A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa  

作　　者：Ting-Ting Liu Danmeng Zhu Wei Chen Wei Deng Hang He Guangming He Baoyan Bai Yijun Qi Runsheng Chen Xing Wang Deng 

机构地区：[1]Peking-Yale Joint Research Center for Plant Molecular Genetics and Agrobiotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China [2]Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing 100101, China [3]National Institute of Biological Sciences, No. 7 zhongguancun Life Science Park Road, Beijing 102206, China [4]Shenzhen Institute of Molecular Crop Design, 5henzhen 518107, China

出　　处：《Molecular Plant》2013年第3期830-846,共17页分子植物（英文版）

基　　金：This work was supported by grants from National Basic Research Program of China （973 Program） （2012CB910900）; National Natural Science Foundation of China （31171156, U1031001）;the Ministry of Science and Technology of China （2011CB100101, 2009DFB30030, 2008AA022301）; and the Ministry of Agriculture of China （2008ZX08012-005, 2009ZX08012-021 B）.We thank Dr. Ning Wei and Abigail Coplin for reading and commenting this manuscript. No conflict of interest declared.

摘　　要：Accumulating evidence suggests that non-coding RNAs （ncRNAs） are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5＇ and 3＇ termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs （snoRNAs） were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGOlb in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.Accumulating evidence suggests that non-coding RNAs （ncRNAs） are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5＇ and 3＇ termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs （snoRNAs） were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGOlb in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.

关 键 词：intermediate-size non-coding RNA small nucleolar RNA rice. 

分 类 号：Q522[生物学—生物化学] S513.01[农业科学—作物学]