Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana

By Edwards Allen, Zhixin Xie, Adam M. Gustafson, G. Sung, J. Spatafora, James C. Carrington. Nature Genetics, 2004

631 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/51cdb3f803e632d324f27998512e421fab0b00a6

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Citations in the corpus

Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis (2005, neutral): “This differs from other ARGONAUTE-catalyzed RNA cleavage sites which occur between nucleotides 10 and 11 (Allen et al., 2004).”
Small RNAs and Their Roles in Plant Development (2009, background): “One model of miRNA origin posits that MIR genes arise from the inverted duplication of target genes (Allen et al. 2004).”
Genomic Organization, Differential Expression, and Interaction of SQUAMOSA Promoter-Binding-Like Transcription Factors and microRNA156 in Rice1[W] (2006, background): “Amechanism of miRNA origination and evolution has been proposed by analysis of two Arabidopsis miR161 and miR163 families (Allen et al., 2004).”
Biosynthesis and Regulation of Phenylpropanoids in Plants (2017, background): “duplication event has been confirmed for other miRNAs, such as MIR161, MIR163, and MIR1444 (Allen et al., 2004; Fahlgren et al., 2007; Wang et al., 2017).”
Origin, biogenesis, and activity of plant microRNAs. (2009, neutral): “Continued selection would enforce further drift of fold-back arm sequences surrounding the miRNA/miRNA*, ultimately generating an old MIR gene unrelated to the parental locus (Figure 1B; Allen et al., 2004; Fahlgren et al., 2007).”
Specialization and evolution of endogenous small RNA pathways (2007, background): “Several non-conserved plant miRNA genes have recently been shown to contain extensive similarity to protein-coding gene”
The evolution of gene regulation by transcription factors and microRNAs (2007, background): “One model of de novo miRNA acquisition, the inverted duplication model, suggests that new miRNAs evolve by inverted duplication of a stretch of coding sequence followed by subsequent erosion of the sequence into an imperfect hairpin structur”
Modulating Hox gene functions during animal body patterning (2005, background): “It has been suggested that miRNAs are derived from inverted duplications of the 3′ UTRs of future target gene”
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities (2008, background): “Second, some ncRNAs have evolved from protein-coding genes [35,36], and so will retain remnant signatures of and homologies to mRNAs.”
Widespread dynamic DNA methylation in response to biotic stress (2012, neutral): “The mutant plant lines met1-3 (17), met1-9 (51), ddm1-8 (52), ddm1-10 (53), drm1-2 drm2-2 cmt3-11 (54), ago4-2 (38), ago6-2 (13), rdr1-1 (55), rdr2-1 (55), rdr6-15 (56), drd1-5 (57), nrpd1a-4 (58), nrpd1b-11 (59), nrpd2a-2 nrpd2b-1 (60), and dcl21 dcl3-1 dcl4-2 (61) have been previously described.”
microRNA-directed phasing during trans-acting siRNA biogenesis in plants. (2005, methodology): “Low molecular weight RNA (5 g) from Arabidopsis inflorescence tissue was isolated and subjected to blot assays as described (Allen et al., 2004).”
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. (2006, background): “To the extent that these transgene hairpins might resemble evolutionary precursors of some miRNAs ( Allen et al. 2004 ), we suggest an adaptive switch from DCL4- to DCL1mediated processing during the course of miRNA gene emergence and evolution, which is driven by selective pressure for enhanced pro”
Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends (2008, background): “2 could be an miRNA that is relatively insensitive to the dcl1-7 mutation, an uncommon but certainly documented characteristic of some bona fide miRNA”