RNA-directed DNA methylation: an epigenetic pathway of increasing complexity (Q38209993)

31 August 2017

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity (English)

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Erratum: RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

31 August 2017

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corrigendum / erratum

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author

Rebecca A Mosher

series ordinal

2

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31 August 2017

Marjori A Matzke

1

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31 August 2017

8 May 2014

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31 August 2017

Nature Reviews Genetics

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31 August 2017

15

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31 August 2017

6

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31 August 2017

394-408

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https://scigraph.springernature.com/pub.10.1038/nrg3683

31 August 2017

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RNA silencing genes control de novo DNA methylation

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Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing

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RNAi triggered by specialized machinery silences developmental genes and retrotransposons

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Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

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Patterns of population epigenomic diversity.

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PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis

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Role of RNA polymerase IV in plant small RNA metabolism

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Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

31 March 2020

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DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

31 March 2020

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In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing

31 March 2020

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SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.

31 March 2020

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An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis

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Regulation of small RNA stability: methylation and beyond.

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AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana

31 March 2020

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The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci

31 March 2020

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Control of female gamete formation by a small RNA pathway in Arabidopsis

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Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes

31 March 2020

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DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

31 March 2020

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Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome

31 March 2020

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RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats.

31 March 2020

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The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin

31 March 2020

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RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes

31 March 2020

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Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin

31 March 2020

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Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.

31 March 2020

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SRA-domain proteins required for DRM2-mediated de novo DNA methylation

31 March 2020

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Developmentally non-redundant SET domain proteins SUVH2 and SUVH9 are required for transcriptional gene silencing in Arabidopsis thaliana

31 March 2020

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SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

31 March 2020

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The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci

31 March 2020

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A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis

31 March 2020

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RNA polymerase V transcription guides ARGONAUTE4 to chromatin

31 March 2020

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An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation.

31 March 2020

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An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II.

31 March 2020

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RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family.

31 March 2020

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An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein.

31 March 2020

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INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

31 March 2020

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Involvement of a GHKL ATPase in RNA-directed DNA methylation in Arabidopsis thaliana

31 March 2020

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IDN2 and its paralogs form a complex required for RNA-directed DNA methylation

31 March 2020

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A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation

31 March 2020

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IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation.

31 March 2020

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A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing

31 March 2020

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Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana

31 March 2020

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Small RNAs prevent transcription-coupled loss of histone H3 lysine 9 methylation in Arabidopsis thaliana

31 March 2020

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HDA6 directly interacts with DNA methyltransferase MET1 and maintains transposable element silencing in Arabidopsis

31 March 2020

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Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1

31 March 2020

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Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation.

31 March 2020

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JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis

31 March 2020

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Interplay between active chromatin marks and RNA-directed DNA methylation in Arabidopsis thaliana

31 March 2020

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Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination

31 March 2020

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The stochastic silencing phenotype of Arabidopsis morc6 mutants reveals a role in efficient RNA-directed DNA methylation

31 March 2020

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MORC family ATPases required for heterochromatin condensation and gene silencing.

31 March 2020

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Spontaneous epigenetic variation in the Arabidopsis thaliana methylome.

31 March 2020

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Transgenerational epigenetic instability is a source of novel methylation variants

31 March 2020

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RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance

31 March 2020

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A role for RNAi in the selective correction of DNA methylation defects.

31 March 2020

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Establishing, maintaining and modifying DNA methylation patterns in plants and animals

31 March 2020

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Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis.

31 March 2020

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Active DNA demethylation in plants and animals.

31 March 2020

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Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis.

31 March 2020

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DNA methylation mediated by a microRNA pathway

31 March 2020

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Transcriptional control of gene expression by microRNAs

31 March 2020

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Roles of dicer-like and argonaute proteins in TAS-derived small interfering RNA-triggered DNA methylation

31 March 2020

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The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs.

31 March 2020

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Reconstructing de novo silencing of an active plant retrotransposon.

31 March 2020

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NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis.

31 March 2020

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Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis

31 March 2020

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Interplay among RNA polymerases II, IV and V in RNA-directed DNA methylation at a low copy transgene locus in Arabidopsis thaliana.

31 March 2020

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Invasion of the Arabidopsis genome by the tobacco retrotransposon Tnt1 is controlled by reversible transcriptional gene silencing

31 March 2020

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An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress.

31 March 2020

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Roles of plant small RNAs in biotic stress responses

31 March 2020

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Geminivirus AL2 and L2 proteins suppress transcriptional gene silencing and cause genome-wide reductions in cytosine methylation

31 March 2020

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C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with beet severe curly top virus

31 March 2020

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BSCTV C2 attenuates the degradation of SAMDC1 to suppress DNA methylation-mediated gene silencing in Arabidopsis

31 March 2020

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Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection

31 March 2020

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The RNA silencing enzyme RNA polymerase v is required for plant immunity

31 March 2020

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Widespread dynamic DNA methylation in response to biotic stress

31 March 2020

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Next-generation systemic acquired resistance.

31 March 2020

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Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

31 March 2020

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DNA methylation mediated control of gene expression is critical for development of crown gall tumors

31 March 2020

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Transgenerational inheritance of modified DNA methylation patterns and enhanced tolerance induced by heavy metal stress in rice (Oryza sativa L.).

