ArticleGenome research2009
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 115 citations in OpenAlex.
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- The biogenesis, regulation and functions of transitive siRNA in plants.Acta biochimica et biophysica Sinica · 2024Review
- Genome-wide identification and characterization of lncRNAs in sunflower endosperm.BMC plant biology · 2022Article
- Recent advances in RNA structurome.Science China. Life sciences · 2022Review
- Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara).BMC genomics · 2021Article
- Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations.Non-coding RNA · 2021Review
- Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions.BMC genomics · 2019Article
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.Plant physiology · 2019Article
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- Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications.BMC plant biology · 2018Article
- Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase.Plant physiology · 2017Article
- Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava.Scientific reports · 2017Article
- Parsing the Regulatory Network between Small RNAs and Target Genes in Ethylene Pathway in Tomato.Frontiers in plant science · 2017Article
- NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes.Scientific reports · 2016Article
- Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods.International journal of molecular sciences · 2015Review
- Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alternifolia Loisel).Molecular biology reports · 2015Article
- Genome-wide view of natural antisense transcripts in Arabidopsis thaliana.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors.The Plant journal : for cell and molecular biology · 2015Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Natural antisense transcripts (NATs) have been shown to play important roles in post-transcriptional regulation through the RNA interference pathway. We have combined pyrophosphate-based high-throughput sequencing and computational analysis to identify and analyze, in genome scale, cis-NAT and trans-NAT small RNAs that are derived under normal conditions and in response to drought and salt stresses in the staple plant Oryza sativa. Computationally, we identified 344 cis-NATs and 7,142 trans-NATs that are formed by protein-coding genes. From the deep sequencing data, we found 108 cis-NATs and 7,141 trans-NATs that gave rise to small RNAs from their overlapping regions. Consistent with early findings, the majority of these 108 cis-NATs seem to be associated with specific conditions or developmental stages. Our analyses also revealed several interesting results. The overlapping regions of the cis-NATs and trans-NATs appear to be more enriched with small RNA loci than non-overlapping regions. The small RNAs generated from cis-NATs and trans-NATs have a length bias of 21 nt, even though their lengths spread over a large range. Furthermore, >40% of the small RNAs from cis-NATs and trans-NATs carry an A as their 5'-terminal nucleotides. A substantial portion of the transcripts are involved in both cis-NATs and trans-NATs, and many trans-NATs can form many-to-many relationships, indicating that NATs may form complex regulatory networks in O. sativa. This study is the first genome-wide investigation of NAT-derived small RNAs in O. sativa. It reveals the importance of NATs in biogenesis of small RNAs and broadens our understanding of the roles of NAT-derived small RNAs in gene regulation, particularly in response to environmental stimuli.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.