subclass differs from the kmt1a subclass in protein domain organization; specifically, these proteins lack the sra domain. a recent study demonstrated that atkmt1b;1/sdg31/suvr possesses h3k9-methyltransferase activities and its binding with ubiquitin converts h3k9me to h3k9me deposition on transposon chromatin. notably, the wiyld domain, which binds ubiquitin, is conserved in brkmt1b;1a, brkmt1b;1b, brkmt1b;2a and brkmt1b;2b. it was reported that atkmt1b;3/sdg6/suvr5/atczs is involved in regulation of flowering time, possibly through deposition of h3k methylation at the flowering time repressor flc. the functions of other members of the kmt1b subclass remain uncharacterized so far. the kmt class proteins the kmt class includes six b. rapa and six a. thaliana proteins in groups. this class features highly conserved set and post-set domains with the yeast h3k4-methyltransferase sckmt2/set nevertheless, some plant proteins have acquired specific domains during evolution, namely pwwp, phd, fyr and/or gyf. the pwwp domain is also found in eukaryotic proteins involved in dna methylation, dna repair, and regulation of transcription, and regulates cell growth and differentiation by mediating protein-protein interactions. the phd domain is found in a number of chromatin-associated proteins and is thought to be involved in protein-protein interactions important for the assembly of multiprotein complexes. the pwwp domain of the animal brpf protein binds h3k36me, and the phd domain is also an important module in proteins that read histone modifications. the fyr domain is composed of fyr-c and fyr-n terminal portions, which are often located close to each other but can also be separated. the gyf domain is proposed to be involved in recognition of proline-rich sequences in protein-protein interactions. kmt group- members contain one pwwp, one fyr and two phd domains. only one member belonging to group- is found in o. sativa or b. distachyon, but two members are found in b. rapa and a. thaliana. our examination revealed that brkmt2;1a has synteny with atkmt2;1a/sdg27/atx and brkmt2;1b with atkmt2;1b/sdg30/atx suggesting that they are derived from two different ancestral copies before the b. rapa/a. thaliana separation. consistent with this, the atx mutant plants exhibit strong and pleiotropic defects, but the atx mutant plants have a normal phenotype. the atx mutation can enhance atx in reduction of expression of the flowering repressor gene flc through reduced levels of h3k4me at the flc locus. the pwwp and fyr domains are absent from the group- members and the phd domain is found only in some monocot proteins. only one group- representative member is found in the dicot species b. rapa or a. thaliana, but the monocot o. sativa has two members and b. distachyon has three members. the b. rapa and a. thaliana proteins, as well as one member each from o. sativa and b. distachyon, contain a gyf domain in the n-terminal part of the protein. the fact that this domain is conserved in kmt2; proteins from all four higher plant species suggests that the acquisition of the gyf domain occurred before the monocot/dicot separation and may have a conserved function in higher plants. genetic analysis demonstrated that atkmt2;2/sdg25/atxr is necessary in preventing early flowering. the recombinant atkmt2;2/sdg25/atxr protein was shown to methylate histone h in vitro and the depletion of atkmt2;2/sdg25/atxr in planta slightly reduced h3k and h3k methylation at flc chromatin. oskmt2;2b/sdg and bdkmt2;2c contain two phd domains, but bdkmt2;2b, like the yeast protein sckmt2/set does not contain a recognizable phd domain. future study of these monocot proteins will likely provide a deeper understanding of the domain evolution of kmt proteins. the group- kmt proteins have a domain organization more similar to group- except that they lack the fyr domain. b. rapa and a. thaliana both have three group- members, but each of the other two higher plant species has only two group- members. synteny was observed for brkmt2;3c with atkmt2;3c/sdg29/atx but not with atkmt2;3b/sdg16/atx suggesting that atkmt2;3b/sdg16/atx was derived from a relatively recent duplication event. this is in agreement with a previous study revealing that atkmt2;3b/sdg16/atx and atkmt2;3c/sdg29/atx are collinearly duplicated with atkmt2;1a/sdg27/atx and atkmt2;1b/sdg30/atx. to date, none of the group- proteins has been functionally characterized. the kmt class proteins the kmt class contains members in a. thaliana but members in b. rapa, and these can be further divided into four groups. the other groups contain a single member per plant species, but group- contains members in a. thaliana and members in