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GC content fluctuation around plant small RNA‐generating sites
Author(s) -
Zhang Yu,
Yan Chenghuan,
Kuang Hanhui
Publication year - 2014
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2014.01.023
Subject(s) - gc content , transposable element , small rna , rna , in silico , biology , arabidopsis thaliana , gene , gene silencing , rna interference , inverted repeat , genetics , gene expression , transfer rna , microbiology and biotechnology , genome , mutant
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.