You will be presented with the abstract, introduction, and discussion section from a biomedical research article. Your task is to create a summary that a layperson can understand, capturing the essence of the research article. Keep essential scientific terms, but ensure that the language remains clear and the concepts are explained in an uncomplicated manner.

Title: Structural Basis of a Histone H3 Lysine 4 Demethylase Required for Stem Elongation in Rice}
Article:
Abstract:
Histone lysine methylation is an important epigenetic modification in regulating chromatin structure and gene expression. Histone H3 lysine 4 methylation( H3K4me), which can be in a mono-, di-, or trimethylated state, has been shown to play an important role in gene expression involved in plant developmental control and stress adaptation. However, the resetting mechanism of this epigenetic modification is not yet fully understood. In this work, we identified a JmjC domain-containing protein, JMJ703, as a histone lysine demethylase that specifically reverses all three forms of H3K4me in rice. Loss-of-function mutation of the gene affected stem elongation and plant growth, which may be related to increased expression of cytokinin oxidase genes in the mutant. Analysis of crystal structure of the catalytic core domain( c-JMJ703) of the protein revealed a general structural similarity with mammalian and yeast JMJD2 proteins that are H3K9 and H3K36 demethylases. However, several specific features were observed in the structure of c-JMJ703. Key residues that interact with cofactors Fe( II) and N-oxalylglycine and the methylated H3K4 substrate peptide were identified and were shown to be essential for the demethylase activity in vivo. Several key residues are specifically conserved in known H3K4 demethylases, suggesting that they may be involved in the specificity for H3K4 demethylation.
Introduction:
Histone methylation is an important epigenetic modification for chromatin structure, genome function, and gene expression in eukaryotic cells[1]. Histone methylation can be reversed by histone demethylases[1]. Lysine Specific Demethylase 1( LSD1) is the first identified histone demethylase characterized as a member of the flavin-dependent amine oxidase family[2]. The second class of histone demethylases featured with the jumonji C( JmjC) domain has been shown to catalyze histone lysine demethylation through ferrous ion( Fe( II)) and α-ketoglutaric acid( α-KG)-dependent oxidative reactions[3]. Structurally related JmjC domain-containing proteins are classified into 7 subgroups based on phylogenetic analysis of members from yeast and animal cells[4]. Among them, the JmjC domain-containing histone demethylase 1( JHDM1) subgroup has been demonstrated to reverse mono- and dimethylated histone H3 lysine 36( H3K36me1/me2)[3]. The JmjC domain-containing histone demethylase 2( JHDM2) subgroup has been identified to reverse dimethylated histone H3 lysine 9( H3K9me2)[5], whereas the JMJD2( also called JHDM3) group specifically reverses methylated H3K9 and/or H3K36[6]. UTX/UTY is involved in the reversal of histone H3 lysine 27 methylation( H3K27me)[7], whereas PHF8 which belongs to PHF2/PHF8 subfamily demethylates H3K9me1/2, H3K27me2 and monomethylated histone H4 lysine 20( H4K20me1)[8]–[10]. Aside from these members, the JARID subgroup is responsible for H3K4 demethylation[11]. The JmjC domain-only subgroup has the smallest molecular architecture; members of which have been shown to catalyze divergent reactions, such as histone arginine demethylation[12] and asparagine protein hydroxylation[13]. More recently, JMJD6 is shown to catalyze protein lysyl-hydroxylation[14]. Plant JmjC proteins have been shown to play important roles in the regulation of epigenetic processes, growth and development[15]. Although conserved with yeast and animal homologues, plant JmjC proteins display several distinct features. For instance, the UTX subgroup proteins that exhibit H3K27 demethylase activity are not found in plants. Recent data show that RELATIVE OF EARLY FLOWERING 6( REF6), a member of the JMJD2 subgroup, can demethylate H3K27 in Arabidopsis[16]. Conversely, there exists a subgroup of plant JmjC proteins that include additional protein modules that are missing from animal or yeast homologues[17]. The amino acid sequence of the JmjC domains of this subgroup is closely related to JARID, while the overall domain organization of the core protein is similar to that of the JMJD2 group[17],[18]. To study this plant specific group of JmjC proteins, we analyzed the developmental function, enzymatic activity, and crystal structure of JMJ703, a member of this subgroup in rice. Our results demonstrate that JMJ703 is essential for plant cell division and stem elongation and specifically demethylates mono-, di-, and trimethylated H3K4 in vivo and in vitro. The high resolution structure of the catalytic core of JMJ703( c-JMJ703) in complex with cofactors and substrate peptide reveals that the overall folding of c-JMJ703 is similar to those defined in animal and yeast JMJD2 that are H3K9 and H3K36 demethylases. However, the crystal structure of c-JMJ703 displays a number of specific features in cofactor interaction and in substrate peptide binding. Substitution mutation analysis indicated that residues implicated in the specific structures are essential for the enzymatic activity, some of which are conserved within JARID proteins and plant H3K4 demethylases and may be involved in the specificity of this class of enzymes.
