TY  - JOUR
A1  - Zhang, Guojie
A1  - Guo, Guangwu
A1  - Hu, Xueda
A1  - Zhang, Yong
A1  - Li, Qiye
A1  - Li, Ruiqiang
A1  - Zhuang, Ruhong
A1  - Lu, Zhike
A1  - He, Zengquan
A1  - Fang, Xiaodong
A1  - Chen, Li
A1  - Tian, Wei
A1  - Tao, Yong
A1  - Kristiansen, Karsten
A1  - Zhang, Xiuqing
A1  - Li, Songgang
A1  - Yang, Huanming
A1  - Wang, Jian
A1  - Wang, Jun
T1  - Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
Y1  - 2010/05/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 646 
EP  - 654 
DO  - 10.1101/gr.100677.109 
VL  - 20 
IS  - 5 
UR  - http://genome.cshlp.org/content/20/5/646.abstract 
N2  - Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in ∼33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed. 
ER  -