Publications by authors named "Yoshiki Habu"

23 Publications

  • Page 1 of 1

Acetic-acid-induced jasmonate signaling in root enhances drought avoidance in rice.

Sci Rep 2021 Mar 18;11(1):6280. Epub 2021 Mar 18.

Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602, Japan.

Conferring drought resistant traits to crops is one of the major aims of current breeding programs in response to global climate changes. We previously showed that exogenous application of acetic acid to roots of various plants could induce increased survivability under subsequent drought stress conditions, but details of the metabolism of exogenously applied acetic acid, and the nature of signals induced by its application, have not been unveiled. In this study, we show that rice rapidly induces jasmonate signaling upon application of acetic acid, resulting in physiological changes similar to those seen under drought. The major metabolite of the exogenously applied acetic acid in xylem sap was determined as glutamine-a common and abundant component of xylem sap-indicating that acetic acid is not the direct agent inducing the observed physiological responses in shoots. Expression of drought-responsive genes in shoot under subsequent drought conditions was attenuated by acetic acid treatment. These data suggest that acetic acid activates root-to-shoot jasmonate signals that partially overlap with those induced by drought, thereby conferring an acclimated state on shoots prior to subsequent drought.
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http://dx.doi.org/10.1038/s41598-021-85355-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7973560PMC
March 2021

Intracellular localization of histone deacetylase HDA6 in plants.

J Plant Res 2019 Sep 23;132(5):629-640. Epub 2019 Jul 23.

Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.

Histone modification is an important epigenetic mechanism in eukaryotes. Histone acetyltransferase and deacetylase regulate histone acetylation levels antagonistically, leading to dynamic control of chromatin structure. One of the histone deacetylases, HDA6, is involved in gene silencing in the heterochromatin regions, chromocenter formation, and metabolic adaptation under drought stress. Although HDA6 plays an important role in chromatin control and response to drought stress, its intracellular localization has not been observed in detail. In this paper, we generated transformants expressing HDA6-GFP in the model plant, Arabidopsis thaliana, and the crops, rice, and cassava. We observed the localization of the fusion protein and showed that HDA6-GFP was expressed in the whole root and localized at the nucleus in Arabidopsis, rice, and cassava. Remarkably, HDA6-GFP clearly formed speckles that were actively colocalized with chromocenters in Arabidopsis root meristem. In contrast, such speckles were unlikely to be formed in rice or cassava. Because AtHDA6 directly binds to the acetate synthesis genes, which function in drought tolerance, we performed live imaging analyses to examine the cellular dynamics of pH in roots and the subnuclear dynamics of AtHDA6 responding to acetic acid treatment. The number of HDA6 speckles increased during drought stress, suggesting a role in contributing to drought stress tolerance.
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http://dx.doi.org/10.1007/s10265-019-01124-8DOI Listing
September 2019

Biosynthesis and accumulation of GABA in rice plants treated with acetic acid.

J Pestic Sci 2018 Aug;43(3):214-219

Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan.

Rice seedlings () that have died from drought cannot be rescued by watering afterward, but pre-treatment with exogenous acetic acid enabled the plants to produce shoots again after being watered (hereinafter referred to as "drought resilience"). To elucidate the metabolism of acetic acid, we treated rice plants with C-labeled acetic acid and traced C-labeled metabolites using LC-MS and C-NMR techniques. The LC-MS and C-NMR spectral data of the root extracts indicated that the acetic acid treatment was absorbed into the plants and then was metabolized to gamma-aminobutyric acid (GABA) by glutamic acid decarboxylase (GAD). GABA accumulation in the roots took place in advance of that in the shoots, and the survival rate against drought stress increased in proportion to the amount of GABA accumulated in the shoots. Therefore, GABA accumulation in shoots may be a key step in drought resilience induced by the acetic acid treatment.
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http://dx.doi.org/10.1584/jpestics.D18-036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173134PMC
August 2018

Direct quantitative evaluation of disease symptoms on living plant leaves growing under natural light.

Breed Sci 2017 Jun 30;67(3):316-319. Epub 2017 May 30.

Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.

