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Microarray analysis of strain EG4 vs. Nipponbare

ABSTRACT: In the japonica rice strain Gimbozu EG4, the DNA transposon mPing is actively transposing to attain over 1,000 copies, whereas in Nipponbare, where this element is virtually silent and has only 50 copies. To analyze the impact of such a massive amplification of transposable element on gene regulation, we performed the rice 44k oligo microarray analysis. Total RNA was extracted from 7-day-old seedlings of EG4 and Nipponbare plants, grown in a greenhouse at at 26ËC and subjected to 44k oligo-DNA microarray with 4 biological replicates.

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Takuji Tsukiyama

PROVIDER: E-GEOD-15021 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Naito Ken K Zhang Feng F Tsukiyama Takuji T Saito Hiroki H Hancock C Nathan CN Richardson Aaron O AO Okumoto Yutaka Y Tanisaka Takatoshi T Wessler Susan R SR

Nature 20091001 7267

High-copy-number transposable elements comprise the majority of eukaryotic genomes where they are major contributors to gene and genome evolution. However, it remains unclear how a host genome can survive a rapid burst of hundreds or thousands of insertions because such bursts are exceedingly rare in nature and therefore difficult to observe in real time. In a previous study we reported that in a few rice strains the DNA transposon mPing was increasing its copy number by approximately 40 per pla ...[more]

PMID: 19847266

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