31 March 2020

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Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development

31 March 2020

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The RdDM pathway is required for basal heat tolerance in Arabidopsis

31 March 2020

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Differential sensitivity of Arabidopsis siRNA biogenesis mutants to genotoxic stress

31 March 2020

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Stress-induced DNA methylation changes and their heritability in asexual dandelions.

31 March 2020

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An epigenetic mutation responsible for natural variation in floral symmetry

31 March 2020

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A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening.

31 March 2020

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Environmental heat and salt stress induce transgenerational phenotypic changes in Arabidopsis thaliana

31 March 2020

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The epigenetic machinery controlling transgenerational systemic acquired resistance

31 March 2020

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Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA

31 March 2020

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DNA methylation dynamics during sexual reproduction in Arabidopsis thaliana.

31 March 2020

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Production of viable gametes without meiosis in maize deficient for an ARGONAUTE protein.

31 March 2020

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Inactivation of a DNA methylation pathway in maize reproductive organs results in apomixis-like phenotypes.

31 March 2020

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Genomic imprinting in plants

31 March 2020

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Extensive demethylation of repetitive elements during seed development underlies gene imprinting

31 March 2020

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Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

31 March 2020

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Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm

31 March 2020

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Genome-wide demethylation of Arabidopsis endosperm.

31 March 2020

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Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes

31 March 2020

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siRNAs and DNA methylation: seedy epigenetics

31 March 2020

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An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs

31 March 2020

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RNA-directed DNA methylation regulates parental genomic imprinting at several loci in Arabidopsis.

31 March 2020

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Maternal control of Pol IV-dependent siRNAs in Arabidopsis endosperm

31 March 2020

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Paramutation: a process for acquiring trans-generational regulatory states

31 March 2020

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RNA-mediated trans-communication can establish paramutation at the b1 locus in maize

31 March 2020

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Epigenetic reprogramming and small RNA silencing of transposable elements in pollen

31 March 2020

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An endogenous, systemic RNAi pathway in plants

31 March 2020

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Small Silencing RNAs in Plants Are Mobile and Direct Epigenetic Modification in Recipient Cells

31 March 2020

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Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana

31 March 2020

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Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor

31 March 2020

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The inheritance pattern of 24 nt siRNA clusters in arabidopsis hybrids is influenced by proximity to transposable elements

31 March 2020

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Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids

31 March 2020

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Repeat associated small RNAs vary among parents and following hybridization in maize

31 March 2020

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Trans chromosomal methylation in Arabidopsis hybrids

31 March 2020

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Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids.

31 March 2020

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Transcriptome and methylome interactions in rice hybrids.

31 March 2020

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Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

31 March 2020

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Wheat hybridization and polyploidization results in deregulation of small RNAs

31 March 2020

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Parent-dependent loss of gene silencing during interspecies hybridization

31 March 2020

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Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat

31 March 2020

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Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs.

31 March 2020

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Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning

31 March 2020

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Are there symplastic connections between the endosperm and embryo in some angiosperms?--a lesson from the Crassulaceae family

31 March 2020

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Pol IV-Dependent siRNA Production is Reduced in Brassica rapa

31 March 2020

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Evolutionary history of plant multisubunit RNA polymerases IV and V: subunit origins via genome-wide and segmental gene duplications, retrotransposition, and lineage-specific subfunctionalization.

31 March 2020

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Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II

31 March 2020

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Functional divergence in the growing family of RNA polymerases

31 March 2020

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Altered expression of the Arabidopsis ortholog of DCL affects normal plant development

31 March 2020

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An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.

31 March 2020

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Functional consequences of subunit diversity in RNA polymerases II and V

31 March 2020

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PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit

31 March 2020

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Iwr1 directs RNA polymerase II nuclear import.

31 March 2020

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A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development

31 March 2020

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RNA-directed DNA methylation and plant development require an IWR1-type transcription factor

31 March 2020

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A multistep process gave rise to RNA polymerase IV of land plants.

31 March 2020

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Conifers have a unique small RNA silencing signature

31 March 2020

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Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

31 March 2020

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The Norway spruce genome sequence and conifer genome evolution

31 March 2020

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Dynamic expression of small RNA populations in larch (Larix leptolepis).

31 March 2020

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Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing.

31 March 2020

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miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii

31 March 2020

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Common functions for diverse small RNAs of land plants

31 March 2020

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Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development

31 March 2020

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A transcription fork model for Pol IV and Pol V-dependent RNA-directed DNA methylation.

31 March 2020

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Proposed mechanism for the initiation of transposable element silencing by the RDR6-directed DNA methylation pathway

31 March 2020

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RNA polymerase IV directs silencing of endogenous DNA.

31 March 2020

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Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.

31 March 2020

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Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.

31 March 2020

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Atypical RNA polymerase subunits required for RNA-directed DNA methylation.

31 March 2020

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NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation

31 March 2020

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A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation

31 March 2020

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Identification of genes required for de novo DNA methylation in Arabidopsis

31 March 2020

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Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation

31 March 2020

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IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana

31 March 2020

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A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation.

31 March 2020

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Genetic evidence that DNA methyltransferase DRM2 has a direct catalytic role in RNA-directed DNA methylation in Arabidopsis thaliana.

31 March 2020

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31 March 2020

Identifiers

DOI

10.1038/NRG3683

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PubMed ID

24805120

Dimensions Publication ID

31 August 2017

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PubMed ID

24805120