Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Kasschau, Kristin D.; Fahlgren, Noah; Chapman, Elisabeth J.; Sullivan, Christopher; Cumbie, Jason S.; Givan, Scott A.; Carrington, James C.

doi:10.1371/journal.pbio.0050057

Cited by 490 publications

(530 citation statements)

References 81 publications

(133 reference statements)

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“…DCL1 mainly processes miRNAs, whereas DCL2 and DCL4 are responsible for producing 22-nt virus-related siRNAs and 21-nt trans-acting siRNAs (ta-siRNAs), respectively. Functional redundancies among the different DCL proteins have been reported or suggested in many studies [27][28][29][30]. Despite the role of DCL3 in generating 24-nt siRNAs, the dcl3 mutant does not exhibit a severe decrease in DNA methylation levels at RdDM loci [31].…”

Section: Introductionmentioning

confidence: 97%

Dicer-independent RNA-directed DNA methylation in Arabidopsis

et al. 2015

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RNA-directed DNA methylation (RdDM) is an important de novo DNA methylation pathway in plants. Small interfering RNAs (siRNAs) generated by Dicers from RNA polymerase IV (Pol IV) transcripts are thought to guide sequence-specific DNA methylation. To gain insight into the mechanism of RdDM, we performed whole-genome bisulfite sequencing of a collection of Arabidopsis mutants, including plants deficient in Pol IV (nrpd1) or Dicer (dcl1/2/3/4) activity. Unexpectedly, of the RdDM target loci that required Pol IV and/or Pol V, only 16% were fully dependent on Dicer activity. DNA methylation was partly or completely independent of Dicer activity at the remaining Pol IV-and/ or Pol V-dependent loci, despite the loss of 24-nt siRNAs. Instead, DNA methylation levels correlated with the accumulation of Pol IV-dependent 25-50 nt RNAs at most loci in Dicer mutant plants. Our results suggest that RdDM in plants is largely guided by a previously unappreciated class of Dicer-independent non-coding RNAs, and that siRNAs are required to maintain DNA methylation at only a subset of loci.

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Section: Introductionmentioning

confidence: 97%

Dicer-independent RNA-directed DNA methylation in Arabidopsis

et al. 2015

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“…It is well established that the relative abundance of the 24-nt and the 21-nt length classes may vary depending on the species and the tissue type, among other factors. In fact, previous reports refer that the 24-nt sRNAs is the predominant size class, for instance in Arabidopsis thaliana, Nicothiana benthamiana, Solano lycopersicum, Oriza sativa and Olea europea (Morin et al 2008;Pantaleo et al 2010;Donaire et al 2011;Kasschau et al 2007), while the 21-nt class is more abundant in species such as Eschscholzia californica, Hordeum vulgare, Vitis vinifera, Pinus contorta and Panax gynseng (Pantaleo et al 2010;Morin et al 2008;Schreiber et al 2011;Barakat et al 2007). The tissue-dependent variation in the pools of 24 and 21-nt classes has also been observed in other plant species (Pantaleo et al 2010) and, in a few cases, striking variation has been detected (Slotkin et al 2009) reflecting the sRNA biogenesis pathways operating in such tissues.…”

Section: Discussionmentioning

confidence: 98%

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

Chaves

Lin

Pinto-Ricardo

et al. 2014

Tree Genetics & Genomes

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The differentiation of cork (phellem) cells from the phellogen (cork cambium) is a secondary growth process observed in the cork oak tree conferring a unique ability to produce a thick layer of cork. At present, the molecular regulators of phellem differentiation are unknown. The previously documented involvement of microRNAs in the regulation of developmental processes, including secondary growth, motivated the search for these regulators in cork oak tissues.We performed deep-sequencing of the small-RNA fraction obtained from cork oak leaves and differentiating phellem. RNA sequences with lengths of 19-25 nt derived from the two libraries were analysed, leading to the identification of 41 families of conserved miRNAs, of which the most abundant were miR167, miR165/166, miR396 and miR159. Thirty novel miRNA candidates were also unveiled, 11 of which were unique to leaves and 13 to phellem. Northern blot detection of a set of conserved and novel-miRNAs confirmed their differential expression profile. Prediction and analysis of putative miRNA target genes provided clues regarding processes taking place in leaf and phellem tissues but further experimental work will be needed for functional characterization. In conclusion, we here provide a first characterization of the miRNA population in a Fagacea species and the comparative analysis of miRNA expression in leaf and phellem libraries represents an important step to uncovering specific regulatory networks controlling phellem differentiation.

