RNA Polymerase IV Directs Silencing of Endogenous DNA

Herr, Alan J.; Jensen, Morten Berg; Dalmay, Tamás; Baulcombe, David C.

doi:10.1126/science.1106910

Cited by 651 publications

(591 citation statements)

References 14 publications

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“…In contrast, RNA-directed DNA methylation has, thus far, only been demonstrated in plants and mammals (Kawasaki and Taira 2004;Matzke and Birchler 2005;Morris et al 2004) and the role of DNA methylation in this type of gene silencing is somewhat debatable in mammals (Ting et al 2005;Weinberg et al 2006). Further, several A. thaliana proteins needed for this process, such as the RdRP Rdr2 and subunits of RNA polymerase IV, do not have mammalian counterparts Herr et al 2005;Kanno et al 2005;Onodera et al 2005;Xie et al 2004). Thus, the ancestral RNAi machinery very likely had the capability to target histone modifications, given the widespread phyletic distribution of this function.…”

Section: Additional (Derived?) Functions Of the Rnai Machinerymentioning

confidence: 99%

On the origin and functions of RNA-mediated silencing: from protists to man

2006

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Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways. We have examined the taxonomic distribution and the phylogenetic relationship of key components of the RNA interference (RNAi) machinery in members of five eukaryotic supergroups. On the basis of the parsimony principle, our analyses suggest that a relatively complex RNAi machinery was already present in the last common ancestor of eukaryotes and consisted, at a minimum, of one Argonautelike polypeptide, one Piwi-like protein, one Dicer, and one RNAdependent RNA polymerase. As proposed before, the ancestral (but non-essential) role of these components may have been in defense responses against genomic parasites such as transposable elements and viruses. From a mechanistic perspective, the RNAi machinery in the eukaryotic ancestor may have been capable of both small-RNA-guided transcript degradation as well as transcriptional repression, most likely through histone modifications. Both roles appear to be widespread among living eukaryotes and this diversification of function could account for the evolutionary conservation of duplicated Argonaute-Piwi proteins. In contrast, additional RNAi-mediated pathways such as RNA-directed DNA methylation, programmed genome rearrangements, meiotic silencing by unpaired DNA, and miRNA-mediated gene regulation may have evolved independently in specific lineages.

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Section: Additional (Derived?) Functions Of the Rnai Machinerymentioning

confidence: 99%

On the origin and functions of RNA-mediated silencing: from protists to man

2006

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“…Alternatively, each species of siRNA and heterochromatin transcripts may be differentially mediated by RNA polymerase IV machinery. (107,108) There is no reason to exclude other post-transcriptional regulatory mechanisms such as RNA stability, (109) alternative splicing, RNA processing and editing, and RNA cache (110) that may be involved in the differential accumulation of transcript levels in the allopolyploids. For example, the stability of mRNAs varied from species to species and the half-life of mRNAs produced from progenitors may be directly correlated with differential accumulation of transcripts in the allopolyploids.…”

