title: Small RNAs in angiosperms: sequence characteristics, distribution and generation.
abstract: High-throughput sequencing (HTS) has opened up a new era for small RNA (sRNA) exploration. Using HTS data for a global survey of sRNAs in 26 angiosperms, elevated GC contents were detected in the monocots, whereas the 5(')-terminal compositions were quite uniform among the angiosperms. Chromosome-wide distribution patterns of sRNAs were investigated by using scrolling-window analysis. We performed de novo natural antisense transcript (NAT) prediction, and found that the overlapping regions of trans-NATs, but not cis-NATs, were hotspots for sRNA generation. One cis-NAT generates phased natural antisense short interfering RNAs (nat-siRNAs) specifically from flowers in Arabidopsis, while one in rice produces phased nat-siRNAs from grains, suggesting their organ-specific regulatory roles.
authors.affiliation: Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences and James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
authors.forename: Dijun
authors.initials: D
authors.lastname: Chen
authors.forename: Yijun
authors.initials: Y
authors.lastname: Meng
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Ma
authors.forename: Chuanzao
authors.initials: C
authors.lastname: Mao
authors.forename: Youhuang
authors.initials: Y
authors.lastname: Bai
authors.forename: Junjie
authors.initials: J
authors.lastname: Cao
authors.forename: Haibin
authors.initials: H
authors.lastname: Gu
authors.forename: Ping
authors.initials: P
authors.lastname: Wu
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology; D017343:Genes, Plant; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry; D012275:Oryza / Q000235:genetics; D016372:RNA, Antisense / Q000737:chemistry / Q000235:genetics; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D035683:MicroRNAs; D016372:RNA, Antisense; D018749:RNA, Plant; D034741:RNA, Small Interfering