HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA.

PubWeight™: 2.64‹?› | Rank: Top 1%

🔗 View Article (PMC 139084)

Published in EMBO J on December 16, 2002

Authors

Werner Aufsatz1, M Florian Mette, Johannes van der Winden, Marjori Matzke, Antonius J M Matzke

Author Affiliations

1: Institute of Molecular Biology, Austrian Academy of Sciences, Billrothstrasse 11, A-5020 Salzburg, Austria.

Articles citing this

Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell (2004) 9.18

Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol (2003) 3.71

Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet (2005) 3.66

Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol (2009) 3.46

Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol (2003) 3.16

Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell (2013) 3.02

Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol (2008) 2.67

The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol (2008) 2.43

Regulation and function of DNA methylation in plants and animals. Cell Res (2011) 2.41

Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell (2009) 2.39

Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res (2004) 2.28

HISTONE DEACETYLASE19 is involved in jasmonic acid and ethylene signaling of pathogen response in Arabidopsis. Plant Cell (2005) 2.06

Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J (2007) 2.05

Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell (2004) 2.03

Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell (2008) 1.94

Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev (2006) 1.92

High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell (2008) 1.85

Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet (2005) 1.83

Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell (2007) 1.64

Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent and locus-specific changes in gene expression during plant development. Genetics (2004) 1.59

Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim Biophys Acta (2007) 1.58

Effects of length and location on the cellular response to double-stranded RNA. Microbiol Mol Biol Rev (2004) 1.57

Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics (2003) 1.52

Stress-induced activation of heterochromatic transcription. PLoS Genet (2010) 1.51

Transgenerational inheritance and resetting of stress-induced loss of epigenetic gene silencing in Arabidopsis. Mol Plant (2010) 1.50

A SNF2-like protein facilitates dynamic control of DNA methylation. EMBO Rep (2005) 1.46

HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates flowering in Arabidopsis. Plant Physiol (2011) 1.30

Adaptive transgenerational plasticity in plants: case studies, mechanisms, and implications for natural populations. Front Plant Sci (2011) 1.30

DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol (2015) 1.29

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci U S A (2013) 1.27

Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1. PLoS Genet (2011) 1.27

HDA6 directly interacts with DNA methyltransferase MET1 and maintains transposable element silencing in Arabidopsis. Plant Physiol (2011) 1.24

Hypermethylation of the human proton-coupled folate transporter (SLC46A1) minimal transcriptional regulatory region in an antifolate-resistant HeLa cell line. Mol Cancer Ther (2009) 1.24

The Arabidopsis HOMOLOGY-DEPENDENT GENE SILENCING1 gene codes for an S-adenosyl-L-homocysteine hydrolase required for DNA methylation-dependent gene silencing. Plant Cell (2005) 1.18

Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics (2011) 1.18

Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet (2009) 1.17

Composition and formation of heterochromatin in Arabidopsis thaliana. Chromosome Res (2006) 1.16

RNA-directed DNA methylation and demethylation in plants. Sci China C Life Sci (2009) 1.14

Chromatin: linking structure and function in the nucleolus. Chromosoma (2008) 1.14

A two-edged role for the transposable element Kiddo in the rice ubiquitin2 promoter. Plant Cell (2005) 1.09

ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. Plant Cell (2005) 1.09

Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis. Proc Natl Acad Sci U S A (2012) 1.07

RNAi-mediated gene silencing reveals involvement of Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation. Proc Natl Acad Sci U S A (2007) 1.06

Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors. Plant Cell (2015) 1.06

Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants. BMC Plant Biol (2009) 1.05

Expression profile and cellular localization of maize Rpd3-type histone deacetylases during plant development. Plant Physiol (2003) 1.05

Arabidopsis homologs of retinoblastoma-associated protein 46/48 associate with a histone deacetylase to act redundantly in chromatin silencing. PLoS Genet (2011) 1.04

Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2. Genetics (2007) 1.00

Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes Dev (2012) 0.99

A two-step process for epigenetic inheritance in Arabidopsis. Mol Cell (2014) 0.98

Maize histone deacetylase hda101 is involved in plant development, gene transcription, and sequence-specific modulation of histone modification of genes and repeats. Plant Cell (2007) 0.97

Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Rep (2014) 0.97

Arabidopsis thaliana histone deacetylase 1 (AtHD1) is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro. Cell Res (2006) 0.95

