RNA-directed DNA methylation inArabidopsis

Abstract

In plants, double-stranded RNA that is processed to short RNAs Ϸ21-24 nt in length can trigger two types of epigenetic gene silencing. Posttranscriptional gene silencing, which is related to RNA interference in animals and quelling in fungi, involves targeted elimination of homologous mRNA in the cytoplasm. RNAdirected DNA methylation involves de novo methylation of almost all cytosine residues within a region of RNA-DNA sequence identity. RNA-directed DNA methylation is presumed to be responsible for the methylation observed in protein coding regions of posttranscriptionally silenced genes. Moreover, a type of transcriptional gene silencing and de novo methylation of homologous promoters in trans can occur if a double-stranded RNA contains promoter sequences. Although RNA-directed DNA methylation has been described so far only in plants, there is increasing evidence that RNA can also target genome modifications in other organisms. To understand how RNA directs methylation to identical DNA sequences and how changes in chromatin configuration contribute to initiating or maintaining DNA methylation induced by RNA, a promoter double-stranded RNA-mediated transcriptional gene silencing system has been established in Arabidopsis. A genetic analysis of this system is helping to unravel the relationships among RNA signals, DNA methylation, and chromatin structure.T he term ''RNA silencing'' refers to epigenetic gene silencing effects that are initiated by double-stranded RNA (dsRNA) (1). Discovered independently in plants, fungi, and animals, RNA silencing phenomena are revealing new ways to repress gene expression and to subdue transposable elements and viruses that produce dsRNA during their replication cycle (2-8). A fundamental step in RNA silencing pathways is cleavage of dsRNA into short RNAs (9), which are believed to act as guides for enzyme complexes that either degrade or modify homologous nucleic acids.The most familiar type of RNA silencing occurs primarily in the cytoplasm and is termed posttranscriptional gene silencing (PTGS) in plants, quelling in Neurospora, and RNA interference (RNAi) in animals. PTGS͞RNAi involves a dsRNA that is processed by an RNase III-like enzyme called Dicer into short interfering (si) RNAs 21-22 nt in length. The antisense siRNAs associate with a ribonuclease complex and guide sequencespecific degradation of complementary mRNAs (5-8).A second form of RNA silencing involves sequence-specific changes at the genome level. RNA-directed DNA methylation (RdDM) (10), which has been described so far only in plants, leads to de novo methylation of almost all cytosine residues within the region of sequence identity between the triggering RNA and the target DNA. Similarly to PTGS͞RNAi, RdDM requires a dsRNA that is cleaved to short RNAs Ϸ21-24 nt in length (11). It is not yet certain whether the short RNAs or dsRNA guide methylation of homologous DNA sequences, although the length of short RNAs is consistent with the minimum DNA target size of RdDM (Ϸ30 bp) (12).RdDM is assumed to be the ...

Arabidopsis histone deacetylase 6: a green link to RNA silencing

“…Importantly, heterochromatin can spread from nucleation sites initially targeted by the RNAi machinery. Small RNAs can also induce de novo cytosine methylation at sequence-homologous DNA in a process called RdDM (Wassenegger, 2000;Aufsatz et al, 2002a;Chan et al, 2004;Mathieu and Bender, 2004). Cytosines in all sequence contexts are modified by RdDM, and methylation is restricted to the site of RNA/DNA identity, suggesting the formation of an RNA/DNA hybrid structure that is in turn recognized by the DNA methylation machinery.…”

“…Cytosines in all sequence contexts are modified by RdDM, and methylation is restricted to the site of RNA/DNA identity, suggesting the formation of an RNA/DNA hybrid structure that is in turn recognized by the DNA methylation machinery. RdDM results in transcriptional repression when promoters are targeted (Aufsatz et al, 2002a). Some of the proteins involved in RdDM seem to be plant-specific (see below).…”

“…A look across kingdom borders might help to develop concepts addressing this important aspect. Plant promoters can also be targeted for de novo methylation, which results in their inactivation (Wassenegger, 2000;Aufsatz et al, 2002a;Melquist and Bender, 2003;Mathieu and Bender, 2004;Cigan et al, 2005). In contrast to the promoters of cancer genes, however, the repressive signal for this silencing of plant promoters is well established.…”

Dynamic and reversibility of heterochromatic gene silencing in human disease

“…In viroid infected plants the cDNA copies integrated into genome undergo DNA methylation directed by RNA. Subsequenly, it was shown that this de novo methylation activity required formation of dsRNA and of processed siRNA [76]. siRNAs direct DNA methyltransferases (MET1, CMT3), histone methyltransferases (DDM1, Kryptonite) and histone deacetylases onto targets promoter regions and induce transcriptional gene silencing in plants [77,78].…”

Des microARN comme s’il en pleuvait…

“…Appréhender cette combinatoire d'interactions ARN:ARN et les réseaux de régulation sous-jacents ajoute un autre niveau de complexité qu'il faudra décrypter pour apprécier pleinement la fonction biologique de cette nouvelle famille d'ARN non codants. Des phénomènes épigéné-tiques de « mise en veille » de gènes faisant intervenir des mécanismes apparentés à l'ARNi ont été récemment décrits, notamment chez les plantes et S. pombe [20,21] …”