RNA-directed de novo methylation of genomic sequences in plants

Wassenegger, Michael; Heimes, Sabine; Riedel, Leonhard; Sänger, Heinz L.

doi:10.1016/0092-8674(94)90119-8

Cited by 838 publications

(540 citation statements)

References 33 publications

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“…The initial observation of dsRNA-induced chromatin change was methylation of endogenous sequences that shared homology with viroids in infected plants [43]. This observation was later followed by the finding that dsRNA sharing sequence homology with promoter regions was able to induce gene silencing.…”

Section: Dsrna and Heterochromatinmentioning

confidence: 98%

RNAi: an ever-growing puzzle

Denli

Hannon

2003

Trends in Biochemical Sciences

270

167

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Section: Dsrna and Heterochromatinmentioning

confidence: 98%

RNAi: an ever-growing puzzle

Denli

Hannon

2003

Trends in Biochemical Sciences

270

167

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“…During viroid infection of tobacco, viroid cDNA copies integrated into nuclear DNA became methylated, implicating replicating viroid RNA in DNA modification [23]. RdDM provides an alternate means to induce the sequence-specific methylation observed in both PTGS and TGS.…”

Section: Methylation and Posttranscriptional Gene Silencingmentioning

confidence: 99%

Gene silencing: Double-stranded RNA mediated mRNA degradation and gene inactivation

2001

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The recent development of gene transfer approaches in plants and animals has revealed that transgene can undergo silencing after integration in the genome. Host genes can also be silenced as a consequence of the presence of a homologous transgene. More and more investigations have demonstrated that doublestranded RNA can silence genes by triggering degradation of homologous RNA in the cytoplasm and by directing methylation of homologous nuclear DNA sequences. Analyses of Arabidopsis mutants and plant viral suppressors of silencing are unraveling RNA-silencing mechanisms and are assessing the role of methylation in transcriptional and posttranscriptional gene silencing. This review will focus on double-stranded RNA mediated mRNA degradation and gene inactivation in plants.

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Section: Introductionmentioning

confidence: 99%

“…DCL1 is responsible for producing various sizes of microRNAs (small RNAs encoded in the genome), whereas DCL2, DCL3, and DCL4 produce 22, 24, and 21 nucleotide (nt) siRNAs, respectively (Bartel, 2004;Dunoyer et al, 2005;Xie et al, 2004). The 24 nt siRNAs are reported to guide RNAdirected DNA methylation (RdDM) in plants (Wassenegger et al, 1994), whereas the 21 and 22 nt siRNAs are known to trigger cognate mRNA degradation and secondary siRNA biogenesis, respectively (Chen et al, 2010;Hamilton et al, 2002).The guide strand of siRNA (usually the antisense strand) associates with AGO proteins to form the core of the RNA silencing effector complexes, which provide RNA-induced silencing complexes (RISCs) with substrate specificity for RNA cleavage (Brodersen and Voinnet, 2006). AGO proteins are characterized by PAZ, middle (Mid) and PIWI domains.…”

mentioning

confidence: 99%

RNA-Dependent RNA Polymerase 6 Is Required for Efficient hpRNA-Induced Gene Silencing in Plants

Harmoko

Fanata

Yoo

et al. 2013

Molecules and Cells

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In plants, transgenes with inverted repeats are used to induce efficient RNA silencing, which is also frequently induced by highly transcribed sense transgenes. RNA silencing induced by sense transgenes is dependent on RNA-dependent RNA polymerase 6 (RDR6), which converts single-stranded (ss) RNA into double-stranded (ds) RNA. By contrast, it has been proposed that RNA silencing induced by self-complementary hairpin RNA (hpRNA) does not require RDR6, because the hpRNA can directly fold back on itself to form dsRNA. However, it is unclear whether RDR6 plays a role in hpRNA-induced RNA silencing by amplifying dsRNA to spread RNA silencing within the plant. To address the efficiency of hpRNA-induced RNA silencing in the presence or absence of RDR6, Wild type (WT, Col-0) and rdr6-11 Arabidopsis thaliana lines expressing green fluorescent protein (GFP) were generated and transformed with a GFP-RNA interference (RNAi) construct. Whereas most GFP-RNAi-transformed WT lines exhibited almost complete silencing of GFP expression in the T1 generation, various levels of GFP expression remained among the GFP-RNAi-transformed rdr6-11 lines. Homozygous expression of GFP-RNAi in the T3 generation was not sufficient to induce complete GFP silencing in several rdr6-11 lines. Our results indicate that RDR6 is required for efficient hpRNA-induced RNA silencing in plants. INTRODUCTIONGene silencing is a mechanism that employs small RNAs and protein effectors to interfere with the expression of homologous genes at the transcriptional and post-transcriptional levels (Voinnet, 2008). Transcriptional gene silencing (TGS), which takes place through repression of transcription, is often associated with methylation of the corresponding homologous promoter (Neuhuber et al., 1994;Park et al., 1996). Post-transcriptional gene silencing (PTGS), occurring through sequencespecific degradation of target mRNAs, is characterized by accumulation of small interfering RNA (siRNA) and methylation of target gene sequences (Depicker and Montagu, 1997;Vaucheret et al., 2001). Gene silencing was first discovered in plants and is highly conserved among multicellular eukaryotes. It initiates with the formation of dsRNA, which is subsequently processed into siRNA. siRNAs are produced from dsRNAs by an RNase III-like enzyme called DICER, which has dsRNA-binding, RNA helicase and P-element-induced wimpy testes (PIWI)-Argonaute (AGO)-Zwille (PAZ) domains (Bernstein et al., 2001). Plants possess four DICER homologs: DCL1, DCL2, DCL3, and DCL4. DCL1 is responsible for producing various sizes of microRNAs (small RNAs encoded in the genome), whereas DCL2, DCL3, and DCL4 produce 22, 24, and 21 nucleotide (nt) siRNAs, respectively (Bartel, 2004;Dunoyer et al., 2005;Xie et al., 2004). The 24 nt siRNAs are reported to guide RNAdirected DNA methylation (RdDM) in plants (Wassenegger et al., 1994), whereas the 21 and 22 nt siRNAs are known to trigger cognate mRNA degradation and secondary siRNA biogenesis, respectively (Chen et al., 2010;Hamilton et al., 2002).The guide str...

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RNA-directed de novo methylation of genomic sequences in plants

Cited by 838 publications

References 33 publications

RNAi: an ever-growing puzzle

RNAi: an ever-growing puzzle

Gene silencing: Double-stranded RNA mediated mRNA degradation and gene inactivation

RNA-Dependent RNA Polymerase 6 Is Required for Efficient hpRNA-Induced Gene Silencing in Plants

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