Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning

Abstract

Small RNAs have several important biological functions. MicroRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) regulate mRNA stability and translation, and siRNAs cause post-transcriptional gene silencing of transposons, viruses and transgenes and are important in both the establishment and maintenance of cytosine DNA methylation. Here, we study the role of the four Arabidopsis thaliana DICER-LIKE genes (DCL1-DCL4) in these processes. Sequencing of small RNAs from a dcl2 dcl3 dcl4 triple mutant showed markedly reduced tasiRNA and siRNA production and indicated that DCL1, in addition to its role as the major enzyme for processing miRNAs, has a previously unknown role in the production of small RNAs from endogenous inverted repeats. DCL2, DCL3 and DCL4 showed functional redundancy in siRNA and tasiRNA production and in the establishment and maintenance of DNA methylation. Our studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs.

The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis

“…There is also a disproportionately high occurrence of small (18-24 nt) microRNAs (miRNA) on chromosome XIX coincident to the region containing the putative gender-determining locus and the major cluster of NBS-LRR genes (Klevebring et al 2009). Such miRNAs are a class of posttranscriptional negative regulators that play a vital role in plant development and growth (Jones-Rhoades et al 2006;Shuklaa et al 2008;Henderson et al 2006;Chan et al 2005). A number of the identified miRNA are predicted to target the NBS-LRR disease resistance genes within the peritelomeric region of chromosome XIX.…”

The Function of RNAi in Plant Development

“…The R2D2-like protein, DRB4, binds to DCL4 (Hiraguri et al 2005) and may assist in its activity because the phenotype of a drb4 mutation resembles dcl4 (Adenot et al 2006). TAS2 and TAS3 are also processed inefficiently by DCL2 into 22-nucleotide siRNAs and by DCL3 into 24-nucleotide siRNAs (Gasciolli et al 2005;Bouche et al 2006;Henderson et al 2006). …”

Deep Sequencing from hen1 Mutants to Identify Small RNA 3' Modifications

“…The Arabidopsis genome includes four DCL genes that are responsible for generating distinct classes of sRNAs and of different sizes, ranging from 21 to 24 nucleotides. Mutant analysis has revealed some functional redundancies among the DCL genes (Deleris et al 2006;Henderson et al 2006). Despite the diversification of sRNA types and biogenesis pathway proteins, current data suggest that all plant sRNAs require 3 0 methylation performed by a protein known as HEN1.…”