Leaf color is an important indicator when evaluating plant growth and responses to biotic/abiotic stress. Acquisition of images by digital cameras allows analysis and long-term storage of the acquired images. However, under field conditions, where light intensity can fluctuate and other factors (shade, reflection, and background, etc.) vary, stable and reproducible measurement and quantification of leaf color are hard to achieve. Digital scanners provide fixed conditions for obtaining image data, allowing stable and reliable comparison among samples, but require detached plant materials to capture images, and the destructive processes involved often induce deformation of plant materials (curled leaves and faded colors, etc.). In this study, by using a lightweight digital scanner connected to a mobile computer, we obtained digital image data from intact plant leaves grown in natural-light greenhouses without detaching the targets. We took images of soybean leaves infected by pv. , and distinctively quantified two disease symptoms (brown lesions and yellow halos) using freely available image processing software. The image data were amenable to quantitative and statistical analyses, allowing precise and objective evaluation of disease resistance.
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http://dx.doi.org/10.1270/jsbbs.16169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515311PMC
June 2017

Ethanol Enhances High-Salinity Stress Tolerance by Detoxifying Reactive Oxygen Species in and Rice.

Front Plant Sci 2017 3;8:1001. Epub 2017 Jul 3.

Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS)Yokohama, Japan.

High-salinity stress considerably affects plant growth and crop yield. Thus, developing techniques to enhance high-salinity stress tolerance in plants is important. In this study, we revealed that ethanol enhances high-salinity stress tolerance in and rice. To elucidate the molecular mechanism underlying the ethanol-induced tolerance, we performed microarray analyses using seedlings. Our data indicated that the expression levels of 1,323 and 1,293 genes were upregulated by ethanol in the presence and absence of NaCl, respectively. The expression of reactive oxygen species (ROS) signaling-related genes associated with high-salinity tolerance was upregulated by ethanol under salt stress condition. Some of these genes encode ROS scavengers and transcription factors (e.g., and ). A RT-qPCR analysis confirmed that the expression levels of and as well as and , which encode cytosolic ascorbate peroxidases (APX), were higher in ethanol-treated plants than in untreated control plants, when exposure to high-salinity stress. Additionally, cytosolic APX activity increased by ethanol in response to salinity stress. Moreover, histochemical analyses with 3,3'-diaminobenzidine (DAB) and nitro blue tetrazolium (NBT) revealed that ROS accumulation was inhibited by ethanol under salt stress condition in and rice, in which DAB staining data was further confirmed by Hydrogen peroxide (HO) content. These results suggest that ethanol enhances high-salinity stress tolerance by detoxifying ROS. Our findings may have implications for improving salt-stress tolerance of agriculturally important field-grown crops.
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http://dx.doi.org/10.3389/fpls.2017.01001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5494288PMC
July 2017

Acetate-mediated novel survival strategy against drought in plants.

Nat Plants 2017 Jun 26;3:17097. Epub 2017 Jun 26.

Plant Genomic Network Research Team, RIKEN Centre for Sustainable Resource Science (CSRS), 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan.

Water deficit caused by global climate changes seriously endangers the survival of organisms and crop productivity, and increases environmental deterioration. Plants' resistance to drought involves global reprogramming of transcription, cellular metabolism, hormone signalling and chromatin modification. However, how these regulatory responses are coordinated via the various pathways, and the underlying mechanisms, are largely unknown. Herein, we report an essential drought-responsive network in which plants trigger a dynamic metabolic flux conversion from glycolysis into acetate synthesis to stimulate the jasmonate (JA) signalling pathway to confer drought tolerance. In Arabidopsis, the ON/OFF switching of this whole network is directly dependent on histone deacetylase HDA6. In addition, exogenous acetic acid promotes de novo JA synthesis and enrichment of histone H4 acetylation, which influences the priming of the JA signalling pathway for plant drought tolerance. This novel acetate function is evolutionarily conserved as a survival strategy against environmental changes in plants. Furthermore, the external application of acetic acid successfully enhanced the drought tolerance in Arabidopsis, rapeseed, maize, rice and wheat plants. Our findings highlight a radically new survival strategy that exploits an epigenetic switch of metabolic flux conversion and hormone signalling by which plants adapt to drought.
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http://dx.doi.org/10.1038/nplants.2017.97DOI Listing
June 2017

DNA Methylation Affects the Efficiency of Transcription Activator-Like Effector Nucleases-Mediated Genome Editing in Rice.

