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Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice.

Ou-Yang F, Luo QJ, Zhang Y, Richardson CR, Jiang Y, Rock CD.

Funct Integr Genomics. 2013 Jun;13(2):207-16. doi: 10.1007/s10142-013-0313-8. Epub 2013 Feb 19.


Domestication of transposable elements into MicroRNA genes in plants.

Li Y, Li C, Xia J, Jin Y.

PLoS One. 2011 May 3;6(5):e19212. doi: 10.1371/journal.pone.0019212.


Profiling microRNAs and their targets in an important fleshy fruit: tomato (Solanum lycopersicum).

Din M, Barozai MY.

Gene. 2014 Feb 10;535(2):198-203. doi: 10.1016/j.gene.2013.11.034. Epub 2013 Dec 4.


The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes.

Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM.

RNA. 2009 Dec;15(12):2219-35. doi: 10.1261/rna.1646909. Epub 2009 Oct 27.


Dual coding of siRNAs and miRNAs by plant transposable elements.

Piriyapongsa J, Jordan IK.

RNA. 2008 May;14(5):814-21. doi: 10.1261/rna.916708. Epub 2008 Mar 26.


A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains.

Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C.

Genome Res. 2008 Sep;18(9):1456-65. doi: 10.1101/gr.075572.107. Epub 2008 Aug 7.


Expression of the rice microRNA miR820 is associated with epigenetic modifications at its own locus.

Nosaka M, Ono A, Ishiwata A, Shimizu-Sato S, Ishimoto K, Noda Y, Sato Y.

Genes Genet Syst. 2013;88(2):105-12.


siRNAs from miRNA sites mediate DNA methylation of target genes.

Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, Vazquez F, Zhang W, Jin H.

Nucleic Acids Res. 2010 Nov;38(20):6883-94. doi: 10.1093/nar/gkq590. Epub 2010 Jul 9.


Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice.

Lacombe S, Nagasaki H, Santi C, Duval D, PiƩgu B, Bangratz M, Breitler JC, Guiderdoni E, Brugidou C, Hirsch J, Cao X, Brice C, Panaud O, Karlowski WM, Sato Y, Echeverria M.

BMC Plant Biol. 2008 Dec 2;8:123. doi: 10.1186/1471-2229-8-123.


Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice.

Wei L, Gu L, Song X, Cui X, Lu Z, Zhou M, Wang L, Hu F, Zhai J, Meyers BC, Cao X.

Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3877-82. doi: 10.1073/pnas.1318131111. Epub 2014 Feb 19.


Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice.

Nosaka M, Itoh J, Nagato Y, Ono A, Ishiwata A, Sato Y.

PLoS Genet. 2012 Sep;8(9):e1002953. doi: 10.1371/journal.pgen.1002953. Epub 2012 Sep 27.


High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice.

Barrera-Figueroa BE, Gao L, Wu Z, Zhou X, Zhu J, Jin H, Liu R, Zhu JK.

BMC Plant Biol. 2012 Aug 3;12:132. doi: 10.1186/1471-2229-12-132.


Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs).

Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher SR, Maher C, Zhang L, Ware D, Liu B, Cao X, Meyers BC, Green PJ.

Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4951-6. doi: 10.1073/pnas.0708743105. Epub 2008 Mar 19.


Uncovering DCL1-dependent small RNA loci on plant genomes: a structure-based approach.

Meng Y, Shao C, Wang H, Chen M.

J Exp Bot. 2014 Feb;65(2):395-400. doi: 10.1093/jxb/ert409. Epub 2013 Dec 11.


Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max.

Zabala G, Campos E, Varala KK, Bloomfield S, Jones SI, Win H, Tuteja JH, Calla B, Clough SJ, Hudson M, Vodkin LO.

BMC Plant Biol. 2012 Oct 2;12:177. doi: 10.1186/1471-2229-12-177.


Construction of gene regulatory networks mediated by vegetative and reproductive stage-specific small RNAs in rice (Oryza sativa).

Meng Y, Shao C, Wang H, Ma X, Chen M.

New Phytol. 2013 Jan;197(2):441-53. doi: 10.1111/nph.12018. Epub 2012 Nov 5.


Genome-wide identification of reverse complementary microRNA genes in plants.

Shao C, Ma X, Xu X, Wang H, Meng Y.

PLoS One. 2012;7(10):e46991. doi: 10.1371/journal.pone.0046991. Epub 2012 Oct 23.


Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs.

Kuang H, Padmanabhan C, Li F, Kamei A, Bhaskar PB, Ouyang S, Jiang J, Buell CR, Baker B.

Genome Res. 2009 Jan;19(1):42-56. doi: 10.1101/gr.078196.108. Epub 2008 Nov 26.

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