Rice jmjC domain-containing gene
            <i>JMJ706</i>
            encodes H3K9 demethylase required for floral organ development

Sun, Qianwen; Zhou, Dao‐Xiu

doi:10.1073/pnas.0805901105

Cited by 163 publications

(134 citation statements)

References 36 publications

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“…In barley, loss of VRS3 function results also in an alteration in floral organ number . JMJ706 affects the histone methylation on the degenerated hell1 locus, which encodes a putative lateral organ boundaries domain transcription factor (Sun and Zhou, 2008). In our analysis, the LOB-domain transcription factor VRS4 was not consistently down-regulated in the vrs3 mutants.…”

Section: Discussionmentioning

confidence: 62%

“…How many of the genes identified as misregulated by RNA sequencing are direct targets of VRS3 is currently unknown, but INT-C and VRS1 are the prime candidates, as they showed low transcript amounts in multiple vrs3 alleles, when compared to wild type and their mutants show similar floral phenotypes. This again leads to functional analogy with rice JMJ706, which regulates floral organ development (Sun and Zhou, 2008). In barley, loss of VRS3 function results also in an alteration in floral organ number .…”

Section: Discussionmentioning

confidence: 96%

“…In rice, the JMJ703, a histone H3 Lys 4 (H3K4) demethylase, is required for stem elongation and transposon silencing (Chen et al, 2013;Cui et al, 2013). The barley VRS3 is similar to the JMJD2 group II of Lys demethylases and exhibits a high similarity to the rice JMJ706, which encodes for a histone H3 Lys 9 di-and tri-(H3K9me2 and H3K9me3) demethylase (Sun and Zhou, 2008). The H3K9me2 and me3 are repressive modifications in heterochromatin and euchromatin contexts, respectively, (Liu et al, 2010), suggesting that JMJ706 is necessary for the activation of specific genes (Sun and Zhou, 2008).…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, comparison of the JmjC domains revealed a 95.97% identity between VRS3 and Os.JMJ706 and an 83.87% identity between VRS3 and At.JMJ13 (Supplemental Table S2). Os.JMJ706 is mainly involved in the removal of a methyl group from the Lys 9 of the histone H3 protein (H3K9me), whereas At.JMJ13 has an H3K27me3 demethylase activity (Sun and Zhou, 2008;Crevillèn et al, 2014). Comparative phenotyping of spike architecture in vrs1, vrs3(int-a.1), vrs4.k, and int-c.5 revealed that these mutants showed quantitative differences in spikelet development.…”

Section: Resultsmentioning

confidence: 99%

“…The barley VRS3 is similar to the JMJD2 group II of Lys demethylases and exhibits a high similarity to the rice JMJ706, which encodes for a histone H3 Lys 9 di-and tri-(H3K9me2 and H3K9me3) demethylase (Sun and Zhou, 2008). The H3K9me2 and me3 are repressive modifications in heterochromatin and euchromatin contexts, respectively, (Liu et al, 2010), suggesting that JMJ706 is necessary for the activation of specific genes (Sun and Zhou, 2008). This scenario may hold true also for VRS3, as suggested by our expression analysis of vrs3(int-a.1).…”

Section: Discussionmentioning

confidence: 99%

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Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

et al. 2017

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The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA sequencing of allelic six-rowed spike3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone Lys demethylase with a conserved zinc finger and Jumonji C and N domain. Sanger sequencing of this candidate gene in independent allelic vrs3 mutants revealed a series of mutations in conserved domains, thus confirming our candidate as the VRS3 gene and suggesting that the row type in barley is determined epigenetically. Global transcriptional profiling in developing shoot apical meristems of vrs3 suggested that VRS3 acts as a transcriptional activator of the row-type genes VRS1 (Hv.HOMEOBOX1) and INTERMEDIUM-C (INT-C; Hv.TEOSINTE BRANCHED1). Comparative transcriptome analysis of the row-type mutants vrs3, vrs4 (Hv.RAMOSA2), and int-c confirmed that all three genes act as transcriptional activators of VRS1 and quantitative variation in the expression levels of VRS1 in these mutants correlated with differences in the number of developed lateral spikelets. The identification of genes and pathways affecting seed number in small grain cereals will enable to further unravel the transcriptional networks controlling this important yield component.