Discussion:
In this work, we have provided evidence that JMJ703 is a histone demethylase specifically reversing the three forms of methylated H3K4. Arabidopsis JMJ14 that belongs to the same group as JMJ703 also has an H3K4 demethylase activity[27]. About two-thirds of plant genes contain at least one type of H3K4me, among which H3K4me3 is associated with gene activation in Arabidopsis and rice[28],[29]. Demethylation of the three forms of H3K4me implies that JMJ703 is important for rice gene expression. The phenotype caused by T-DNA insertion and RNAi and increased expression of CKX genes suggest that JMJ703 may regulate growth hormone metabolism in rice, which is different from JMJ14 that has functions in floral transition, DNA methylation, and RNA silencing in Arabidopsis[27],[30]–[33]. H3K4me3 on specific plant genes can be induced by external signals, such as light, drought, and submergence, among others[34]–[36]. H3K4me3 is suggested to be a mark of active genes and may play a role in plant adaptation to environmental cues. Whether JMJ703 is involved in resetting stress-induced gene expression requires further analysis. Although JmjC domain of JMJ703 is closely related to that of the JARID proteins[17], the domain organization of the catalytic core of the enzyme( JmjN- long β-hairpin-mixed domain-JmjC) resembles that of JMJD2 members( c-JMJD2A and c-Rph1). However, our functional analysis has revealed that JMJ703( i. e. FA-J3NCZ) was unable to demethylate H3K9me1/2/3 or H3K36me1/2/3( Figure S2A–S2B). This suggests that the enzymatic specificity may be determined essentially in the JmjC domain. Our data indicate that the helix-rich region( α8–α11, aa 419–459) of the JmjC domain of JMJ703 is substantially divergent from that of JMJD2A and Rph1. For instance, K241 of c-JMJD2A, which is conserved in c-Rph1, is considered to be a key catalytic residue that recruits and positions O2 between Fe( II) and the methyl group to participate in the reaction[25]. Substitution mutation of K241L abolishes the activity of c-JMJD2A[25]. However, this position is replaced by a leucine in JMJ703( L447) and in other plant homologues and JARID proteins( Figure 4). L447 was found to be essential for the H3K4 demethylase activity of JMJ703( Table 1, Figure S6). This leucine together with the other residues that are specifically conserved in JARID/H3K4 demethylases and mostly found in the helix-rich region( α8–α11, aa 419–459) of c-JMJ703( Table 1, Figure 4 and Figure S6), may be involved in the specificity of H3K4 demethylases. Our data indicate that although most of the JMJ703 residues in α-KG/NOG stabilization showed a high structural similarity with JMJD2 proteins, the residues Y321 and N404 displayed specific features( Figure 8, Figure S5). The conformation of Y321 in c-JMJ703 indicates that the residue may not be in direct contact with α-KG or NOG. Substitution mutation of Y321 only affected H3K4me1 demethylase activity. In addition, N404A substitution did not clearly alter the H3K4 demethylase activity. The methyl group binding pocket in c-JMJ703 differs also from that of c-JMJD2A and Rph1 in one key residue( A494 in JMJ703 compared to S288 in JMJD2A or S355 in Rph1). S288 of JMJD2A has been shown to be important to reverse di- and trimethylated H3K9[25],[26],[37]. However, JMJD2D, which harbors an alanine in this position, is 7-fold and 60-fold more efficient than JMJD2A in the demethylation of H3K9me3 and H3K9me2, respectively. JMJD2D has residual activity to H3K9me1 that is absent from JMJD2A[26]. The presence of alanine at this position in JMJ703( A494) supports the demethylation function of the protein of all three forms of methylated H3K4( Figure 