b. rapa. our examination indicates that brkmt3;4a and brkmt3;4c are syntenic with atkmt3;4a/sdg7/ashh and brkmt3;4b and brkmt3;4d with atkmt3;4b/sdg24/ashh the ests found in the current databases match all four brkmt3; genes, and thus do not allow us to distinguish expression of each gene. our rt-pcr analysis indicated that brkmt3;4a and brkmt3;4c are expressed at higher levels and more broadly in different examined organs/tissues, whereas only weak expression was detected for brkmt3;4b and brkmt3;4d in some organs/tissues. the kmt class plant proteins share high sequence similarity and share the aws, set and post-set domain organization with the yeast h3k36-methyltransferase sckmt3/set. the group- proteins have a long sequence and contain an additional cw domain specific to this group. the cw domain of atkmt3;1/sdg8/ashh2/efs/ccr was recently shown to bind h3k4me1/me, suggesting a novel link between h3k and h3k methylation in plants. atkmt3;1/sdg8/ashh2/efs/ccr is the major h3k36-methyltransferase specifically required for h3k36me and h3k36me deposition, and activates expression of hundreds of genes including flc and mafs. depletion of atkmt3;1/sdg8/ashh2/efs/ccr causes pleiotropic phenotypes, including early flowering, reduced organ size, increased shoot branching, perturbed fertility and carotenoid composition, and impaired plant defenses against pathogens. the other group of kmt plant proteins have a shorter sequence and do not contain the cw domain; interestingly the depletion of atkmt3;2/sdg26/ashh resulted in a late-flowering phenotype associated with elevated levels of flc expression. the group- kmt proteins, with the exception of bdkmt3;3b and oskmt3;3b/sdg contain a phd domain; and atkmt3;3/sdg4/ashr was reported to be involved in pollen and stamen development possibly through mediating h3k4me and h3k36me deposition. the functions of the group- proteins remain unexamined so far. examination of this group in b. rapa could be a challenge because of gene multiplication and more diverged sequences. the kmt6a subclass proteins the kmt6a subclass includes members in b. rapa and well-characterized members in a. thaliana, atkmt6a;1/sdg1/clf, atkmt6a;2/sdg10/eza1/swn and atkmt6a;3/sdg5/mea, which represent three distinct groups. atkmt6a;1/sdg1/clf and atkmt6a;2/sdg10/eza1/swn are broadly expressed and partially redundant in regulation of vegetative and reproductive development, whereas atkmt6a;3/sdg5/mea appears to function specifically in gametophyte and seed development. the three arabidopsis proteins can act as a key component of the evolutionarily conserved polycomb repressive complex, which trimethylates h3k involved in transcriptional repression. atkmt6a;1/sdg1/clf and atkmt6a;2/sdg10/eza1/swn represent group- and group- respectively, and each has an orthologue in different higher plant species. atkmt6a;3/sdg5/mea, which belongs to group- has no orthologue in monocots but has two orthologues in b. rapa. both brkmt6a;3a and brkmt6a;3b are syntenic with atkmt6a;3/sdg5/mea, and brkmt6a;3a has a more similar protein domain organization to atkmt6a;3/sdg5/mea than does brkmt6a;3b, suggesting that brkmt6a;3b may have diverged after the a. thaliana/b. rapa separation during evolution. the sant domain is found in most of the plant kmt6a subclass proteins. this domain is also found in a number of other chromatin remodeling proteins with multiple activities such as dna-binding, histone tail binding, and protein-protein interactions. nevertheless, the precise role of the sant domain in kmt6a proteins is currently unknown. notably, brkmt6a;3b does not contain a sant domain. as expected from restricted atkmt6a;3/sdg5/mea expression in only a small number of cells during reproduction, expression of both brkmt6a;3a and brkmt6a;3b is barely detectable in the examined tissues. it will be interesting to investigate brkmt6a;3a and brkmt6a;3b expression during reproduction and to examine whether both genes are functionally important. the kmt6b subclass proteins the kmt6b subclass includes two members each in a. thaliana, b. distachyon and o. sativa, and four members in b. rapa, which together can be divided into two distinct groups. the two members from a. thaliana, atkmt6b;1/sdg15/atxr and atkmt6b;2/sdg34/atxr were classified as trithorax-related in the first genome analysis of arabidopsis set-domain proteins. however, our study as well as two previous studies that included a more complete set of plant set-domain proteins clearly show that atkmt6b;1/sdg15/atxr and atkmt6b;2/sdg34/atxr belong to the kmt6b subclass. consistent with this, functional analysis revealed that atkmt6b;1/sdg15/atxr and atkmt6b;2/sdg34/atxr are involved in monomethylation of