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“…Furthermore, as shown for AGO4, AGO6 and AGO9, members of a given protein family may participate to different degrees in RdDM as a result of functional diversification (Zheng et al, 2007;Havecker et al, 2010). Moreover, the observation that Pol IV and Pol V are not involved in the production of strand-specific clusters of 24-nt siRNAs that match long inverted duplications (Kasschau et al, 2007;Zhang et al, 2007) implies that at least in this case, siRNAs must derive from transcripts produced by one of the three canonical RNA polymerases, presumably Pol II. In fact, transcripts produced by Pol II are likely to be the initial trigger for RdDM in other situations as well, notably immediately after TE insertion, with the Pol IV/Pol V loop serving only in a second step, after Pol II activity has ceased or has been altered by the process of heterochromatin formation.…”

Section: Fk Teixeira and V Colot 15mentioning

confidence: 98%

Repeat elements and the Arabidopsis DNA methylation landscape

Teixeira

Colot

2010

Heredity

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DNA methylation is an epigenetic mark that has key roles in the control of genome activity in plants and mammals. It is critical for the stable silencing of repeat elements and is also involved in the epigenetic regulation of some genes. Despite similarities in the controlling functions of DNA methylation, its dynamics and deposition patterns differ in several respects between plants and mammals. One of the most striking differences is that plants tend to propagate pre-existing DNA methylation states across generations, whereas mammals re-establish them genome wide at every generation. Here, we review our current understanding of DNA methylation in the flowering plant Arabidopsis. We discuss in particular the role of RNAi in the incremental methylation and silencing of repeat elements over successive generations. We argue that paramutation, an epigenetic phenomenon first described in maize, is an extreme manifestation of this RNAi-dependent pathway. Heredity (2010) 105, 14-23; doi:10.1038/hdy.2010.52; published online 12 May 2010Keywords: DNA methylation; repeat elements; Arabidopsis; RNAi; paramutation Introduction DNA methylation refers to the enzymatic transfer of a methyl group to specific nucleotides within the DNA sequence. In eukaryotes, this modification almost exclusively affects cytosines. Although clearly ancestral, cytosine methylation is not universally present in the eukaryotic tree of life. Thus, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, as well as the nematode Caenorhabditis elegans have no DNA methyltransferases (DNA MTases;Goll and Bestor, 2005). Furthermore, Drosophila contains a single, enigmatic DNA MTase-like protein (Goll and Bestor, 2005) and it is unclear if this species actually methylates DNA. By contrast, DNA methylation is readily detected in plants and mammals, where it is critical for normal development and genome stability. Although numerous hypotheses have been proposed (Bird, 1995;Yoder et al., 1997;Martienssen, 1998;Regev et al., 1998;Colot and Rossignol, 1999;Suzuki and Bird, 2008), it is still a mystery as to why these organisms cannot dispense with cytosine methylation when many lower eukaryotes can.In plants and mammals, most methylated cytosines are found over repeat elements (Goll and Bestor, 2005;Suzuki and Bird, 2008;Law and Jacobsen, 2010) and loss of this modification is associated with transcriptional reactivation as well as increased mobilization of transposable elements (TEs; Slotkin and Martienssen, 2007). These observations likely reflect the ancestral role of cytosine methylation in the defence against invasive DNA. Methylation of repeat elements is also thought to have been exapted recurrently during eukaryotic evolution to exert other essential functions, notably in the epigenetic regulation of genes. Thus, genomic imprinting, which results in parent-of-origin-dependent expression, may have evolved in plants and mammals from situations in which methylation of repeat elements influences the activity of neighbouring genes (Barlow, 1993;M...

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Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Cited by 490 publications

References 81 publications

Dicer-independent RNA-directed DNA methylation in Arabidopsis

Dicer-independent RNA-directed DNA methylation in Arabidopsis

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

Repeat elements and the Arabidopsis DNA methylation landscape

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