Front Plant Sci 2017 13;8:302. Epub 2017 Mar 13.

Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO) Tsukuba, Japan.

Genome editing in plants becomes popular since the advent of sequence-specific nucleases (SSNs) that are simple to set up and efficient in various plant species. Although transcription activator-like effector nucleases (TALENs) are one of the most prevalent SSNs and have a potential to provide higher target specificity by their dimeric property, TALENs are sensitive to methylated cytosines that are present not only in transposons but also in active genes in plants. In mammalian cells, the methylation sensitivity of TALENs could be overcome by using a base-recognition module (N) that has a higher affinity to methylated cytosine. In contrast to mammals, plants carry DNA methylation at all cytosine contexts (CG, CHG, and CHH, where H represents A, C, or T) with various degrees and effectiveness of N module in genome editing in plants has not been explored. In this study, we designed sets of TALENs with or without N modules and examined their efficiency in genome editing of methylated regions in rice. Although improvement in genome editing efficiency was observed with N-TALENs designed to a stably methylated target, another target carrying cytosines with various levels of methylation showed resistance to both normal and N-TALENs. The results suggest that variability of cytosine methylation in target regions is an additional factor affecting the genome editing efficiency of TALENs.
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http://dx.doi.org/10.3389/fpls.2017.00302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5346537PMC
March 2017

Gene Body CG and CHG Methylation and Suppression of Centromeric CHH Methylation are Mediated by DECREASE IN DNA METHYLATION1 in Rice.

Mol Plant 2015 Oct 12;8(10):1560-2. Epub 2015 Aug 12.

Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan; CREST, JST, Kawaguchi, Saitama 332-0012, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2015.08.002DOI Listing
October 2015

Does the upstream region possessing MULE-like sequence in rice upregulate PsbS1 gene expression?

PLoS One 2014 26;9(9):e102742. Epub 2014 Sep 26.

Institute for Environmental Science and Technology, Saitama University, Saitama city, Saitama, Japan.

The genomic nucleotide sequences of japonica rice (Sasanishiki and Nipponbare) contained about 2.7-kb unique region at the point of 0.4-kb upstream of the OsPsbS1 gene. In this study, we found that japonica rice with a few exceptions possessing such DNA sequences [denoted to OsMULE-japonica specific sequence (JSS)] is distinct by the presence of Mutator-like-element (MULE). Such sequence was absent in most of indica cultivars and Oryza glaberrima. In OsMULE-JSS1, we noted the presence of possible target site duplication (TSD; CTTTTCCAG) and about 80-bp terminal inverted repeat (TIR) near TSD. We also found the enhancement ofOsPsbS1 mRNA accumulation by intensified light, which was not associated with the DNA methylation status in OsMULE/JSS. In addition, O. rufipogon, possible ancestor of modern rice cultivars was found to compose PsbS gene of either japonica (minor) or indica (major) type. Transient gene expression assay showed that the japonica type promoter elevated a reporter gene activity than indica type.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102742PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178011PMC
June 2015

RICE SALT SENSITIVE3 forms a ternary complex with JAZ and class-C bHLH factors and regulates jasmonate-induced gene expression and root cell elongation.

Plant Cell 2013 May 28;25(5):1709-25. Epub 2013 May 28.

Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan.

Plasticity of root growth in response to environmental cues and stresses is a fundamental characteristic of land plants. However, the molecular basis underlying the regulation of root growth under stressful conditions is poorly understood. Here, we report that a rice nuclear factor, RICE SALT SENSITIVE3 (RSS3), regulates root cell elongation during adaptation to salinity. Loss of function of RSS3 only moderately inhibits cell elongation under normal conditions, but it provokes spontaneous root cell swelling, accompanied by severe root growth inhibition, under saline conditions. RSS3 is preferentially expressed in the root tip and forms a ternary complex with class-C basic helix-loop-helix (bHLH) transcription factors and JASMONATE ZIM-DOMAIN proteins, the latter of which are the key regulators of jasmonate (JA) signaling. The mutated protein arising from the rss3 allele fails to interact with bHLH factors, and the expression of a significant portion of JA-responsive genes is upregulated in rss3. These results, together with the known roles of JAs in root growth regulation, suggest that RSS3 modulates the expression of JA-responsive genes and plays a crucial role in a mechanism that sustains root cell elongation at appropriate rates under stressful conditions.
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http://dx.doi.org/10.1105/tpc.113.112052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694701PMC
May 2013

3' fragment of miR173-programmed RISC-cleaved RNA is protected from degradation in a complex with RISC and SGS3.

