Dicer-like 3 Produces Transposable Element-associated 24-nt SiRNAs that Control Agricultural Traits in Rice

Apr 01, 2014     Email"> PrintText Size

Transposable elements (TEs) are pieces of DNA that are competent to integrate into new positions in the genome. In the 1940s, transposons were firstly discovered in maize by Barbara McClintock (1983 Nobel Laureate in Physiology or Medicine). Rice (Oryza sativa) is an important food crops and monocot model plant, TEs and repetitive sequences make up over 35% of the rice genome. Miniature inverted repeat transposable elements (MITEs) are the most abundant type of TEs in rice, and vast majority of MITEs are inserted in close proximity of rice genes.

This is also typical of other cereal genomes such as maize, sorghum, etc. Because TEs are frequently targeted by several silencing pathways including siRNA, DNA methylation and H3K9me2, it is possible that the presence of MITE may affect the expression of nearby genes through chromatin-related pathways. However, this hypothesis has yet been tested, in part due to the fact that most silencing mutants were isolated and studied in Arabidopsis, a species with a small and lean genome with relative less number of TEs compared with rice.

Researchers in CAO Xiaofeng's group from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, addressed the functional relationship of transposons and small RNAs in the study of gene expression and its effect on agronomic traits.

They used deep sequencing of small RNAs to provide the first evidence that the rice Dicer-like 3 homolog OsDCL3a produced 24-nt small interfering RNAs (siRNAs) predominantly associated with MITEs. These 24-nt siRNAs target genes adjacented to TEs and acted as broadly functioning regulators of gene expression. In particular, OsDCL3a directly targeted genes involved in gibberellin and brassinosteroid homeostasis, thus controlling important agricultural traits such as plant height and leaf angle. This mechanism of fine-tuning gene expression mediated by MITEs might be conserved in organisms with genomes rich in dispersed repeats or TEs.

This work was published online in PNAS on February 19, 2014. WEI Liya, GU Lianfeng and SONG Xianwei contributed equally to this work. This work was supported by National Basic Research Program of China, Ministry of Agriculture of China and National Natural Science Foundation of China.