气候变化领域集成服务门户(CCPortal): Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice

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DOI	10.1186/1471-2164-13-721
	Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice
	Lu, Tingting; Zhu, Chuanrang; Lu, Guojun; Guo, Yunli; Zhou, Yan; Zhang, Zhiyong; Zhao, Yan; Li, Wenjun; Lu, Ying; Tang, Weihua; Feng, Qi; Han, Bin
发表日期	2012
ISSN	1471-2164
卷号	13
英文摘要	Background: Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs), which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs. Results: We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq) to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa). Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set), 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data. Among them, 503 cis-NATs seemed to be associated with specific conditions. The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.0% of cis-NATs were expressed simultaneously in a population of homogenous cells. Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation. Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks. Conclusions: Our study profiles an abundance of cis-NATs and nat-siRNAs in rice. These data are valuable for gaining insight into the complex function of the rice transcriptome.
关键词	Oryza sativa Cis-NATs Nat-siRNAs SsRNA-seq Transcriptome
学科领域	Biotechnology & Applied Microbiology; Genetics & Heredity
语种	英语
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
来源期刊	BMC GENOMICS
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/111666
作者单位	Chinese Acad Sci, Shanghai Inst Biol Sci, Natl Ctr Gene Res, Shanghai 200233, Peoples R China
推荐引用方式 GB/T 7714	Lu, Tingting,Zhu, Chuanrang,Lu, Guojun,et al. Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice[J]. 中国科学院西北生态环境资源研究院,2012,13.
APA	Lu, Tingting.,Zhu, Chuanrang.,Lu, Guojun.,Guo, Yunli.,Zhou, Yan.,...&Han, Bin.(2012).Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.BMC GENOMICS,13.
MLA	Lu, Tingting,et al."Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice".BMC GENOMICS 13(2012).