A biochemical framework for RNA silencing in plants.

By Guiliang Tang, B. Reinhart, David P. Bartel, Phillip D. Zamore. Genes & Development, 2003

1,047 citations recorded by the source corpus.

RNA silencing phenomena were first discovered in plants, yet only the RNA interference pathway in animals has been subject to biochemical analysis. Here, we extend biochemical analysis to plant RNA silencing. We find that standard wheat germ extract contains Dicer-like enzymes that convert double-stranded RNA (dsRNA) into two classes of small interfering RNAs, as well as an RNA-dependent RNA polymerase activity that can convert exogenous single-stranded RNA into dsRNA. In this plant embryo extract, an endogenous microRNA (miRNA) that lacks perfect complementarity to its RNA targets nonetheless acts as a small interfering RNA. The miRNA guides an endonuclease to cleave efficiently wild-type Arabidopsis PHAVOLUTA mRNA, but not a dominant mutant previously shown to perturb leaf development. This finding supports the view that plant miRNAs direct RNAi and that miRNA-specified mRNA destruction is important for proper plant development. Thus, endonuclease complexes guided by small RNAs are a common feature of RNA silencing in both animals and plants.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/096e4fb10238a1ea2193055da97e8c9d7bac975b

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Citations in the corpus

MicroRNA targets in Drosophila (2003, neutral): “Many of these plant mRNA targets encode transcription factors that regulate morphogenesis [15-19].”
The Functions of MicroRNAs: mRNA Decay and Translational Repression. (2015, background): “Many aspects of plant RNA silencing, for example, target cleavage and RNAdependent RNA polymerization, have been recapitulated in lysates derived from Arabidopsis inflorescence tissue and cultured cells as well as in wheat germ extract [71,124].”
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. (2006, background): “As expected based on initial sequencing efforts ( Tang et al. 2003 ), the 24mers were enriched for a 5-terminal adenosine (Supplementary Fig. 1E,F).”
Small silencing RNAs: an expanding universe (2009, neutral): “In plants, inverted-repeat transgenes or co-expressed sense and antisense transcripts produce two sizes of siRNAs: 21 and 24 nucleotide”
MicroRNAs and complex diseases: from experimental results to computational models (2019, neutral): “In vitro programming of active RISCs by synthetic miRNA duplexes in plant systems needs further exploration [81, 83].”
SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. (2004, background): “Although we are intrigued by the hypothesis that SGS3 and RDR6 are involved in miRNA-initiated transitive PTGS, Tang et al. (2003) noted that this phenomenon is inconsistent with the observation that mutations in miRNA cognate sites are typically dominant to the wild-type allele (McConnell et al. 20”
MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. (2004, methodology): “We used an in vitro assay that relies on miRNA-pro-grammed RISC endogenously present in wheat-germ extract [30] to determine whether miR164-directed cleavage of 5mCUC1 RNA is reduced.”
Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. (2005, background): “Cloning of the 3# cleavage products resulting from near-perfect duplex formation between a miRNA and an mRNA sequence has been a powerful means of experimentally validating targets of miRNA action (Jones-Rhoades and Bartel, 2004; Kasschau et al., 2003; Llave et al., 2002; Mansfield et al., 2004; Ta”
Computational identification of Drosophila microRNA genes (2003, background): “Interestingly, perfect or near-perfect target complementarity is associated with mRNA degradation [24-26], similar to the effects of siRNA, whereas imperfect base-pairing is associated with regulation by translational inhibition [6,27].”
Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis (2004, background): “…Bartel, 2003; Bartel, 2004). miRNAs are known to silence genes posttranscriptionally by targeting cognate mRNAs for degradation (Llave et al., 2002a; Palatnik et al., 2003; Tang et al., 2003) or translation repression (Lee et al., 1993; Reinhart et al., 2000; Aukerman and Sakai, 2003; Chen, 2004).”
RNA Interference: Biology, Mechanism, and Applications (2003, background): “(205) found that the dsRNA was chopped into siRNAs of two discrete size classes, one 21 nucleotides and the other 24 to 25 nucleotides long, whereas D.”
The microRNAs of Caenorhabditis elegans. (2003, background): “2002), and the plant miR171 and miR165/166 have been shown to specify cleavage of their mRNA targets (Llave et al. 2002b; Tang et al. 2003).”
microPrimer: the biogenesis and function of microRNA (2005, background): “Upon binding to their mRNA targets, the miRNA-containing RISCs function as endonucleases, cleaving the mRNA (Llave et al., 2002; Tang et al., 2003).”
Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation (2004, background): “Plant miRNAs apparently also inhibit translation [19], but many plant miRNAs are precisely complementary to their targets, and in these cases they act as guides to trigger transcript degradation through RNA interference (RNAi) [ 20-22 ].”
Oncomirs — microRNAs with a role in cancer (2006, background): “This mechanism of miRNA-mediated gene silencing is commonly found in plant”
MicroRNA-Directed Regulation of Arabidopsis AUXIN RESPONSE FACTOR17 Is Essential for Proper Development and Modulates Expression of Early Auxin Response Genesw⃞ (2005, methodology): “…of 5mARF17 RNA was reduced, we used an in vitro assay that relies on miRNAprogrammed silencing complexes endogenously present in wheat germ extract (Tang et al., 2003), which can direct cleavage of wild-type ARF17 RNA (G. Tang, M. Jones-Rhoades, D.P. Bartel, and P. Zamore, unpublished data),…”
A two-hit trigger for siRNA biogenesis in plants. (2006, methodology): “We next tested, using wheat-germ extract (Tang et al., 2003), the biochemical properties of the miR390 complementary sites.”