MiRNAs target conserved motifs of diverse genes encoding NB-LRRs to trigger trans-acting siRNAs in legumes.
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PROVIDER: PRJNA146213 | ENA |
REPOSITORIES: ENA
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Project description:Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide 'phased' intervals. TasiRNAs have not been extensively described in many plant species. We identified dozens of new miRNAs in Medicago and soybean and confirmed 119 Medicago targets. A search for phased tasiRNA-like small RNAs ('phasiRNAs') found at least 114 Medicago loci, the majority of which were NB-LRR encoding genes. Notably, conserved domains in NB-LRR-encoding RNAs are targeted by several 22-nt miRNA families to trigger phasiRNA production. DCL2 and SGS3 transcripts were also cleaved by these 22-nt miRNAs, generating phased small RNAs, suggesting synchronization between silencing and pathogen defense pathways. A second example of 'two-hit' phasiRNA processing was identified, utilizing miR156-miR172 sites. Our data illustrate a complex tasiRNA-mediated regulatory circuit that potentially modulates plant-microbe interactions. A few miRNA triggers regulate an extremely large gene family by targeting highly conserved protein motif-encoding sequences, representing a new paradigm for miRNA function. Examination of different tissue types in legumes (Medicago, soybean, common bean, peanut) by high throughput sequencing for small RNA profiling
2011-10-24 | E-GEOD-31061 | biostudies-arrayexpress
Project description:Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide 'phased' intervals. TasiRNAs have not been extensively described in many plant species. We identified dozens of new miRNAs in Medicago and soybean and confirmed 119 Medicago targets. A search for phased tasiRNA-like small RNAs ('phasiRNAs') found at least 114 Medicago loci, the majority of which were NB-LRR encoding genes. Notably, conserved domains in NB-LRR-encoding RNAs are targeted by several 22-nt miRNA families to trigger phasiRNA production. DCL2 and SGS3 transcripts were also cleaved by these 22-nt miRNAs, generating phased small RNAs, suggesting synchronization between silencing and pathogen defense pathways. A second example of 'two-hit' phasiRNA processing was identified, utilizing miR156-miR172 sites. Our data illustrate a complex tasiRNA-mediated regulatory circuit that potentially modulates plant-microbe interactions. A few miRNA triggers regulate an extremely large gene family by targeting highly conserved protein motif-encoding sequences, representing a new paradigm for miRNA function.
2011-10-24 | GSE31061 | GEO
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Project description:Small RNAs are a class of noncoding RNAs which are of great importance in gene expression regulatory networks. Different families of small RNAs are generated via distinct biogenesis pathways. One such family specific to plants is that of phased, secondary siRNAs (phasiRNAs); these require RDR6, DCL4, and microRNA (miRNA) trigger for their biogenesis. Protein-encoding genes are an important source of phasiRNAs. The model legume Medicago truncatula generates phasiRNAs from many PHAS loci, and we aimed to investigate their biogenesis and mechanism by which miRNAs trigger these molecules. We modulated miRNA abundances in transgenic tissues showing that the abundance of phasiRNAs correlates with the levels of both miRNA triggers and the target, precursor transcripts. We identified sets of phasiRNAs or PHAS loci that predominantly and substantially increase in response to miRNA overexpression. In the process of validating targets from miRNA overexpression tissues, we found that in the miRNA-mRNA target pairing, the 3’ terminal nucleotide (the 22nd position), but not the 10th position, is important for phasiRNA production. Mutating the single 3’ terminal nucleotide dramatically diminishes phasiRNA production. Ectopic expression of Medicago NB-LRR-targeting miRNAs in Arabidopsis showed that only a few NB-LRRs are capable of phasiRNA production; our data indicate that this is due to target inaccessibility determined by sequences flanking target sites. We propose that target accessibility is an important component of miRNA-target interactions that could be utilized in target prediction, and the evolution of mRNA sequences flanking miRNA target sites may be impacted.
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