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This article is part of the supplement: Ninth International Conference on Bioinformatics (InCoB2010): Computational Biology

Open Access Proceedings

RNA editing of nuclear transcripts in Arabidopsis thaliana

Yijun Meng123, Dijun Chen12, YongFeng Jin3, Chuanzao Mao2, Ping Wu2 and Ming Chen12*

Author Affiliations

1 Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China

2 State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China

3 Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China

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BMC Genomics 2010, 11(Suppl 4):S12  doi:10.1186/1471-2164-11-S4-S12

Published: 2 December 2010

Abstract

Background

RNA editing is a transcript-based layer of gene regulation. To date, no systemic study on RNA editing of plant nuclear genes has been reported. Here, a transcriptome-wide search for editing sites in nuclear transcripts of Arabidopsis (Arabidopsis thaliana) was performed.

Results

MPSS (massively parallel signature sequencing) and PARE (parallel analysis of RNA ends) data retrieved from public databases were utilized, focusing on one-base-conversion editing. Besides cytidine (C)-to-uridine (U) editing in mitochondrial transcripts, many nuclear transcripts were found to be diversely edited. Interestingly, a sizable portion of these nuclear genes are involved in chloroplast- or mitochondrion-related functions, and many editing events are tissue-specific. Some editing sites, such as adenosine (A)-to-U editing loci, were found to be surrounded by peculiar elements. The editing events of some nuclear transcripts are highly enriched surrounding the borders between coding sequences (CDSs) and 3′ untranslated regions (UTRs), suggesting site-specific editing. Furthermore, RNA editing is potentially implicated in new start or stop codon generation, and may affect alternative splicing of certain protein-coding transcripts. RNA editing in the precursor microRNAs (pre-miRNAs) of ath-miR854 family, resulting in secondary structure transformation, implies its potential role in microRNA (miRNA) maturation.

Conclusions

To our knowledge, the results provide the first global view of RNA editing in plant nuclear transcripts.