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Section: Discussionmentioning

confidence: 62%

Section: Discussionmentioning

confidence: 96%

Section: Discussionmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

et al. 2017

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The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

Fambrini

Usai

Vangelisti

et al. 2020

Genesis

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Transposable elements (TEs) are DNA sequences that can change their position within genomes. TEs are present in most organisms and can be an important genomic component. Their activities are manifold: restructuring of genome size, chromosomal rearrangements, induction of gene mutations, and alteration of gene activity by insertion near or within promoters, intronic regions, or enhancer. There are several examples of mutations and other genetic variations determined by the activity of TEs, associated with the evolution of prokaryotic and eukaryotic organisms and the domestication of plants. Generally, TE mobilization occurs when the organism is subjected to stress, which can include both biotic and abiotic stresses, polyploidy conditions, and interspecific hybridizations, very common events in plants. TEs are widely distributed among organisms. TEs also play essential roles in evolution, but most of them are either dormant or inactive. This is mainly determined by epigenetic silencing mechanisms, regulatory systems, and control systems that aim to limit its proliferation. Furthermore, the host has recruited many genes originated from TEs as transcriptional regulators, especially in defense against pathogens and invasive genetic elements; this phenomenon is called molecular domestication. Therefore, TEs are responsible for horizontal gene transfer and the movement of genetic material between organisms, even phylogenetically distant, with a consequent remixing of their gene pools.

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Molecular basis underlying the successful invasion of hexaploid cytotypes of Solidago canadensis L.: Insights from integrated gene and miRNA expression profiling

Chen

Wang

2019

Ecology and Evolution

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Dissecting complex connections between cytogenetic traits (ploidy levels) and plant invasiveness has emerged as a popular research subject in the field of invasion biology. Although recent work suggests that polyploids are more likely to be invasive than their corresponding diploids, the molecular basis underlying the successful invasion of polyploids remains largely unexplored. To this end, we adopted an RNA‐seq and sRNA‐seq approach to describe how polyploids mediate invasiveness differences in two contrasting cytotypes of Solidago canadensis L., a widespread wild hexaploid invader with localized cultivated diploid populations. Our analysis of the leaf transcriptome revealed 116,801 unigenes, of which 12,897 unigenes displayed significant differences in expression levels. A substantial number of these differentially expressed unigenes (DEUs) were significantly associated with the biosynthesis of secondary metabolites, carbohydrate metabolism, lipid metabolism, and environmental adaptation pathways. Gene Ontology term enrichment‐based categorization of DEU‐functions was consistent with this observation, as terms related to single‐organism, cellular, and metabolic processes including catalytic, binding, transporter, and enzyme regulator activity were over‐represented. Concomitantly, 186 miRNAs belonging to 44 miRNA families were identified in the same leaf tissues, with 59 miRNAs being differentially expressed. Furthermore, we discovered 83 miRNA‐target interacting pairs that were oppositely regulated, and a meticulous study of these targets depicted that several unigenes encoding transcription factors, DNA methyltransferase, and leucine‐rich repeat receptor‐like kinases involved in the stress response were greatly influenced. Collectively, these transcriptional and epigenetic data provide new insights into miRNA‐mediated gene expression regulatory mechanisms that may operate in hexaploid cytotypes to favor successful invasion.

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Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development

Cited by 163 publications

References 36 publications

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

Molecular basis underlying the successful invasion of hexaploid cytotypes of Solidago canadensis L.: Insights from integrated gene and miRNA expression profiling

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