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

Guojie Zhang; Guangwu Guo; Xueda Hu; Yong Zhang; Qiye Li; Ruiqiang Li; Ruhong Zhuang; Zhike Lu; Zengquan He; Xiaodong Fang; Li Chen; Wei Tian; Yong Tao; Karsten Kristiansen; Xiuqing Zhang; Songgang Li; Huanming Yang; Jian Wang; Jun Wang

doi:10.1101/gr.100677.109

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

Guojie Zhang, Guangwu Guo, Xueda Hu, Yong Zhang, Qiye Li, Ruiqiang Li, Ruhong Zhuang, Zhike Lu, Zengquan He, Xiaodong Fang, Li Chen, Wei Tian, Yong Tao, Karsten Kristiansen, Xiuqing Zhang, Songgang Li, Huanming Yang, Jian Wang, Jun Wang

Department of Biology

360 Citations (Scopus)

Abstract

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 transsplicing, 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.

Original language	English
Journal	Genome Research
Volume	20
Issue number	5
Pages (from-to)	646-54
Number of pages	8
ISSN	1088-9051
DOIs	https://doi.org/10.1101/gr.100677.109
Publication status	Published - May 2010

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

abstract = "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 transsplicing, 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.",

author = "Guojie Zhang and Guangwu Guo and Xueda Hu and Yong Zhang and Qiye Li and Ruiqiang Li and Ruhong Zhuang and Zhike Lu and Zengquan He and Xiaodong Fang and Li Chen and Wei Tian and Yong Tao and Karsten Kristiansen and Xiuqing Zhang and Songgang Li and Huanming Yang and Jian Wang and Jun Wang",

year = "2010",

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doi = "10.1101/gr.100677.109",

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pages = "646--54",

journal = "Genome Research",

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T1 - Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

AU - Zhang, Guojie

AU - Guo, Guangwu

AU - Hu, Xueda

AU - Zhang, Yong

AU - Li, Qiye

AU - Li, Ruiqiang

AU - Zhuang, Ruhong

AU - Lu, Zhike

AU - He, Zengquan

AU - Fang, Xiaodong

AU - Chen, Li

AU - Tian, Wei

AU - Tao, Yong

AU - Kristiansen, Karsten

AU - Zhang, Xiuqing

AU - Li, Songgang

AU - Yang, Huanming

AU - Wang, Jian

AU - Wang, Jun

PY - 2010/5

Y1 - 2010/5

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 transsplicing, 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.

AB - 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 transsplicing, 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.

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DO - 10.1101/gr.100677.109

M3 - Journal article

C2 - 20305017

SN - 1088-9051

VL - 20

SP - 646

EP - 654

JO - Genome Research

JF - Genome Research

IS - 5

ER -

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

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