ArticleGenome biology2012
Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
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Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis revealed insights into the sources, conservation and impact of microRNA 5'-isoforms in four model species.Nucleic acids research · 2014Pooled it
- The Rice Cis-Natural Antisense Transcript NAT1850 of Pri-miR1850 Negatively Regulates Cold Tolerance by Repressing NPR3.Plant biotechnology journal · 2026Article
- Small RNAs regulation and genomic harmony: insights into allopolyploid evolution in marsh orchids (Dactylorhiza).The New phytologist · 2026Article
- Non-coding RNAs in plant stress responses: molecular insights and agricultural applications.Plant biotechnology journal · 2025Review
- Arabidopsis SGS3 is recruited to chromatin by CHR11 to select RNA that initiate siRNA production.Nature communications · 2025Article
- Classification of and detection techniques for RNAi-induced effects in GM plants.Frontiers in plant science · 2025Review
- Biochemical Defence of Plants against Parasitic Nematodes.Plants (Basel, Switzerland) · 2024Review
- The biogenesis, regulation and functions of transitive siRNA in plants.Acta biochimica et biophysica Sinica · 2024Review
- Genome-wide view and characterization of natural antisense transcripts in Cannabis Sativa L.Plant molecular biology · 2024Article
- The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling.Non-coding RNA · 2024Review
- The plant siRNA landscape.The Plant cell · 2024Review
- The non-coding RNA SVALKA locus produces a cis-natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures.Plant communications · 2023Article
- Biogenesis, Mode of Action and the Interactions of Plant Non-Coding RNAs.International journal of molecular sciences · 2023Review
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- Investigating nicotine pathway-related long non-coding RNAs in tobacco.Frontiers in genetics · 2022Article
- Biogenesis, Trafficking, and Function of Small RNAs in Plants.Frontiers in plant science · 2022Article
- An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection.Scientific reports · 2021Article
- Influence of virus-host interactions on plant response to abiotic stress.Plant cell reports · 2021Review
- The Critical Role of Small RNAs in Regulating Plant Innate Immunity.Biomolecules · 2021Review
- Identification of Small RNAs During High Light Acclimation inFrontiers in plant science · 2021Article
13 more citing papers are in PubMed but not listed here.
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19 authors.
Funding
Abstract
backgroundMany eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, and yeasts. However, many questions remain regarding the features and biogenesis of nat-siRNAs.
resultsThrough deep sequencing, we identified more than 17,000 unique siRNAs corresponding to cis-NATs from biotic and abiotic stress-challenged Arabidopsis thaliana and 56,000 from abiotic stress-treated rice. These siRNAs were enriched in the overlapping regions of NATs and exhibited either site-specific or distributed patterns, often with strand bias. Out of 1,439 and 767 cis-NAT pairs identified in Arabidopsis and rice, respectively, 84 and 119 could generate at least 10 siRNAs per million reads from the overlapping regions. Among them, 16 cis-NAT pairs from Arabidopsis and 34 from rice gave rise to nat-siRNAs exclusively in the overlap regions. Genetic analysis showed that the overlapping double-stranded RNAs could be processed by Dicer-like 1 (DCL1) and/or DCL3. The DCL3-dependent nat-siRNAs were also dependent on RNA-dependent RNA polymerase 2 (RDR2) and plant-specific RNA polymerase IV (PolIV), whereas only a fraction of DCL1-dependent nat-siRNAs was RDR- and PolIV-dependent. Furthermore, the levels of some nat-siRNAs were regulated by specific biotic or abiotic stress conditions in Arabidopsis and rice.
conclusionsOur results suggest that nat-siRNAs display distinct distribution patterns and are generated by DCL1 and/or DCL3. Our analysis further supported the existence of nat-siRNAs in plants and advanced our understanding of their characteristics.
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