Histone Methylation in Higher Plants

Liu, Chunyan; Lu, Falong; Cui, Xia; Cao, Xiaofeng

doi:10.1146/annurev.arplant.043008.091939

Cited by 586 publications

(508 citation statements)

References 154 publications

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“…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%

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: 99%

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

et al. 2017

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“…Histone H3 Lys 9 dimethylation (H3K9me2) and H3 Lys 27 trimethylation (H3K27me3) are two crucial epigenetic marks involved in heterochromatin silencing and transcriptional repression, respectively (Fischle et al, 2003;Liu et al, 2010). H3K9me2 is often associated with DNA methylation.…”

Section: Introductionmentioning

confidence: 99%

Identification and Characterization of an Epi-Allele of FIE1 Reveals a Regulatory Linkage between Two Epigenetic Marks in Rice

et al. 2012

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DNA methylation and histone H3 Lys 9 dimethylation (H3K9me2) are important epigenetic repression marks for silencing transposons in heterochromatin and for regulating gene expression. However, the mechanistic relationship to other repressive marks, such as histone H3 Lys 27 trimethylation (H3K27me3) is unclear. FERTILIZATION-INDEPENDENT ENDOSPERM1 (FIE1) encodes an Esc-like core component of the Polycomb repressive complex 2, which is involved in H3K27me3-mediated gene repression. Here, we identify a gain-of-function epi-allele (Epi-df) of rice (Oryza sativa) FIE1; this allele causes a dwarf stature and various floral defects that are inherited in a dominant fashion. We found that Epi-df has no changes in nucleotide sequence but is hypomethylated in the 59 region of FIE1 and has reduced H3K9me2 and increased H3K4me3. In Epi-df, FIE1 was ectopically expressed and its imprinting was disrupted. FIE1 interacted with rice Enhancer of Zeste homologs, consistent with its role in H3K27me3 repression. Ectopic expression of FIE1 in Epi-df resulted in alteration of H3K27me3 levels in hundreds of genes. In summary, this work identifies an epi-allele involved in H3K27me3-mediated gene repression that itself is highly regulated by DNA methylation and histone H3K9me2, thereby shedding light on the link between DNA methylation and histone methylation, the two important epigenetic marks regulating rice development.

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“…Histone methylation is one type of epigenetic marker that serves an essential regulatory function in the organization of chromatin structure and genome function (Yu et al, 2009b;Liu et al, 2010). Enzymes that catalyze histone Lys methylation contain an evolutionarily conserved SET domain (Tschiersch et al, 1994).…”

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confidence: 99%

“…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). However, studies on these SET domain proteins are still limited, and the biological functions of a large number of SET domain-containing proteins in chloroplast development remain a mystery.…”

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confidence: 99%

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

et al. 2011

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The SET domain-containing protein, pTAC14, was previously identified as a component of the transcriptionally active chromosome (TAC) complexes. Here, we investigated the function of pTAC14 in the regulation of plastid-encoded bacterialtype RNA polymerase (PEP) activity and chloroplast development. The knockout of pTAC14 led to the blockage of thylakoid formation in Arabidopsis (Arabidopsis thaliana), and ptac14 was seedling lethal. Sequence and transcriptional analysis showed that pTAC14 encodes a specific protein in plants that is located in the chloroplast associated with the thylakoid and that its expression depends on light. In addition, the transcript levels of all investigated PEP-dependent genes were clearly reduced in the ptac14-1 mutants, while the accumulation of nucleus-encoded phage-type RNA polymerase-dependent transcripts was increased, indicating an important role of pTAC14 in maintaining PEP activity. pTAC14 was found to interact with pTAC12/ HEMERA, another component of TACs that is involved in phytochrome signaling. The data suggest that pTAC14 is essential for proper chloroplast development, most likely by affecting PEP activity and regulating PEP-dependent plastid gene transcription in Arabidopsis together with pTAC12.

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Histone Methylation in Higher Plants

Cited by 586 publications

References 154 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

Identification and Characterization of an Epi-Allele of FIE1 Reveals a Regulatory Linkage between Two Epigenetic Marks in Rice

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

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