Small RNAs in angiosperms: sequence characteristics, distribution and generation.
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.
Chen
Dijun
D
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.
Meng
Yijun
Y
Ma
Xiaoxia
X
Mao
Chuanzao
C
Bai
Youhuang
Y
Cao
Junjie
J
Gu
Haibin
H
Wu
Ping
P
Chen
Ming
M
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
D035683:MicroRNAs; D016372:RNA, Antisense; D018749:RNA, Plant; D034741:RNA, Small Interfering