Post-transcriptional small RNA pathways in plants: mechanisms and regulations

Abstract

For a long period of time, DNA, the support of heredity, and proteins, the actors of the cellular machinery, have been considered the most important components of biological systems. By contrast, RNA was originally considered as an intermediate molecule, bridging the gap between DNA and protein (mRNA), or serving functional roles during splicing (snRNA) and translation (tRNA and rRNA). The recent discovery of an increasing number of large and small non-protein-coding RNAs with specific regulatory roles has changed our view of gene expression. In particular, 20-to 27-nucleotide (nt) small RNAs belonging to two classes, microRNAs (miRNAs) and short interfering RNAs (siRNAs), are known to play essential roles in the four Eukaryote kingdoms (protists, fungi, plants, animals), with the surprising exception of the yeast Saccharomyces cerevisiae. Small RNAs are involved in a variety of phenomena that are essential for genome stability, development, and adaptive responses to biotic and abiotic stresses. Their mode of action also is diverse. They guide DNA elimination during the formation of the macronucleus in protists and heterochromatin assembly in fungi and plants. They target endogenous mRNAs for cleavage and translational repression in plants and animals, and protect both plant and animal cells against virus infection through an RNA-based immune system. They also control the movement of transposable elements at the transcriptional and post-transcriptional level in plants and animals. Cis-acting siRNAs as an RNA-based immune mechanism and a silencing toolBecause small RNAs are repressors of gene expression, small RNA-mediated regulation is often referred to as RNA silencing, gene silencing, or RNA interference (RNAi). RNA silencing was discovered in plants more than 15 years ago during the course of transgenic experiments that eventually led to silencing of the introduced transgene and, in some cases, of homologous endogenous genes or resident transgenes (Matzke et al. 1989;Linn et al. 1990;Napoli et al. 1990;Smith et al. 1990;van der Krol et al. 1990). Gene silencing results from transcription inhibition (transcriptional gene silencing [TGS]) or from RNA degradation (post-transcriptional gene silencing [PTGS]), and correlates with the accumulation of siRNAs corresponding to the silenced promoter or to the degraded RNA, respectively (Hamilton and Baulcombe 1999;Mette et al. 2000). The production of virus-derived siRNAs was observed in response to virus infection (Hamilton and Baulcombe 1999), and plant mutants defective in PTGS were hypersusceptible to virus infection (Mourrain et al. 2000;Dalmay et al. 2001;Qu et al. 2005;Schwach et al. 2005). Studies in worm revealed that mutants defective in RNAi (the animal counterpart of PTGS) lose control of their transposable elements (Ketting et al. 1999). Altogether, these results suggested that the PTGS/RNAi pathway corresponds to an RNA-based immune system that allows cells to control endogenous (transposons) or exogenous (virus, transgenes) nucleic acid invaders through...

A single transgene locus triggers both transcriptional and post-transcriptional silencing through double-stranded RNA production

“…mRNA cleavage in RISC is directed by short interfering RNAs (siRNAs) that derive from the processing of long dsRNAs that are complementary to target mRNAs by the RNase III Dicer. Mechanistically, PTGS is very similar to mRNA cleavage directed by endogenous miRNAs and trans-acting siRNAs (Vaucheret 2006).…”

Approaches for Studying MicroRNA and Small Interfering RNA Methylation In Vitro and In Vivo

“…In contrast to miRNAs that are derived from single-stranded precursors, siRNAs are generated by Dicer-like proteins from long doublestranded RNAs. Several types of endogenous siRNAs have been found in Arabidopsis, such as trans-acting siRNAs, nat-siRNAs, and heterochromatic siRNAs (reviewed in Brodersen and Voinnet, 2006;Vaucheret, 2006). In addition to the endogenous siRNAs, viruses and transgenes also give rise to siRNAs (reviewed in Brodersen and Voinnet, 2006;Vaucheret, 2006).…”

The Cornucopia of Small RNAs in Plant Genomes

“…MicroRNAs are mainly bound by AGO1, and ta-siRNAs are bound by AGO6 and AGO2, whereas most of the 24 nt small RNAs are directed to AGO4 and AGO5 [5,[17][18][19]. During the process of sorting certain classes of small RNAs into their corresponding AGOs, the 5′ terminal nucleotide of the small RNAs plays a significant role, as it was recently reported that different AGOs have a strong bias for a distinct 5′ terminal nucleotide: U for AGO1, A for AGO2, A for AGO4, and C for AGO5 [19,20].…”

“…Plant sRNAs may also be categorized as miRNAs or siRNAs based on their origin: miRNAs are derived from imperfectly matched stem-loop structures that are formed from single-stranded RNA (ssRNA) precursors, whereas siRNAs are derived from perfectly-or nearly perfectlymatched double-stranded RNAs (dsRNAs) produced by the activity of RNA-dependent RNA polymerases (with genes named as "RDR1," "RDR2," etc.) or from ssRNA transcripts including inverted repeats that fold back to form a dsRNA region [4,5]. The larger class of siRNAs can be further subdivided into categories including trans-acting siRNAs (ta-siRNAs), natural cis-antisense transcript derived siRNAs (nat-siRNAs) and heterochromatic siRNAs (hc-siRNAs).…”

“…The larger class of siRNAs can be further subdivided into categories including trans-acting siRNAs (ta-siRNAs), natural cis-antisense transcript derived siRNAs (nat-siRNAs) and heterochromatic siRNAs (hc-siRNAs). This division is based on the distinct biogenesis pathway of each subgroup [5].…”