Proc Natl Acad Sci U S A 2013 Mar 15;110(10):4117-22. Epub 2013 Feb 15.

Division of Plant Sciences and Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.

trans-acting small interfering RNAs (tasiRNAs) are plant-specific endogenous siRNAs produced via a unique pathway whose first step is the microRNA (miRNA)-programmed RNA-induced silencing complex (RISC)-mediated cleavage of tasiRNA gene (TAS) transcripts. One of the products is subsequently transformed into tasiRNAs by a pathway that requires several factors including SUPPRESSOR OF GENE SILENCING3 (SGS3) and RNA-DEPENDENT RNA POLYMERASE6. Here, using in vitro assembled ARGONAUTE (AGO)1-RISCs, we show that SGS3 is recruited onto RISCs only when they bind target RNA. Following cleavage by miRNA173 (miR173)-programmed RISC, SGS3 was found in complexes containing cleaved TAS2 RNA and RISC. The 3' cleavage fragment (the source of tasiRNAs) was protected from degradation in this complex. Depletion of SGS3 did not affect TAS2 RNA cleavage by miR173-programmed RISC, but did affect the stability of the 3' cleavage fragment. When the 3' nucleotide of 22-nt miR173 was deleted or the corresponding nucleotide in TAS2 RNA was mutated, the complex was not observed and the 3' cleavage fragment was degraded. Importantly, these changes in miR173 or TAS2 RNA are known to lead to a loss of tasiRNA production in vivo. These results suggest that (i) SGS3 associates with AGO1-RISC via the double-stranded RNA formed by the 3'-terminal nucleotides of 22-nt miR173 and corresponding target RNA, which probably protrudes from the AGO1-RISC molecular surface, (ii) SGS3 protects the 3' cleavage fragment of TAS2 RNA from degradation, and (iii) the observed SGS3-dependent stabilization of the 3' fragment of TAS2 RNA is key to tasiRNA production.
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http://dx.doi.org/10.1073/pnas.1217050110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593843PMC
March 2013

DDM1 (decrease in DNA methylation) genes in rice (Oryza sativa).

Mol Genet Genomics 2012 Oct 24;287(10):785-92. Epub 2012 Aug 24.

CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan.

Regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. Relative tolerance of plant to deficiency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. The Decrease in DNA Methylation 1 (DDM1) of Arabidopsis thaliana is one of the best characterized plant epigenetic regulators that are necessary for maintenance of cytosine methylation in genomic DNA. Although cytosine methylation could affect various aspects of plant growth and development including those related to agricultural importance, orthologs of DDM1 in plants other than Arabidopsis has not been studied in detail. In this study, we identified two rice genes with similarity to Arabidopsis DDM1 and designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development and their amino acid sequences are 93 % identical to each other. Transgenic rice lines expressing the OsDDM1a cDNA in the antisense orientation exhibited genomic DNA hypomethylation. In those lines, repeated sequences were more severely affected than a single copy sequence as is the case in Arabidopsis ddm1 mutants. Transcripts derived from endogenous transposon-related loci were up-regulated in the antisense OsDDM1 lines, opening a possibility to identify and utilize potentially active transposons for rice functional genomics.
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http://dx.doi.org/10.1007/s00438-012-0717-5DOI Listing
October 2012

Tandemly arranged chalcone synthase A genes contribute to the spatially regulated expression of siRNA and the natural bicolor floral phenotype in Petunia hybrida.

Plant J 2012 Jun 30;70(5):739-49. Epub 2012 Mar 30.

Institute of Floricultural Science, National Agriculture and Food Research Organization, Tsukuba 305-8519, Japan.

