A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana.

By R. Rajagopalan, H. Vaucheret, Jerry Trejo, David P. Bartel. Genes & Development, 2006

1,341 citations recorded by the source corpus.

To better understand the diversity of small silencing RNAs expressed in plants, we employed high-throughput pyrosequencing to obtain 887,000 reads corresponding to Arabidopsis thaliana small RNAs. They represented 340,000 unique sequences, a substantially greater diversity than previously obtained in any species. Most of the small RNAs had the properties of heterochromatic small interfering RNAs (siRNAs) associated with DNA silencing in that they were preferentially 24 nucleotides long and mapped to intergenic regions. Their density was greatest in the proximal and distal pericentromeric regions, with only a slightly preferential propensity to match repetitive elements. Also present were 38 newly identified microRNAs (miRNAs) and dozens of other plausible candidates. One miRNA mapped within an intron of DICER-LIKE 1 (DCL1), suggesting a second homeostatic autoregulatory mechanism for DCL1 expression; another defined the phase for siRNAs deriving from a newly identified trans-acting siRNA gene (TAS4); and two depended on DCL4 rather than DCL1 for their accumulation, indicating a second pathway for miRNA biogenesis in plants. More generally, our results revealed the existence of a layer of miRNA-based control beyond that found previously that is evolutionarily much more fluid, employing many newly emergent and diverse miRNAs, each expressed in specialized tissues or at low levels under standard growth conditions.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/0d3549f769c37e59debe18cb185e85c70ba17c90

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Citations in the corpus

Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing1[W][OA] (2009, background): “TAS4-siR81(2) targets a group of MYB transcription factors, PAP1/MYB75, PAP2/MYB90, and MYB113, that are involved in the biosynthesis of anthocyanin (Rajagopalan et al., 2006).”
Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing (2010, background): “The notion that these miRNAs and their targets ultimately derived from the same ancestral elements is reminiscent of the origin of some plant miRNAs, whichderive from duplicated fragments of their cleavage targets (Allen et al., 2004; Rajagopalan et al., 2006).”
Applications of next-generation sequencing technologies in functional genomics. (2008, background): “thaliana [74–80]; wheat, Triticum aestivum [81]; the basal eudicot species Eschscholzia californica [82]; the lycopod Selaginella moellendorffii [74]; the unicellular alga Chlamydomonas rein-”
High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes (2007, background): “[47] describing results from deep sequencing of Arabidopsis small RNAs (887,000 reads) was published.”
Evolution and Functional Diversification of MIRNA Genes (2011, background): “This supports the earlier finding that most young miRNAs in A. thaliana have few bona fide targets (Rajagopalan et al., 2006; Fahlgren et al., 2007).”
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. (2007, background): “quencing approach has not been used previously in insects, but in other lineages it has revealed miRNAs and miRNA candidates that escaped earlier detection because they are rare or not well conserved in related genomes (Berezikov et al. 2006; Lu et al. 2006; Rajagopalan et al. 2006; Ruby et al. 2006”
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. (2008, methodology): “Next-generation miRNA profiling has already been realized in a few organisms (Rajagopalan et al. 2006; Fahlgren et al. 2007; Kasschau et al. 2007; Yao et al. 2007) using the massively parallel signature sequencing (MPSS) methodology (Nakano et al. 2006) and more recently the Roche/454 platform…”
Gene silencing in plants using artificial microRNAs and other small RNAs. (2008, background): “More recent analyses have, however, revealed that a 21-base form of miR319a predominates, as is typical for plant miRNAs (Fahlgren et al., 2007; Rajagopalan et al., 2006).”
Small RNAs and Their Roles in Plant Development (2009, background): “Second, DCL1 pre-mRNA harbors the pre-miR838 hairpin, and DCL1-mediated processing of DCL1 pre-mRNA to release premiR838 results in nonproductive fragments of DCL1 pre-mRNA (Rajagopalan et al. 2006).”
Criteria for Annotation of Plant MicroRNAs (2008, background): “Because of the presence of several miRNAs whose accumulation depends upon DCL4 (Rajagopalan et al., 2006), DCL1 dependency is not necessary for miRNA annotation.”
psRNATarget: a plant small RNA target analysis server (2017 release) (2018, background): “Most of the plant miRNA targets identified to date have extensive complementarity to their cognate miRNA mature sequences, yet perfect matches between them were not often found (1,4,5).”
Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends (2008, background): “One of the candidates, Small13, identified via its target in this study and previously reported as “miRNA candidate S&rdquo”
PMRD: plant microRNA database (2009, methodology): “Using high-throughput sequencing, Rajagopalan et al. ( 9 ) identified 38 new miRNAs in”