Histone deacetylase HDA6 is functionally associated with AS1 in repression of KNOX genes in arabidopsis. PLoS Genet (2012) 0.94

The RdDM pathway is required for basal heat tolerance in Arabidopsis. Mol Plant (2013) 0.94

H2B- and H3-specific histone deacetylases are required for DNA methylation in Neurospora crassa. Genetics (2010) 0.93

Effect of 27nt small RNA on endothelial nitric-oxide synthase expression. Mol Biol Cell (2008) 0.93

A Pol V-mediated silencing, independent of RNA-directed DNA methylation, applies to 5S rDNA. PLoS Genet (2009) 0.92

HISTONE DEACETYLASE6-Defective Mutants Show Increased Expression and Acetylation of ENHANCER OF TRIPTYCHON AND CAPRICE1 and GLABRA2 with Small But Significant Effects on Root Epidermis Cellular Pattern. Plant Physiol (2015) 0.91

RNA-directed DNA methylation: mechanisms and functions. Plant Signal Behav (2010) 0.89

High frequency, cell type-specific visualization of fluorescent-tagged genomic sites in interphase and mitotic cells of living Arabidopsis plants. Plant Methods (2010) 0.88

Transgenerational maintenance of transgene body CG but not CHG and CHH methylation. Epigenetics (2012) 0.87

Histone deacetylase AtHDA7 is required for female gametophyte and embryo development in Arabidopsis. Plant Physiol (2013) 0.86

The RNAs of RNA-directed DNA methylation. Biochim Biophys Acta (2016) 0.84

Chromatin dynamics and Arabidopsis development. Chromosome Res (2003) 0.82

HISTONE DEACETYLASE6 Controls Gene Expression Patterning and DNA Methylation-Independent Euchromatic Silencing. Plant Physiol (2015) 0.81

Quantification and Gene Expression Analysis of Histone Deacetylases in Common Bean during Rust Fungal Inoculation. Int J Genomics (2015) 0.81

Inhibition of histone deacetylation alters Arabidopsis root growth in response to auxin via PIN1 degradation. Plant Cell Rep (2013) 0.81

RNA-directed DNA methylation in plants. Plant Cell Rep (2015) 0.80

Extra views on RNA-dependent DNA methylation and MBD6-dependent heterochromatin formation in nucleolar dominance. Nucleus (2010) 0.79

Heat-induced release of epigenetic silencing reveals the concealed role of an imprinted plant gene. PLoS Genet (2014) 0.79

Hybrid incompatibility caused by an epiallele. Proc Natl Acad Sci U S A (2017) 0.79

Identification and characterization of histone deacetylases in tomato (Solanum lycopersicum). Front Plant Sci (2015) 0.79

Non-coding RNAs in the plant response to abiotic stress. Planta (2012) 0.79

Epigenetic memory of DNAi associated with cytosine methylation and histone modification in fern. Plant Signal Behav (2012) 0.78

Epiallelic variation in Arabidopsis thaliana. Cold Spring Harb Symp Quant Biol (2012) 0.77

DEAD-box RNA helicases and epigenetic control of abiotic stress-responsive gene expression. Plant Signal Behav (2014) 0.77

Epigenetic interplay of histone modifications and DNA methylation mediated by HDA6. Plant Signal Behav (2012) 0.77

POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. Elife (2016) 0.77

H3K36ac Is an Evolutionary Conserved Plant Histone Modification That Marks Active Genes. Plant Physiol (2016) 0.77

The ben1-1 brassinosteroid-catabolism mutation is unstable due to epigenetic modifications of the intronic T-DNA insertion. G3 (Bethesda) (2013) 0.77

Transformation of rice with large maize genomic DNA fragments containing high content repetitive sequences. Plant Cell Rep (2015) 0.76

Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants. J Exp Bot (2016) 0.75

The Second Subunit of DNA Polymerase Delta Is Required for Genomic Stability and Epigenetic Regulation. Plant Physiol (2016) 0.75

Accurate Chromosome Segregation at First Meiotic Division Requires AGO4, a Protein Involved in RNA-Dependent DNA Methylation in Arabidopsis thaliana. Genetics (2016) 0.75

Two domain-disrupted hda6 alleles have opposite epigenetic effects on transgenes and some endogenous targets. Sci Rep (2015) 0.75

POWERDRESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis. Proc Natl Acad Sci U S A (2016) 0.75

Telomere-binding protein regulates the chromosome ends through the interaction with histone deacetylases in Arabidopsis thaliana. Nucleic Acids Res (2016) 0.75

Articles cited by this

Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J (1998) 97.93

RNA interference. Nature (2002) 22.28

MicroRNAs in plants. Genes Dev (2002) 20.12

A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J (1993) 19.68

Prediction of plant microRNA targets. Cell (2002) 19.20

Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science (2002) 18.37

Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science (2002) 17.04

CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol (2002) 15.13

Endogenous and silencing-associated small RNAs in plants. Plant Cell (2002) 10.07

Establishment and maintenance of a heterochromatin domain. Science (2002) 9.34

Two classes of short interfering RNA in RNA silencing. EMBO J (2002) 8.54

Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci U S A (2000) 8.12

Gene silencing in mammals by small interfering RNAs. Nat Rev Genet (2002) 7.80

Activation tagging in Arabidopsis. Plant Physiol (2000) 7.09

Arabidopsis thaliana DNA methylation mutants. Science (1993) 6.63

An expanding universe of noncoding RNAs. Science (2002) 5.96

Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science (2001) 5.50

Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol (2002) 5.47

Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J (2000) 5.41

RNA-directed de novo methylation of genomic sequences in plants. Cell (1994) 5.26

RNA silencing in plants--defense and counterdefense. Science (2001) 5.01

Ancient pathways programmed by small RNAs. Science (2002) 4.94

RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol Cell (2002) 4.90

RNA silencing as a plant immune system against viruses. Trends Genet (2001) 4.49

Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell (2002) 4.38

Computational genomics of noncoding RNA genes. Cell (2002) 3.90

A role for histone deacetylase activity in HDAC1-mediated transcriptional repression. Proc Natl Acad Sci U S A (1998) 3.85

RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing. Plant Cell (1999) 3.70

Reversible methylation and inactivation of marker genes in sequentially transformed tobacco plants. EMBO J (1989) 3.61

Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev (1997) 3.56

Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiol (2002) 3.27

Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev (2001) 3.27

Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature (2000) 3.23

Functional analysis of regulatory elements in a plant embryo-specific gene. Proc Natl Acad Sci U S A (1986) 3.14

RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr Biol (2001) 3.03

Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo. Genes Dev (1998) 2.71

RNA: guiding gene silencing. Science (2001) 2.50

RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci U S A (2002) 2.46

Transcriptional and posttranscriptional gene silencing are mechanistically related. Curr Biol (2001) 2.39

RNA-directed DNA methylation. Plant Mol Biol (2000) 2.38

Plant DNA methyltransferases. Plant Mol Biol (2000) 2.31

Major chromosomal rearrangements induced by T-DNA transformation in Arabidopsis. Genetics (1998) 2.10

Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci U S A (2001) 2.05

Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell (2001) 1.87

Distinct in vivo requirements for establishment versus maintenance of transcriptional repression. Nat Genet (2002) 1.83

T-DNA-associated duplication/translocations in Arabidopsis. Implications for mutant analysis and functional genomics. Plant Physiol (2001) 1.76

Size constraints for targeting post-transcriptional gene silencing and for RNA-directed methylation in Nicotiana benthamiana using a potato virus X vector. Plant J (2001) 1.75

Sequences for two cDNAs encoding Arabidopsis thaliana eukaryotic protein synthesis initiation factor 4A. Gene (1992) 1.67

Using RNA interference to identify genes required for RNA interference. Proc Natl Acad Sci U S A (2002) 1.63

Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-directed DNA methylation. Nucleic Acids Res (1999) 1.62

Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell (2001) 1.52

Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus. Plant Mol Biol (2001) 1.44

Histone modification and replacement in chromatin activation. Genes Dev (2002) 1.38

DNA methyltransferases get connected to chromatin. Trends Genet (2002) 1.38

Homology-dependent gene silencing mechanisms in fungi. Annu Rev Microbiol (2001) 1.32

A DNA target of 30 bp is sufficient for RNA-directed DNA methylation. RNA (2000) 1.27

Endogenous viral sequences and their potential contribution to heritable virus resistance in plants. EMBO J (2002) 1.19

Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants. Proc Natl Acad Sci U S A (1999) 1.15