The natural bicolor floral traits of the horticultural petunia (Petunia hybrida) cultivars Picotee and Star are caused by the spatial repression of the chalcone synthase A (CHS-A) gene, which encodes an anthocyanin biosynthetic enzyme. Here we show that Picotee and Star petunias carry the same short interfering RNA (siRNA)-producing locus, consisting of two intact CHS-A copies, PhCHS-A1 and PhCHS-A2, in a tandem head-to-tail orientation. The precursor CHS mRNAs are transcribed from the two CHS-A copies throughout the bicolored petals, but the mature CHS mRNAs are not found in the white tissues. An analysis of small RNAs revealed the accumulation of siRNAs of 21 nucleotides that originated from the exon 2 region of both CHS-A copies. This accumulation is closely correlated with the disappearance of the CHS mRNAs, indicating that the bicolor floral phenotype is caused by the spatially regulated post-transcriptional silencing of both CHS-A genes. Linkage between the tandemly arranged CHS-A allele and the bicolor floral trait indicates that the CHS-A allele is a necessary factor to confer the trait. We suppose that the spatially regulated production of siRNAs in Picotee and Star flowers is triggered by another putative regulatory locus, and that the silencing mechanism in this case may be different from other known mechanisms of post-transcriptional gene silencing in plants. A sequence analysis of wild Petunia species indicated that these tandem CHS-A genes originated from Petunia integrifolia and/or Petunia inflata, the parental species of P. hybrida, as a result of a chromosomal rearrangement rather than a gene duplication event.
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http://dx.doi.org/10.1111/j.1365-313X.2012.04908.xDOI Listing
June 2012

siRNA-mediated chromatin maintenance and its function in Arabidopsis thaliana.

Biochim Biophys Acta 2011 Aug 13;1809(8):444-51. Epub 2011 May 13.

National Institute of Agrobiological Sciences, Ibaraki, Japan.

Small interfering RNAs (siRNAs) are widespread in various eukaryotes and are involved in maintenance of chromatin modifications, especially those for inert states represented by covalent modifications of cytosine and/or histones. In contrast to mammalian genomes, in which cytosine methylation is restricted mostly to CG dinucleotide sequences, inert chromatin in plants carries cytosine methylation in all sequence contexts, and siRNAs play a major role in directing cytosine methylation through the process of RNA-directed DNA methylation. Recent advances in this field have revealed that siRNA-mediated maintenance of inert chromatin has diverse roles in development as well as in plant responses to the environment. Various proteinaceous factors required for siRNA-mediated chromatin modification have been identified in Arabidopsis thaliana, and much effort has been invested in understanding their function and interaction, resulting in the assignment of many of these factors to specific biochemical activities and engagement with specific steps such as transcription of intergenic RNAs, RNA processing, and cytosine methylation. However, the precise functions of a number of factors remain undesignated, and interactions of distinct pathways for siRNA-mediated chromatin modification are largely unknown. In this review, we summarize the roles of siRNA-mediated chromatin modification in various biological processes of A. thaliana, and present some speculation on the functions and interactions of silencing factors that, while not yet assigned to defined biochemical activities, have been loosely assigned to specific events in siRNA-mediated chromatin modification pathways. Special Issue entitled: Epigenetic control of cellular and developmental processes in plants.
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http://dx.doi.org/10.1016/j.bbagrm.2011.05.002DOI Listing
August 2011

Epigenetic silencing of endogenous repetitive sequences by MORPHEUS' MOLECULE1 in Arabidopsis thaliana.

Authors:
Yoshiki Habu

Epigenetics 2010 Oct;5(7):562-5

Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan.

Morpheus' molecule1 (MOM1) is a plant-specific epigenetic regulator of transcriptional gene silencing. Mutants of MOM1 release silencing of subsets of endogenous repetitive elements and transgenes without affecting their cytosine methylation status. Although MOM1 is evolutionarily related to chromodomain helicase DNA binding protein3 (CHD3), a family of chromatin remodeling proteins involved in repression of gene expression, MOM1 does not carry the functional ATPase/helicase domain essential for chromatin remodeling activity, and therefore, its mode of action is unknown. We recently performed a genome-wide survey for endogenous targets silenced by MOM1 and identified loci that are concentrated around centromeres and rich in sequences homologous to the 24-nt small interfering RNAs (siRNAs) that accumulate in wild type plants. Further and independent analyses indicated that the degree of contribution of MOM1 to maintenance of the silent states varies in different loci and that other silencing machineries, including those in the RNA-directed DNA methylation (RdDM) pathway, interact genetically with MOM1. In this short article, I review what we know about MOM1 and discuss its possible functions in silencing through examination of other silencing factors that interact genetically with MOM1.
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http://dx.doi.org/10.4161/epi.5.7.12518DOI Listing
October 2010

Locus-specific dependency of endogenous silent loci on MOM1 and non-CG methylation in Arabidopsis thaliana.

