Genetic and Functional Diversification of Small RNA Pathways in Plants

By Zhixin Xie, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, James C. Carrington. PLoS Biology, 2004

1,652 citations recorded by the source corpus.

Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense.

Subfields: Endocrinology, Plant Science

View Paper: https://www.semanticscholar.org/paper/caf3dfcf243a415c5dd4f337c8560e4bc04d2fa2

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Citations in the corpus

Approaches to Minimize Variation of Transgene Expression in Plants (2005, background): “…PTGS-machinery, including genes encoding a putative RNA-dependent RNA polymerase (RdRp) (SGS2/SDE1/ RDR6; Dalmay et al. 2000; Mourrain et al. 2000; Xie et al. 2004), a coiled-coil protein of unknown function (SGS3; Mourrain et al. 2000), a RNA helicase (SDE3; Dalmay et al. 2001) and a protein…”
Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana (2004, background): “Biogenesis of these siRNAs may or may not require an RNA-dependent RNA polymerase, and they may form through the activity of DCL1 (as do most or all miRNAs) or another DCL protein associated with other classes of endogenous siRNA”
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. (2006, background): “Conventional cloning and sequencing of small RNAs from Arabidopsis has suggested that plants have a remarkable diversity of endogenous small RNAs (Llave et al. 2002; Park et al. 2002; Reinhart et al. 2002; Sunkar and Zhu 2004; Xie et al. 2004).”
Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels (2019, background): “In plants, RdDM is an epigenetic modification process that primarily relies on two core proteins: Dicer-like 3 (DCL3), which cleaves long double-stranded RNA to produce small interfering RNAs (siRNAs), and Argonaute 4 (AGO4), which binds siRNAs to function [37,38].”
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes (2007, background): “Arabidopsis mutants and microarray samples Mutant lines for dcl1-7, dcl2-1, dcl3-1, dcl4-2, rdr1-1, rdr2-1, rdr6-15 and hen1-1 were described previously [34,36–38,48,49].”
Silencing a cotton bollworm P450 monooxygenase gene by plant-mediated RNAi impairs larval tolerance of gossypol (2007, methodology): “To generate plants that predominately produce the long dsRNA of the transgene, we used a dcl2 dcl3 dcl4 triple mutan”
Applications of next-generation sequencing technologies in functional genomics. (2008, background): “While miRNAs and siRNAs are similar in size and are both involved in posttranscriptional regulation of gene expression, their biogenesis and exact functions are different [71].”
Gene silencing in plants using artificial microRNAs and other small RNAs. (2008, background): “This process requires the activity of an RNAdependent RNA polymerase, RDR2 in Arabidopsis, which mediates unprimed dsRNA formation from low-abundance transcripts that originate from repeats and various classes of transposons (Xie et al., 2004).”
microRNA-directed phasing during trans-acting siRNA biogenesis in plants. (2005, background): “…cooperate in the heterochromatin-associated RNAi pathway, resulting in 24-nucleotide siRNAs from various retroelements and transposons, ribosomal arrays, endogenous direct and inverted repeats, and transgenes containing direct repeats (Chan et al., 2004; Xie et al., 2004; Zilberman et al., 2003).”