h3k. they appear to act redundantly, because depletion of h3k monomethylation is only detectable in the atxr atxr double mutant. kmt6a-mediated h3k27me is mainly present in euchromatic regions and is important for gene silencing, but kmt6b-mediated h3k27me is found in heterochromatic chromocenters and is important for heterochromatin condensation and replication in arabidopsis. distinct from kmt6a proteins containing a sant domain, many plant kmt6b subclass proteins contain a phd domain. the phd domain of both atkmt6b;1/sdg15/atxr and atkmt6b;2/sdg34/atxr strongly bind unmethylated h tail peptides, and this binding is negatively affected by methylation on h3k. this binding preference may help to assure that these kmt6b proteins are not targeted to euchromatin and active genes enriched in h3k methylation. remarkably, both group- and group- members are duplicated in b. rapa. both brkmt6b;1a and brkmt6b;1b are syntenic with atkmt6b;1/sdg15/atxr and both brkmt6b;2a and brkmt6b;2b with atkmt6b;2/sdg34/atxr expression of brkmt6b;1a, brkmt6b;2a and brkmt6b;2b was detected in different tissues, but we failed to detect brkmt6b;1b expression. it is reasonable to speculate that brkmt6b;1a, brkmt6b;2a and brkmt6b;2b might have redundant functions. the kmt class proteins the kmt class contains a single member each in a. thaliana, o. sativa and b. distachyon, but three members in b. rapa. although the arabidopsis protein atkmt7;1/sdg2/atxr was considered to be related to members of the kmt class in some previous studies, it was located outside of any classes in the phylogenetic tree analysis by springer and colleagues, and our analysis here revealed that it is grouped together with some other green lineage proteins, forming the plant kmt class. unlike the classes described above, the plant and animal kmt classes do not cluster although they are predicted to have similar functions in h3k methylation. representatives of the animal kmt class are only found in mammals and include the human set7/ which monomethylates h3k and also methylates a number of nonhistone proteins. the plant kmt proteins did not show the highest sequence similarities with the human set7/ and depletion of atkmt7;1/sdg2/atxr resulted in a global reduction of h3k4me and caused pleiotropic defects in both sporophyte and gametophyte development. both brkmt7;1a and brkmt7;1b but not brkmt7;1c have synteny with atkmt7;1/sdg2/atxr and phylogenetic analysis showed that brkmt7;1a is more closely related to atkmt7;1/sdg2/atxr rt-pcr analysis revealed that brkmt7;1b is expressed at a higher level than brkmt7;1a. in view of the important function of atkmt7;1a/sdg2/atxr it will be interesting to investigate roles of brkmt7;1a and brkmt7;1b in histone methylation and plant development in b. rapa. discussion over last years, a number of set-domain genes in arabidopsis and in rice have been characterized and shown to exert crucial chromatin-based functions via histone methylation during plant growth and development. however, the nomenclature of plant set-domain proteins remains complex, and multiple synonyms exist for many arabidopsis proteins, which could cause considerable confusion in this important field. nomenclature based on sequence similarity has several advantages, informing the prediction of kmt enzyme substrate specificity for its histone lysine residue and providing a global view of kmt types in an organism once its whole genome sequence becomes available. however, the sdg nomenclature failed to provide information concerning enzyme substrate specificity and the number following "sdg" could be long and difficult to remember, e.g., the first sdg from b. rapa would have been named sdg while the nomenclature by baumbusch and colleagues provided information about homology to animal proteins, an incomplete list of arabidopsis set-domain proteins and the limitation of having only one plant species with a genome-wide analysis restricted the precision and correctness of phylogenetic grouping in this study. in addition, animal kmt nomenclature had also been noncoherent; a rational nomenclature was proposed only recently. therefore, the nomenclature we propose here is in line with the latest advances in the field. in accordance with the guidelines of the commission on plant gene nomenclature, the nomenclature of plant kmts is defined by species initials before kmt, which is followed by the class number. the class number is based on the yeast and animal systems indicating the enzyme substrate specificity, i.e. kmt for h3k kmt for h3k kmt for h3k kmt for h3k and kmt also for h3k. multiple subclasses are indicated by upper-case letters, and distinct groups within the class/subclass are indicated