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Unexpected consequences of a sudden and massive transposon amplification on rice gene expression.

Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR.

Nature. 2009 Oct 22;461(7267):1130-4. doi: 10.1038/nature08479.


Early embryogenesis-specific expression of the rice transposon Ping enhances amplification of the MITE mPing.

Teramoto S, Tsukiyama T, Okumoto Y, Tanisaka T.

PLoS Genet. 2014 Jun 12;10(6):e1004396. doi: 10.1371/journal.pgen.1004396. eCollection 2014 Jun.


Dramatic amplification of a rice transposable element during recent domestication.

Naito K, Cho E, Yang G, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR.

Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17620-5. Epub 2006 Nov 13.


An active DNA transposon family in rice.

Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR, Wessler SR.

Nature. 2003 Jan 9;421(6919):163-7.


Mobilization of a transposon in the rice genome.

Nakazaki T, Okumoto Y, Horibata A, Yamahira S, Teraishi M, Nishida H, Inoue H, Tanisaka T.

Nature. 2003 Jan 9;421(6919):170-2.


The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice.

Robb SM, Lu L, Valencia E, Burnette JM 3rd, Okumoto Y, Wessler SR, Stajich JE.

G3 (Bethesda). 2013 Jun 21;3(6):949-57. doi: 10.1534/g3.112.005348.


mPing: The bursting transposon.

Naito K, Monden Y, Yasuda K, Saito H, Okumoto Y.

Breed Sci. 2014 Jun;64(2):109-14. doi: 10.1270/jsbbs.64.109. Epub 2014 Jun 1. Review.


Rice transposable elements are characterized by various methylation environments in the genome.

Takata M, Kiyohara A, Takasu A, Kishima Y, Ohtsubo H, Sano Y.

BMC Genomics. 2007 Dec 20;8:469.


cDNA microarray analysis of rice anther genes under chilling stress at the microsporogenesis stage revealed two genes with DNA transposon Castaway in the 5'-flanking region.

Yamaguchi T, Nakayama K, Hayashi T, Yazaki J, Kishimoto N, Kikuchi S, Koike S.

Biosci Biotechnol Biochem. 2004 Jun;68(6):1315-23.


The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean.

Hancock CN, Zhang F, Floyd K, Richardson AO, Lafayette P, Tucker D, Wessler SR, Parrott WA.

Plant Physiol. 2011 Oct;157(2):552-62. doi: 10.1104/pp.111.181206. Epub 2011 Aug 15.


Selective acquisition and retention of genomic sequences by Pack-Mutator-like elements based on guanine-cytosine content and the breadth of expression.

Ferguson AA, Zhao D, Jiang N.

Plant Physiol. 2013 Nov;163(3):1419-32. doi: 10.1104/pp.113.223271. Epub 2013 Sep 12.


Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana.

Yang G, Zhang F, Hancock CN, Wessler SR.

Proc Natl Acad Sci U S A. 2007 Jun 26;104(26):10962-7. Epub 2007 Jun 19.


Nested insertions and accumulation of indels are negatively correlated with abundance of mutator-like transposable elements in maize and rice.

Zhao D, Jiang N.

PLoS One. 2014 Jan 27;9(1):e87069. doi: 10.1371/journal.pone.0087069. eCollection 2014.


A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica.

Oki N, Yano K, Okumoto Y, Tsukiyama T, Teraishi M, Tanisaka T.

Genes Genet Syst. 2008 Aug;83(4):321-9.


Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses.

Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K.

Plant Physiol. 2003 Dec;133(4):1755-67. Epub 2003 Nov 26.


Loss-of-function of a ubiquitin-related modifier promotes the mobilization of the active MITE mPing.

Tsukiyama T, Teramoto S, Yasuda K, Horibata A, Mori N, Okumoto Y, Teraishi M, Saito H, Onishi A, Tamura K, Tanisaka T.

Mol Plant. 2013 May;6(3):790-801. doi: 10.1093/mp/sst042. Epub 2013 Feb 27.


Low temperature-responsive changes in the anther transcriptome's repeat sequences are indicative of stress sensitivity and pollen sterility in rice strains.

Ishiguro S, Ogasawara K, Fujino K, Sato Y, Kishima Y.

Plant Physiol. 2014 Feb;164(2):671-82. doi: 10.1104/pp.113.230656. Epub 2013 Dec 27.


Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.).

Mizuno H, Kawahara Y, Sakai H, Kanamori H, Wakimoto H, Yamagata H, Oono Y, Wu J, Ikawa H, Itoh T, Matsumoto T.

BMC Genomics. 2010 Dec 2;11:683. doi: 10.1186/1471-2164-11-683.


DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements.

Wang J, Yu Y, Tao F, Zhang J, Copetti D, Kudrna D, Talag J, Lee S, Wing RA, Fan C.

Genome Biol. 2016 May 6;17(1):92. doi: 10.1186/s13059-016-0954-8.

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