Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

Abstract

To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from mature leaves and developing roots, shoots, and inflorescences. Using a spatial clustering algorithm, we identified 36,780 genomic groups of small RNAs. Most consisted of 24-nt RNAs that are expressed in all four tissues and enriched in repeat regions of the genome; 1029 clusters were composed primarily of 21-nt small RNAs and, strikingly, 831 of these contained phased RNAs and were preferentially expressed in developing inflorescences. Thirty-eight of the 24-mer clusters were also phased and preferentially expressed in inflorescences. The phased 21-mer clusters derive from nonprotein coding, nonrepeat regions of the genome and are grouped together into superclusters containing 10-46 clusters. The majority of these 21-mer clusters (705/831) are flanked by a degenerate 22-nt motif that is offset by 12 nt from the main phase of the cluster. Small RNAs complementary to these flanking 22-nt motifs define a new miRNA family, which is conserved in maize and expressed in developing reproductive tissues in both plants. These results suggest that the biogenesis of phased inflorescence RNAs resembles that of tasiRNAs and raise the possibility that these novel small RNAs function in early reproductive development in rice and other monocots.

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

“…5), eight of these corresponding to known tasiRNA triggers, including miR167 (ref. 27), the miR472/ 482/2118 superfamily 16,28 , and the miR7122 and the related miR4376/1432/391 superfamilies 29 . Interestingly, a prevalence of 22-nucleotide species was also observed for miR479, whose Figure 3 | Sequence abundance and conservation across Tracheophyta species.…”

22-nucleotide RNAs trigger secondary siRNA biogenesis in plants

“…Thus, an AGO1 bound to 22-nt miRNA is likely to be distorted relative to the form with an associated 21-nt miRNA. The miR2775 is likely to trigger 24-nt rather than 21-nt phased siRNA production in developing inflorescences of rice (20), but it nevertheless conforms to the 22-nt rule and has a 5′ U (Fig. 1C).…”

“…The sRNA cleavage sites are normally opposite positions 10 and 11 of the sRNA guide molecule, and this position corresponds to the 22-nt form rather than the 21-nt form of tasiR2140 (4,6). Two rice miRNAs, miR2118 and miR2775, that may direct the 21-nt or 24-nt phased siRNA production in developing inflorescences are also 22 nt in size (Table S1) (20). Thus, a size of 22 nt is a common feature shared by many diverse triggers of secondary siRNA production.…”

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

“…If large numbers of targets for a single miRNA are found, there should be direct experimental evidence to support the assertions. Such exceptional cases do exist, such as the thousands of targets of the miR2118 family in rice that are experimentally supported by phasiRNA accumulation (Johnson et al, 2009). Those attempting to find plant miRNA targets should also be skeptical of inferring mechanistic attributes from the complementarity pattern.…”