2). Substitution of this alanine by a serine abolished the demethylase activity of H3K4me1/2, but retained the activity toward H3K4me3( Table 1, Figure S6). Interestingly, this alanine residue is conserved in most of the plant JMJD2 members( Figure S4), suggesting that these plant proteins may be able to demethylate the three methylated forms of relevant histone lysines. In addition, the zinc finger that overlaps partially with the JmjC domain of JMJD2A is not found in JMJ703. Although the residues involved in the zinc finger formation in JMJD2A are conserved in Rph1, no zinc ion is observed in its structure and this domain is disordered and invisible in the c-Rph1 structure[20]. By contrast, JMJ703 contains a distal zinc finger motif relative to the JmjC domain( about 100 amino acids downstream the JmjC domain), which is present in Rph1, but absent from JMJD2A. The distal zinc finger is found in a number of other JmjC proteins and is shown to be involved in nuclear localization of JMJ706[17]. These observations together with our data showing that the inclusion of the motif increased the substrate peptide( H3K4me1/2/3) binding activity to two-folds but not alter the binding specificity, suggest that this zinc finger may not be a component of the catalytic core of JmjC proteins, but is important for their enzymatic activity. Our data also revealed a number of other clear structural differences in the plant JmjC protein. The N-terminal end of c-JMJ703 adopted a completely different conformation from that of c-JMJD2A and c-Rph1. The long β-hairpin domain and mixed domain of c-JMJ703 also showed significant divergence at the amino acid sequence level compared to c-JMJD2A and c-Rph1( Figure S4). However, the divergent regions are mostly invisible in c-JMJ703 and c-Rph1, indicating intrinsic disorder. In summary, we have shown that JMJ703 is an H3K4 demethylase that is important for rice plant development. Although JMJ703 displays an overall structure similar to that of JMJD2 H3K9 and H3K36 demethylases, it exhibits a number of important structural features which are conserved within JARID and plant H3K4 demethylases. In particular, our data suggest that the helix-rich region( α8–α11, aa 419–459) of the catalytic JmjC domain of JMJ703 may be involved in the determination of substrate specificity of the H3K4 demethylase.
Genomic DNA is associated with histone proteins to form the basic structure of chromatin . Lysine residues within the N-terminal end of histones H3 and H4 can be methylated , which may have a positive or a negative effect on the activity of associated DNA or genes , depending on the position of the lysines in the histones . Histone lysine methylation can be reversed by histone demethylases . However , it is not very clear how the specificity of histone demethylases to different histone lysines is determined . In this work we have identified a rice histone demethylase , namely JMJ703 , which specifically demethylates methylated histone H3 lysine 4 . We found that loss of the enzyme reduces cell division rate of the stem and the size of plant stature , indicating the importance of the protein in plant growth . The crystal structure of the catalytic domain of the protein shares a general similarity with that of mammalian and yeast proteins that demethylate methylated histone H3 lysine 9 and lysine 36 , but displays several distinct structural features that are important for substrate and cofactor binding and enzymatic activity of the protein . We found that key amino acids involved in the specific structures are conserved within known H3 lysine 4 demethylases , which may be involved in the specificity to histone H3 lysine 4 .