Plant Signal Behav 2010 Jun 1;5(6):724-6. Epub 2010 Jun 1.

Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan.

RNA-directed modification of histones is essential for maintenance of heterochromatin in higher eukaryotes. In plants, cytosine methylation, especially in non-CG sequence contexts, is tightly related to inactive chromatin, but the mechanisms regulating the coexistence of cytosine methylation and repressive histone modification remain obscure. We recently revealed that MORPHEUS' MOLECULE1 (MOM1) of Arabidopsis thaliana silences endogenous loci related to transposons and homologous to the 24-nt siRNAs accumulated in wild type plants, and suggested that MOM1 transduces RNA-directed DNA methylation (RdDM) signals to repressive histone modification. In this addendum, we focus on the involvement of MOM1 in multiple transcriptional gene silencing (TGS) pathways.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001571PMC
http://dx.doi.org/10.4161/psb.5.6.11663DOI Listing
June 2010

Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana.

EMBO J 2010 Jan 10;29(2):352-62. Epub 2009 Dec 10.

Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Japan.

RNA-directed modification of histones is essential for the maintenance of heterochromatin in higher eukaryotes. In plants, cytosine methylation is an additional factor regulating inactive chromatin, but the mechanisms regulating the coexistence of cytosine methylation and repressive histone modification remain obscure. In this study, we analysed the mechanism of gene silencing mediated by MORPHEUS' MOLECULE1 (MOM1) of Arabidopsis thaliana. Transcript profiling revealed that the majority of up-regulated loci in mom1 carry sequences related to transposons and homologous to the 24-nt siRNAs accumulated in wild-type plants that are the hallmarks of RNA-directed DNA methylation (RdDM). Analysis of a single-copy gene, SUPPRESSOR OF drm1 drm2 cmt3 (SDC), revealed that mom1 activates SDC with concomitant reduction of di-methylated histone H3 lysine 9 (H3K9me2) at the tandem repeats in the promoter region without changes in siRNA accumulation and cytosine methylation. The reduction of H3K9me2 is not observed in regions flanking the tandem repeats. The results suggest that MOM1 transduces RdDM signals to repressive histone modification in the core region of RdDM.
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http://dx.doi.org/10.1038/emboj.2009.374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824457PMC
January 2010

Inheritance and alteration of genome methylation in F1 hybrid rice.

Electrophoresis 2008 Oct;29(19):4088-95

Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan.

We analyzed the inheritance of DNA methylation in the first filial generation(F1) hybrid of Oryza sativa L. ("Nipponbare"x"Kasalath") by restriction landmark genome scanning (RLGS). Most parental RLGS spots were found in the F1, but eight spots (4%) showed abnormal inheritance: seven of the eight spots were missing in the F1, and one was newly detected in the F1. Here we show demethylation at restriction enzyme sites in the F1. We also found a candidate site of stable heterozygous methylation in the genome. These results show the applicability of the RLGS method for analysis of the inheritance and alteration of methylation in F1 hybrid plants.
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http://dx.doi.org/10.1002/elps.200700784DOI Listing
October 2008

Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants.

PLoS Genet 2008 Aug 22;4(8):e1000165. Epub 2008 Aug 22.

Laboratory of Plant Genetics, University of Geneva, Geneva, Switzerland.

Arabidopsis MOM1 is required for the heritable maintenance of transcriptional gene silencing (TGS). Unlike many other silencing factors, depletion of MOM1 evokes transcription at selected loci without major changes in DNA methylation or histone modification. These loci retain unusual, bivalent chromatin properties, intermediate to both euchromatin and heterochromatin. The structure of MOM1 previously suggested an integral nuclear membrane protein with chromatin-remodeling and actin-binding activities. Unexpected results presented here challenge these presumed MOM1 activities and demonstrate that less than 13% of MOM1 sequence is necessary and sufficient for TGS maintenance. This active sequence encompasses a novel Conserved MOM1 Motif 2 (CMM2). The high conservation suggests that CMM2 has been the subject of strong evolutionary pressure. The replacement of Arabidopsis CMM2 by a poplar motif reveals its functional conservation. Interspecies comparison suggests that MOM1 proteins emerged at the origin of vascular plants through neo-functionalization of the ubiquitous eukaryotic CHD3 chromatin remodeling factors. Interestingly, despite the divergent evolution of CHD3 and MOM1, we observed functional cooperation in epigenetic control involving unrelated protein motifs and thus probably diverse mechanisms.
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http://dx.doi.org/10.1371/journal.pgen.1000165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507757PMC
August 2008

Epigenetic regulation of transcription in intermediate heterochromatin.

