GC content fluctuation around plant small RNA-generating sites.
GC content of small RNA-generating sites and their flanking sequences in Arabidopsis thaliana and rice was systematically analyzed in silico. High GC content fluctuation (GCF) is observed at the borders of sRNA sites, while the GCF within sRNA sites is low. Furthermore, the GC content along sequences of some miniature inverted-repeat transposable element (MITE) families coincides with the abundance of MITE-derived small RNAs. The GCF within tasiRNA clusters is negatively correlated with its phasing score. We conclude that high GC content and low GCF could increase the expression of small RNA. Our results provide further insights on small RNA expression, which may be applied to improve the silencing efficiency of RNAi and virus-induced gene silencing.
Key Laboratory of Horticulture Biology, Ministry of Education, Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, PR China.
Yu
Y
Zhang
Key Laboratory of Horticulture Biology, Ministry of Education, Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, PR China.
Chenghuan
C
Yan
Key Laboratory of Horticulture Biology, Ministry of Education, Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: kuangfile@gmail.com.
Hanhui
H
Kuang
D017360:Arabidopsis / Q000235:genetics*; D001482:Base Composition; D017343:Genes, Plant; D055029:Inverted Repeat Sequences; D012275:Oryza / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*
D018749:RNA, Plant; D058727:RNA, Small Untranslated
GC content; GC fluctuation; MITEs; Small RNA expression; TasiRNA