title: Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis.
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 biological 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 significantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epigenetic 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.
authors.affiliation: College of Life Sciences, Beijing Normal University, Beijing 100875, China.
authors.forename: Yuqiu
authors.initials: Y
authors.lastname: Wang
authors.forename: Xuncheng
authors.initials: X
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.forename: Xiuduo
authors.initials: X
authors.lastname: Fan
authors.forename: Ting-Ting
authors.initials: TT
authors.lastname: Liu
authors.forename: Guangming
authors.initials: G
authors.lastname: He
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: William
authors.initials: W
authors.lastname: Terzaghi
authors.forename: Danmeng
authors.initials: D
authors.lastname: Zhu
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D022661:RNA, Untranslated / Q000235:genetics*
chemical_list: D022661:RNA, Untranslated
keywords: Arabidopsis; RNomics.; intermediate-sized non-coding RNAs