Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

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	Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
	Zhang GJ 1,2; Guo GW 1; Hu XD 1; Zhang Y 1; Li QY 1,3; Li RQ 1,4; Zhuang RH 1; Lu ZK 1; He ZQ 1; Fang XD 1; Chen L 1; Tian W 1; Tao Y 5; Kristiansen K 1,4; Zhang XQ 1; Li SG 1; Yang HM 1; Wang J*1; wangj@genomics.org.cn
	2010
发表期刊	GENOME RESEARCH
ISSN	1088-9051
卷号	20 期号:5 页码:646-654
合作性质	其它
摘要	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 similar to 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.
资助者	This project is supported by the Chinese Academy of Science (KSCX2-YWN-023, GJHZ0701-6), the National Natural Science Foundation of China (30725008), and the Chinese 973 program (2007CB815701, 2007CB815703, 2007CB815705). This project is also funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Danish Plat- form for Integrative Biology, and the Ole Rømer grant from the Danish Natural Science Research Council (272-07-0196). ; This project is supported by the Chinese Academy of Science (KSCX2-YWN-023, GJHZ0701-6), the National Natural Science Foundation of China (30725008), and the Chinese 973 program (2007CB815701, 2007CB815703, 2007CB815705). This project is also funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Danish Plat- form for Integrative Biology, and the Ole Rømer grant from the Danish Natural Science Research Council (272-07-0196). ; This project is supported by the Chinese Academy of Science (KSCX2-YWN-023, GJHZ0701-6), the National Natural Science Foundation of China (30725008), and the Chinese 973 program (2007CB815701, 2007CB815703, 2007CB815705). This project is also funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Danish Plat- form for Integrative Biology, and the Ole Rømer grant from the Danish Natural Science Research Council (272-07-0196). ; This project is supported by the Chinese Academy of Science (KSCX2-YWN-023, GJHZ0701-6), the National Natural Science Foundation of China (30725008), and the Chinese 973 program (2007CB815701, 2007CB815703, 2007CB815705). This project is also funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Danish Plat- form for Integrative Biology, and the Ole Rømer grant from the Danish Natural Science Research Council (272-07-0196).
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收录类别	SCI
语种	英语
资助者	This project is supported by the Chinese Academy of Science (KSCX2-YWN-023, GJHZ0701-6), the National Natural Science Foundation of China (30725008), and the Chinese 973 program (2007CB815701, 2007CB815703, 2007CB815705). This project is also funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Danish Plat- form for Integrative Biology, and the Ole Rømer grant from the Danish Natural Science Research Council (272-07-0196). ; This project is supported by the Chinese Academy of Science (KSCX2-YWN-023, GJHZ0701-6), the National Natural Science Foundation of China (30725008), and the Chinese 973 program (2007CB815701, 2007CB815703, 2007CB815705). This project is also funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Danish Plat- form for Integrative Biology, and the Ole Rømer grant from the Danish Natural Science Research Council (272-07-0196). ; This project is supported by the Chinese Academy of Science (KSCX2-YWN-023, GJHZ0701-6), the National Natural Science Foundation of China (30725008), and the Chinese 973 program (2007CB815701, 2007CB815703, 2007CB815705). This project is also funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Danish Plat- form for Integrative Biology, and the Ole Rømer grant from the Danish Natural Science Research Council (272-07-0196). ; This project is supported by the Chinese Academy of Science (KSCX2-YWN-023, GJHZ0701-6), the National Natural Science Foundation of China (30725008), and the Chinese 973 program (2007CB815701, 2007CB815703, 2007CB815705). This project is also funded by the Shenzhen Municipal Government and the Yantian District local government of Shenzhen, the Danish Plat- form for Integrative Biology, and the Ole Rømer grant from the Danish Natural Science Research Council (272-07-0196).
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/4859
专题	基因起源组遗传资源与进化国家重点实验室
通讯作者	wangj@genomics.org.cn
作者单位	1.Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China 2.CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 3.School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China 4.Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark; 5.Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
推荐引用方式 GB/T 7714	Zhang GJ,Guo GW,Hu XD,et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome[J]. GENOME RESEARCH,2010,20(5):646-654.
APA	Zhang GJ.,Guo GW.,Hu XD.,Zhang Y.,Li QY.,...&wangj@genomics.org.cn.(2010).Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.GENOME RESEARCH,20(5),646-654.
MLA	Zhang GJ,et al."Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome".GENOME RESEARCH 20.5(2010):646-654.

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