EMBO Rep 2006 Dec 3;7(12):1279-84. Epub 2006 Nov 3.

National Institute of Agrobiological Sciences, Kannondai 2-1-2, 305-8602 Tsukuba, Japan.

Constitutive heterochromatin is a compact, transcriptionally inert structure formed in gene-poor and repeat- and transposon-rich regions. In Arabidopsis, constitutive heterochromatin is characterized by hypermethylated DNA and histone H3 dimethylated at lysine (K) 9 (H3K9me2) together with depletion of histone H3 dimethylated at lysine 4 (H3K4me2). Here, we describe loci with intermediate properties of heterochromatin in which transcription downregulation is inherited in a manner similar to constitutive heterochromatin, although the loci are associated with opposing histone marks--H3K4me2 and H3K9me2. In the ddm1 (decrease in DNA methylation 1) mutants, their transcriptional activation is accompanied by the expected shift in the H3 modifications--depletion of H3K9me2 and enrichment in H3K4me2. In mom1 (Morpheus' molecule 1) mutants, however, a marked increase in transcription is not accompanied by detectable changes in the levels of H3K4me2 and H3K9me2. Therefore, transcriptional regulation in the intermediate heterochromatin involves two distinct epigenetic mechanisms. Interestingly, silent transgenic inserts seem to acquire properties characteristic of the intermediate heterochromatin.
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http://dx.doi.org/10.1038/sj.embor.7400835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794695PMC
December 2006

Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin.

Proc Natl Acad Sci U S A 2003 Jul 9;100(15):8823-7. Epub 2003 Jul 9.

Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.

In mammals and plants, formation of heterochromatin is associated with hypermethylation of DNA at CpG sites and histone H3 methylation at lysine 9. Previous studies have revealed that maintenance of DNA methylation in Neurospora and Arabidopsis requires histone H3 methylation. A feedback loop from DNA methylation to histone methylation, however, is less understood. Its recent examination in Arabidopsis with a partial loss of function in DNA methyltransferase 1 (responsible for maintenance of CpG methylation) yielded conflicting results. Here we report that complete removal of CpG methylation in an Arabidopsis mutant null for DNA maintenance methyltransferase results in a clear loss of histone H3 methylation at lysine 9 in heterochromatin and also at heterochromatic loci that remain transcriptionally silent. Surprisingly, these dramatic alterations are not reflected in heterochromatin relaxation.
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http://dx.doi.org/10.1073/pnas.1432939100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC166397PMC
July 2003

Depletion of MOM1 in non-dividing cells of Arabidopsis plants releases transcriptional gene silencing.

EMBO Rep 2002 Oct 13;3(10):951-5. Epub 2002 Sep 13.

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Mitotic and meiotic inheritance of epigenetic information is coupled to the reproduction of chromatin conformation and DNA methylation patterns. This implies that the S phase of the cell cycle provides a window of opportunity for changes in epigenetic determination. Recent studies, however, have suggested that chromatin structure is also rather dynamic in quiescent cells of multicellular eukaryotes and that silent heterochromatic regions can become accessible to transcription. Such epigenetic flexibility in differentiated tissues could be of physiological importance. The mechanisms and molecular components involved are of great interest but as yet unknown. We examined MOM1 (Morpheus' Molecule 1), a regulator of transcriptional gene silencing (TGS) that acts independently of DNA methylation, for its role in the maintenance of TGS in non-dividing, differentiated cells. The results provide evidence that TGS maintenance mediated by MOM1 is a dynamic process that can be modified in non-dividing cells of mature plant organs by depletion of MOM1.
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http://dx.doi.org/10.1093/embo-reports/kvf195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1307620PMC
October 2002
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