by an arabic numeral suffix. members within the group are indicated by lower-case letters. subgroups are not currently defined but may be designated in the future as functional analysis and an increasing number of sequenced genomes demonstrate sequence conservation between species or distinct functions for several members of a defined kmt group. the use of a given subgroup suffix should indicate highly similar sequences or equivalent functional roles between several species. the new nomenclature may be difficult to adopt in arabidopsis because the original names for a number of set-domain proteins are familiar to researchers, but a coherent and rational nomenclature for different species is important and useful because of the enormous interest in kmts. the guidelines proposed here will be particularly useful for nomenclature of newly identified set-domain proteins, which are being discovered at an exponentially increasing rate as genome sequences become available for additional plant species. we identified set-domain proteins from the recently completed whole genome sequence of b. rapa. among them, proteins belong to the s-et class likely involved in nonhistone protein methylation, proteins belong to the kmt class potentially involved in h3k methylation, proteins belong to the kmt class potentially involved in h3k methylation, proteins belong to the kmt class potentially involved in h3k methylation, proteins belong to the kmt class potentially involved in h3k methylation, and belong to the kmt class also potentially involved in h3k methylation. this in silico survey is useful for future functional analysis of this important family of epigenetic regulators in brassica. h4k methylation was detected in arabidopsis using antibodies, but the catalyzing enzyme involved is not yet known and the current phylogenetic analysis did not allow prediction of a specific kmt class involved in h4k methylation. it is possible that some members of the aforementioned kmt classes catalyze h4k methylation. the total number of kmts in b. rapa is slightly higher than that identified in a. thaliana, o. sativa and b. distachyon. nevertheless, we could not exclude the possibility that a few more kmts may be missing from the currently available genome sequence of b. rapa. gene duplication is one of the primary driving forces in the evolution of genomes and genetic systems, and is considered to be a major mechanism for the establishment of new gene functions and the generation of evolutionary novelty. contrary to what would be expected from the chromosome number duplication in b. rapa compared to a. thaliana, the number of kmt genes in b. rapa is much less than double the number of a. thaliana kmts. many duplicated genes show synteny with their a. thaliana homologues, suggesting that they are derived from chromosome/genome segment duplications. three alternative outcomes can occur in the evolution of duplicated genes: one copy may simply become silenced by degenerative mutations; one copy may acquire a novel, beneficial function and become preserved by natural selection; both copies may become partially compromised by mutation so that their total capacity adds up to the capacity of the single-copy ancestral gene. these different outcomes likely apply to different duplicated kmt genes, judging from their expression patterns. expression of brkmt1a;4c and brkmt6b;1b was undetectable, suggesting that they might have been nonfunctionalized. the duplicated pairs brkmt1b;2a and brkmt1b;2b, brkmt3;4b and brkmt3;4d, or brkmt7;1a and brkmt7;1b are differentially expressed in plant organs, suggesting that they might have acquired distinct tissue-specific functions. finally, expression of some duplicated genes, e.g. brkmt1a;2a and brkmt1a;2c, brkmt1b;1a and brkmt1b;1b, or brkmt6a;3a and brkmt6a;3b showed similar patterns, suggesting that they might be subfunctionalized and/or have redundant functions. among the groups showing gene duplications in b. rapa, it is worth to note that in arabidopsis, atkmt6a;3/sdg5/mea is critical for parental gene imprinting and seed development, atkmt6b;1/sdg15/atx and atkmt6b;2/sdg34/atx are important for heterochromatin condensation and replication in arabidopsis, and atkmt7;1/sdg2/atxr is essential for both sporophyte and gametophyte development. it will be of great interest to investigate these groups of genes for their regulation and function in chromatin organization, plant growth and development in b. rapa.  our study shows that the plant set-domain kmt proteins can be phylogenetically grouped into distinct classes and that the classes involved in histone methylation can be named in accordance with the nomenclature proposed for animal and yeast set-domain kmts. such a coherent and rational nomenclature in different organisms will help avoid confusion caused by the existence of multiple names for the same protein or gene. the information provided on the b. rapa kmts will also be beneficial for future research to unravel the mechanisms of epigenetic regulation in brassica crops. 
