Unknown,Transcriptomics,Genomics,Proteomics

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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 26˚C 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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Publications

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]

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