Two small regulatory RNAs establish opposing fates of a developmental axis

Abstract

Small RNAs are important regulators of gene expression. In maize, adaxial/abaxial (dorsoventral) leaf polarity is established by an abaxial gradient of microRNA166 (miR166), which spatially restricts the expression domain of class III homeodomain leucine zipper (HD-ZIPIII) transcription factors that specify adaxial/upper fate. Here, we show that leafbladeless1 encodes a key component in the trans-acting small interfering RNA (ta-siRNA) biogenesis pathway that acts on the adaxial side of developing leaves and demarcates the domains of hd-zipIII and miR166 accumulation. Our findings indicate that tasiR-ARF, a ta-siRNA, and miR166 establish opposing domains along the adaxial-abaxial axis, thus revealing a novel mechanism of pattern formation.Supplemental material is available at www.genesdev.org.Received January 8, 2007; revised version accepted February 20, 2007. In both animals and plants, many developmentally important regulatory genes are predicted targets of microRNAs (miRNAs), which suggests that such small RNAs constitute a class of developmental determinants (Alvarez-Garcia and Miska 2005;Jones-Rhoades et al. 2006). Patterning and outgrowth of lateral organs in plants depend on the specification of adaxial/abaxial (dorsoventral) polarity in the incipient primordium. This asymmetry is established through the polarized expression of class III homeodomain leucine zipper (HD-ZIPIII) transcription factors that specify adaxial/upper cell fate (McConnell et al. 2001;Emery et al. 2003;Juarez et al. 2004a). The adaxial-specific expression of hd-zipIII family members is delineated by the expression pattern of a 21-nucleotide (nt) miRNA, miR166, which directs the cleavage of hd-zipIII transcripts (Juarez et al. 2004a;Kidner and Martienssen 2004). In maize, miR166 accumulates most abundantly immediately below the incipient leaf, but a gradient of miR166 extends into the abaxial side of the initiating organ that establishes organ polarity (Juarez et al. 2004a).Specification of adaxial/abaxial organ polarity in maize also requires the activity of leafbladeless1 (lbl1). Recessive mutations in lbl1 lead to a variable abaxialization of leaves (Timmermans et al. 1998). The weak lbl1-ref allele causes a partial loss of adaxial identity revealed as patches of abaxial cells on the upper leaf surface, whereas leaves of the severe ragged seedling1 allele (lbl1-rgd1) are often radially symmetric and completely abaxialized (Fig. 1A). Expression of the hd-zipIII family member rld1 is reduced in lbl1 mutants. Conversely, increased levels of hd-zipIII expression in Rld1-O mutants, which carry a miR166-insensitive allele of rld1, can fully suppress the vegetative defects of lbl1 (Juarez et al. 2004b). lbl1 thus contributes to organ polarity by regulating the accumulation of rld1 transcripts on the adaxial side of the developing leaf.Here, we show that lbl1 encodes a homolog of SUPPRESSOR-OF-GENE-SILENCING3 (SGS3), which is specifically required for the biogenesis of trans-acting small interfering RNAs (ta-siRNAs) (Peragine et al. 2...

The small interfering RNA production pathway is required for shoot meristem initiation in rice

“…Mutations in LEAF BLADELESS in maize, which encodes a homologue of SUPRESSOR of GENE SILENCING3 (SGS3) in Arabidopsis and is involved in the ta-siRNA production pathway, result in a similar seedling phenotype to sho1 and sho2, including defects in leaf polarity. This phenotype in maize is due to reduced expression of tasiR-ARF and increased accumulation of miR166 (28). In our microarray analysis, expression levels of some of the rice ETT/ARF genes were up-regulated in sho mutants (SI Table 2 and SI Fig.…”

“…The phenotype is caused by reduced expression of a ta-siRNA, tasiR-ARF, and overexpression of its targets, the ETT/ARF genes (25)(26)(27). tasiR-ARF and its target genes are conserved among Arabidopsis, maize, and rice (21,28). Mutations in LEAF BLADELESS in maize, which encodes a homologue of SUPRESSOR of GENE SILENCING3 (SGS3) in Arabidopsis and is involved in the ta-siRNA production pathway, result in a similar seedling phenotype to sho1 and sho2, including defects in leaf polarity.…”

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

“…Among the sRNA loci down-regulated in wild type by drought stress (during the treatment or after the recovery), five were TAS3 loci (TAS3c-e, TAS3g, and TAS3i). Plant TAS3 genes are important regulators of leaf polarity and vegetative phase change (Peragine et al, 2004;Nogueira et al, 2007). Our finding that their expression is affected by long-term drought stress implies a connection between control of development and environmental conditions in maize leaves.…”

“…In Arabidopsis, miR156 was proposed to regulate leaf cell number and size (Usami et al, 2009), and its induction under stress conditions was shown to maintain the plant in the juvenile state for a relatively longer period of time, which helps it withstand unfavorable environmental conditions (Cui et al, 2014;Stief et al, 2014). Another two miRNAs involved in the control of normal leaf growth and development were altered by the abiotic stress treatments miR166 and miR396 (Nogueira et al, 2007;Liu et al, 2009). MiR399 controls inorganic phosphate (Pi) homeostasis and its response to Pi is highly specific (Bari et al, 2006).…”

Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation

“…leaf primordia (Supplemental Figures 2B and 2C). According to a model proposed by Waites and Hudson (1995), the juxtaposition of adaxial (upper leaf) and abaxial (lower leaf) developmental fields generates a new leaf axis that promotes laminar outgrowth (Waites and Hudson, 1995;Timmermans et al, 1998;Nogueira et al, 2007;Candela et al, 2008;Douglas et al, 2010). This mechanism may have been co-opted to generate new growth axes in leaves with nonplanar morphologies, such as the maize prophyll (Johnston et al, 2010).…”