the results obtained in this study will provide a base for nomenclature of kmts in other plant species and facilitate the functional characterization of these important epigenetic regulatory genes in brassica crops. we showed that plant set-domain proteins can be grouped into distinct classes, namely kmt kmt kmt kmt kmt and s-et. apart from the s-et class, which has an interrupted set domain and may be involved in methylation of nonhistone proteins, the other classes have characteristics of histone methyltransferases exhibiting different substrate specificities: kmt for h3k kmt for h3k kmt for h3k kmt for h3k and kmt also for h3k we also propose a coherent and rational nomenclature for plant set-domain proteins. the substrate specificity and activity of kmts are determined by sequences within the set domain and other regions of the protein. we performed sequence similarity and protein domain organization analysis of these proteins, along with the set-domain proteins from the dicot arabidopsis thaliana, the monocots oryza sativa and brachypodium distachyon, and the green alga ostreococcus tauri. comparisons of sequence similarity and synteny of b. rapa and a. thaliana set-domain proteins revealed recent gene duplication events for some kmts. here we identified set-domain proteins from the recently sequenced brassica rapa genome. kmts perform many crucial biological functions via histone methylation of chromatin. histone methylation marks are interpreted differently depending on the histone type, the lysine position and the number of added methyl groups. phylogenetic analysis data allowed the development of a coherent and rational nomenclature of this important family of proteins in plants, as in animals. for example, h3k4me and h3k36me are associated with transcriptional activation, but h3k9me and h3k27me are associated with gene silencing. the set 3- enhancer-of-zeste, trithorax) domain is an evolutionarily conserved sequence of approximately 130- amino acids, and constitutes the catalytic site of lysine methyltransferases. this study provides the first characterization of the set-domain kmt proteins of b. rapa.
 the set 3- enhancer-of-zeste, trithorax) domain is an evolutionarily conserved sequence of approximately 130- amino acids, and constitutes the catalytic site of lysine methyltransferases. kmts perform many crucial biological functions via histone methylation of chromatin. histone methylation marks are interpreted differently depending on the histone type, the lysine position and the number of added methyl groups. for example, h3k4me and h3k36me are associated with transcriptional activation, but h3k9me and h3k27me are associated with gene silencing. the substrate specificity and activity of kmts are determined by sequences within the set domain and other regions of the protein.  here we identified set-domain proteins from the recently sequenced brassica rapa genome. we performed sequence similarity and protein domain organization analysis of these proteins, along with the set-domain proteins from the dicot arabidopsis thaliana, the monocots oryza sativa and brachypodium distachyon, and the green alga ostreococcus tauri. we showed that plant set-domain proteins can be grouped into distinct classes, namely kmt kmt kmt kmt kmt and s-et. apart from the s-et class, which has an interrupted set domain and may be involved in methylation of nonhistone proteins, the other classes have characteristics of histone methyltransferases exhibiting different substrate specificities: kmt for h3k kmt for h3k kmt for h3k kmt for h3k and kmt also for h3k we also propose a coherent and rational nomenclature for plant set-domain proteins. comparisons of sequence similarity and synteny of b. rapa and a. thaliana set-domain proteins revealed recent gene duplication events for some kmts.  this study provides the first characterization of the set-domain kmt proteins of b. rapa. phylogenetic analysis data allowed the development of a coherent and rational nomenclature of this important family of proteins in plants, as in animals. the results obtained in this study will provide a base for nomenclature of kmts in other plant species and facilitate the functional characterization of these important epigenetic regulatory genes in brassica crops. chromatinhistonelysine methylationset domaingene duplicationnomenclature 