Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis  

作　　者：Yuqiu Wang Xuncheng Wang Wei Deng Xiuduo Fan Ting-Ting Liu Guangming He Runsheng Chen William Terzaghi Danmeng Zhu Xing Wang Deng 

机构地区：[1]College of Life Sciences, Beijing Normal University, Beijing 100875, China [2]Peking-Yale Joint ResearchCenter for Plant Molecular Genetics and Agrobiotechnology, National Laboratory of Protein and Plant Gene Research,College of Life Sciences, Peking University, Beijing 100871, China [3]Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China [4]Bioinformatics Laboratory and National Laboratory of Biomacromolecules,-Institute of Biophysics. Beijing 100101, China [5]Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA [6]Department of Biology, Wilkes University, Wilkes-Barre, PA 1B766, USA

出　　处：《Molecular Plant》2014年第3期514-527,共14页分子植物（英文版）

基　　金：grants from the National Basic Research Program of China (973 Program)，the National Natural Science Foundation of China，in part by the Peking-Tsinghua Center for Life Sciences and a grant from the Next-Generation BioGreen 21 Program，Rural Development Administration,Republic of Korea

摘　　要：ABSTRACT Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biologi- cal processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs （im-ncRNAs） （50-300 nt） have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half （58%） are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5＇-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited signifi- cantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epige- netic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.ABSTRACT Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biologi- cal processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs （im-ncRNAs） （50-300 nt） have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half （58%） are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5＇-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited signifi- cantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epige- netic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.

关 键 词：intermediate-sized non-coding RNAs ARABIDOPSIS RNomics. 

分 类 号：Q522[生物学—生物化学] Q987