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Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development.

Cho SH, Addo-Quaye C, Coruh C, Arif MA, Ma Z, Frank W, Axtell MJ.

PLoS Genet. 2008 Dec;4(12):e1000314. doi: 10.1371/journal.pgen.1000314. Epub 2008 Dec 19.


Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa.

Zhou X, Sunkar R, Jin H, Zhu JK, Zhang W.

Genome Res. 2009 Jan;19(1):70-8. doi: 10.1101/gr.084806.108. Epub 2008 Oct 29.


Selection and mutation on microRNA target sequences during rice evolution.

Guo X, Gui Y, Wang Y, Zhu QH, Helliwell C, Fan L.

BMC Genomics. 2008 Oct 2;9:454. doi: 10.1186/1471-2164-9-454.


Characterization of unique small RNA populations from rice grain.

Heisel SE, Zhang Y, Allen E, Guo L, Reynolds TL, Yang X, Kovalic D, Roberts JK.

PLoS One. 2008 Aug 6;3(8):e2871. doi: 10.1371/journal.pone.0002871.


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.


Genomics: protein fossils live on as RNA.

Sasidharan R, Gerstein M.

Nature. 2008 Jun 5;453(7196):729-31. doi: 10.1038/453729a. No abstract available. Erratum in: Nature. 2008 Jun 19;453(7198):1001.


Molecular biology. Slicing and dicing for small RNAs.

Birchler JA, Kavi HH.

Science. 2008 May 23;320(5879):1023-4. doi: 10.1126/science.1159018. Epub 2008 May 8. No abstract available.


Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells.

Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada TN, Siomi MC, Siomi H.

Nature. 2008 Jun 5;453(7196):793-7. doi: 10.1038/nature06938. Epub 2008 May 7.


The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs.

Okamura K, Chung WJ, Ruby JG, Guo H, Bartel DP, Lai EC.

Nature. 2008 Jun 5;453(7196):803-6. doi: 10.1038/nature07015. Epub 2008 May 7.


Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes.

Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ.

Nature. 2008 May 22;453(7194):534-8. doi: 10.1038/nature06904. Epub 2008 Apr 10.


Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes.

Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H.

Nature. 2008 May 22;453(7194):539-43. doi: 10.1038/nature06908. Epub 2008 Apr 10.


Characterization of paralogous protein families in rice.

Lin H, Ouyang S, Egan A, Nobuta K, Haas BJ, Zhu W, Gu X, Silva JC, Meyers BC, Buell CR.

BMC Plant Biol. 2008 Feb 19;8:18. doi: 10.1186/1471-2229-8-18.


A novel class of bacteria-induced small RNAs in Arabidopsis.

Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H.

Genes Dev. 2007 Dec 1;21(23):3123-34. Epub 2007 Nov 14.


Patterns of selective constraints in noncoding DNA of rice.

Guo X, Wang Y, Keightley PD, Fan L.

BMC Evol Biol. 2007 Nov 1;7:208.


The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race.

Aravin AA, Hannon GJ, Brennecke J.

Science. 2007 Nov 2;318(5851):761-4. Review.


Targets of RNA-directed DNA methylation.

Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ.

Curr Opin Plant Biol. 2007 Oct;10(5):512-9. Epub 2007 Aug 16. Review.


Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB.

Genome Res. 2007 Jun;17(6):839-51.


A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish.

Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RH, Hannon GJ, Draper BW, Ketting RF.

Cell. 2007 Apr 6;129(1):69-82.


The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?

Zheng D, Gerstein MB.

Trends Genet. 2007 May;23(5):219-24. Epub 2007 Mar 26.

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