Section: Transcriptional Regulation In Allopolyploidsmentioning

confidence: 99%

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

2006

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SummaryPolyploidy is produced by multiplication of a single genome (autopolyploid) or combination of two or more divergent genomes (allopolyploid). The available data obtained from the study of synthetic (newly created or human-made) plant allopolyploids have documented dynamic and stochastic changes in genomic organization and gene expression, including sequence elimination, inter-chromosomal exchanges, cytosine methylation, gene repression, novel activation, genetic dominance, subfunctionalization and transposon activation. The underlying mechanisms for these alterations are poorly understood. To promote a better understanding of genomic and gene expression changes in polyploidy, we briefly review origins and forms of polyploidy and summarize what has been learned from genome-wide gene expression analyses in newly synthesized autoand allopolyploids. We show transcriptome divergence between the progenitors and in the newly formed allopolyploids. We propose models for transcriptional regulation, chromatin modification and RNA-mediated pathways in establishing locus-specific expression of orthologous and homoeologous genes during allopolyploid formation and evolution. Polyploidy and its formsPolyploidy occurs throughout the evolutionary history of all eukaryotes, (1,2) predominately in flowering plants (3,4) including many important agricultural crops. (5) Compared to plants, polyploidy occurs rarely in animals, but clearly exists in some invertebrates (e.g. insects) and vertebrates (e.g. fish, amphibians and reptiles). (4,6) The relative paucity of polyploidy in animals is attributed to the delicate schemes of sex determination and animal development, which are disrupted by polyploidization. (7,8) Therefore, polyploid animals rarely exist. (9) Moreover, aneuploid and polyploid cells in animals and human are often associated with malignant cell proliferation or carcinogenesis. (10) However, endopolyploidy (somatic polyploid cells within a diploid individual) appears to be a physiological response to developmental changes in plants and some animals, (11,12) indicating plasticity of plant and animal genomes. In the post-sequencing era, polyploidy is proving to be a fascinating and challenging field of plant biology, stimulating many research advances and insightful reviews. (2,13 -24) Here we attempt to update the views using genomic-scale results and provide new mechanistic insights.Historically, Winkler (1916) introduced the term polyploidy, (25) and Winge (1917) called attention to the general importance of polyploidy in the evolution of angiosperms. (26) At that time, research in polyploidy was somewhat limited by the plant and animal materials that were available in nature. In 1937, Blakeslee and Avery induced polyploidy in plants using colchicine, a chemical inhibitor of mitotic cell divisions. (27) The technique has been successfully used to induce chromosome doubling in meristemic cells of diploids and interspecific hybrids. Doubling a single 'diploid' genome results in an autotetraploid, while doubling c...

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“…Their biogenesis and function is controlled by a specialized set of RNAi proteins, which are DICER-LIKE 3 (DCL3), the RNA-dependent RNA polymerase RDR2 and the Argonaute protein AGO4 Xie et al, 2004). In addition, siRNA generation and function is dependent on RNA polymerase IV, which is unique to plants (Herr et al, 2005;Kanno et al, 2005;Onodera et al, 2005;Pontier et al, 2005) and a plant-specific SNF2-like protein, DRD1 (Kanno et al, 2004). Pol IV exists as two distinct complexes in Arabidopsis, which are functionally diverse and specified by their unique largest subunits, respectively.…”

Section: Athda6: An Intimate Relationship With Transcriptional Rna Simentioning

confidence: 99%

Arabidopsis histone deacetylase 6: a green link to RNA silencing

et al. 2007

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Epigenetic reprogramming is at the base of cancer initiation and progression. Generally, genome-wide reduction in cytosine methylation contrasts with the hypermethylation of control regions of functionally wellestablished tumor suppressor genes and many other genes whose role in cancer biology is not yet clear. While insight into mechanisms that induce aberrant cytosine methylation in cancer cells is just beginning to emerge, the initiating signals for analogous promoter methylation in plants are well documented. In Arabidopsis, the silencing of promoters requires components of the RNA interference machinery and promoter double-stranded RNA (dsRNA) to induce a repressive chromatin state that is characterized by cytosine methylation and histone deacetylation catalysed by the RPD3-type histone deacetylase AtHDA6. Similar mechanisms have been shown to occur in fission yeast and mammals. This review focuses on the connections between cytosine methylation, dsRNA and AtHDA6-controlled histone deacetylation during promoter silencing in Arabidopsis and discusses potential mechanistic similarities of these silencing events in cancer and plant cells.

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RNA Polymerase IV Directs Silencing of Endogenous DNA

Cited by 651 publications

References 14 publications

On the origin and functions of RNA-mediated silencing: from protists to man

On the origin and functions of RNA-mediated silencing: from protists to man

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

Arabidopsis histone deacetylase 6: a green link to RNA silencing

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