Plant chromatin: development and gene control. Bioessays (2002) 1.00

Application of gene silencing in plants. Curr Opin Plant Biol (2002) 0.97

Articles by these authors

A uniform system for microRNA annotation. RNA (2003) 20.28

Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet (2005) 5.48

Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol (2003) 4.27

RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol (2009) 4.11

Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiol (2002) 3.27

Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J (2006) 3.19

Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol (2003) 3.16

Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol (2004) 2.88

Targets of RNA-directed DNA methylation. Curr Opin Plant Biol (2007) 2.81

A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet (2008) 2.74

RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci U S A (2002) 2.46

The role of MET1 in RNA-directed de novo and maintenance methylation of CG dinucleotides. Plant Mol Biol (2004) 2.11

RNA silencing and the mobile silencing signal. Plant Cell (2002) 2.03

A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J (2008) 1.93

Involvement of a GHKL ATPase in RNA-directed DNA methylation in Arabidopsis thaliana. Curr Biol (2012) 1.92

Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta (2004) 1.91

An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature (2010) 1.82

RNA-directed DNA methylation mediated by DRD1 and Pol IVb: a versatile pathway for transcriptional gene silencing in plants. Biochim Biophys Acta (2007) 1.53

Unexpected silencing effects from T-DNA tags in Arabidopsis. Trends Plant Sci (2008) 1.48

A SNF2-like protein facilitates dynamic control of DNA methylation. EMBO Rep (2005) 1.46

Does the intrinsic instability of aneuploid genomes have a causal role in cancer? Trends Genet (2003) 1.35

RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep (2009) 1.32

Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana. PLoS Genet (2008) 1.19

Homology-dependent gene silencing and host defense in plants. Adv Genet (2002) 1.18

Methylation and demethylation of the Arabidopsis genome. Curr Opin Plant Biol (2010) 1.17

RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants. Annu Rev Plant Biol (2014) 1.16

AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana. PLoS One (2011) 1.09

Planting the seeds of a new paradigm. PLoS Biol (2004) 1.07

Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). PLoS One (2013) 1.01

Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species. BMC Plant Biol (2007) 0.96

A distinct endogenous pararetrovirus family in Nicotiana tomentosiformis, a diploid progenitor of polyploid tobacco. Plant Physiol (2004) 0.92

Ion channels at the nucleus: electrophysiology meets the genome. Mol Plant (2010) 0.91

Interplay among RNA polymerases II, IV and V in RNA-directed DNA methylation at a low copy transgene locus in Arabidopsis thaliana. Plant Mol Biol (2013) 0.91

Use of two-color fluorescence-tagged transgenes to study interphase chromosomes in living plants. Plant Physiol (2005) 0.90

Genetic evidence that DNA methyltransferase DRM2 has a direct catalytic role in RNA-directed DNA methylation in Arabidopsis thaliana. Genetics (2011) 0.90

Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing. Methods Mol Biol (2005) 0.88

High frequency, cell type-specific visualization of fluorescent-tagged genomic sites in interphase and mitotic cells of living Arabidopsis plants. Plant Methods (2010) 0.88

RNAi extends its reach. Science (2003) 0.86

Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biol (2012) 0.86

Pol V transcribes to silence. Cell (2008) 0.82

Studies on the effects of a flanking repetitive sequence on the expression of single-copy transgenes in Nicotiana sylvestris and in N. sylvestris-N. tomentosiformis hybrids. Plant Mol Biol (2003) 0.81

Unusual case of apparent hypermutation in Arabidopsis thaliana. Genetics (2012) 0.81

Fluorescent transgenes to study interphase chromosomes in living plants. Methods Mol Biol (2008) 0.81

Membrane "potential-omics": toward voltage imaging at the cell population level in roots of living plants. Front Plant Sci (2013) 0.81

Distinct and concurrent pathways of Pol II- and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana. Plant J (2014) 0.80

Nuclear membrane ion channels mediate root nodule development. Trends Plant Sci (2009) 0.79

The genome in context: biologists and philosophers on epigenetics. Bioessays (2002) 0.78

A novel strategy for obtaining kanamycin resistance in Arabidopsis thaliana by silencing an endogenous gene encoding a putative chloroplast transporter. Biotechnol J (2009) 0.78

The RNA world is alive and well. Trends Plant Sci (2008) 0.78

Plants, RNAi, and the Nobel Prize. Science (2006) 0.75