Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

Abstract

Transposable elements (TEs) and repetitive sequences make up over 35% of the rice (Oryza sativa) genome. The host regulates the activity of different TEs by different epigenetic mechanisms, including DNA methylation, histone H3K9 methylation, and histone H3K4 demethylation. TEs can also affect the expression of host genes. For example, miniature inverted repeat TEs (MITEs), dispersed high copy-number DNA TEs, can influence the expression of nearby genes. In plants, 24-nt small interfering RNAs (siRNAs) are mainly derived from repeats and TEs. However, the extent to which TEs, particularly MITEs associated with 24-nt siRNAs, affect gene expression remains elusive. Here, we show that the rice Dicer-like 3 homolog OsDCL3a is primarily responsible for 24-nt siRNA processing. Impairing OsDCL3a expression by RNA interference caused phenotypes affecting important agricultural traits; these phenotypes include dwarfism, larger flag leaf angle, and fewer secondary branches. We used small RNA deep sequencing to identify 535,054 24-nt siRNA clusters. Of these clusters, ∼82% were OsDCL3a-dependent and showed significant enrichment of MITEs. Reduction of OsDCL3a function reduced the 24-nt siRNAs predominantly from MITEs and elevated expression of nearby genes. OsDCL3a directly targets genes involved in gibberellin and brassinosteroid homeostasis; OsDCL3a deficiency may affect these genes, thus causing the phenotypes of dwarfism and enlarged flag leaf angle. Our work identifies OsDCL3a-dependent 24-nt siRNAs derived from MITEs as broadly functioning regulators for fine-tuning gene expression, which may reflect a conserved epigenetic mechanism in higher plants with genomes rich in dispersed repeats or TEs.

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

“…In A. thaliana, complete removal of hc-siRNAs has only modest effects on genome-wide DNA methylation patterns (Stroud et al, 2013) and causes no obvious defects in organismal phenotype. In contrast, loss of hc-siRNAs in rice de-represses hundreds of proteincoding mRNAs, many of which are proximal to 24 nt-generating Miniature Inverted repeat Transposable Elements (MITEs) (Wei et al, 2014). These features are relevant in the context of miRNA annotation, because MITEs often contain miRNA-like inverted repeats, and heterochromatic regions may be low copy in the genome; hc-siRNAs from such regions may thus confound miRNA prediction algorithms and end up on output lists as candidate miRNAs.…”

RNAi in Plants: An Argonaute-Centered View

“…AGO4a, AGO4b, and AGO16 can bind lmiRNAs and 24-nucleotide siRNAs that are mainly produced from miniature inverted repeat TEs and other TEs (Wu et al, 2010). Knocking down AGO4a and AGO4b affects GA and BR homeostasis-related genes and causes dwarfism phenotype, likely through affecting DNA methylation mediated by the 24-nucleotide siRNAs associated with miniature inverted repeat TEs (Wei et al, 2014).…”

Dynamic Cytology and Transcriptional Regulation of Rice Lamina Joint Development

“…In addition, LEAF IN-CLINATION2 (LC2), a VIN3-like protein, controls leaf inclination by inhibiting adaxial cell division (Zhao et al, 2010). Suppression of small RNA-producing genes, including RNA-dependent RNA polymerase2, RNase III-class Dicer-like3, and OsAGO4a and OsAGO4b (members of the Argonaute family), results in the increased bending of the lamina joint (Wei et al, 2014), while increased expression of OsAGO7 leads to the leaf erectness (Shi et al, 2007).…”