ArticleGenome biology2005
Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana.
Article in Genome biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers.
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Who cites it
141 citing papers in PubMed.
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- The plant siRNA landscape.The Plant cell · 2024Review
- Global identification of natural antisense transcripts iniScience · 2023Article
- 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
- Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.The Plant cell · 2023Review
- Recent insights into the functions and mechanisms of antisense RNA: emerging applications in cancer therapy and precision medicine.Frontiers in chemistry · 2023Review
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- Regulation of small RNA-mediated high temperature stress responses in crop plants.Plant cell reports · 2022Review
- An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development.Genome biology · 2022Article
- Small RNAs Participate in Plant-Virus Interaction and Their Application in Plant Viral Defense.International journal of molecular sciences · 2022Review
- Genome-wide identification of antisense lncRNAs and their association with susceptibility toFrontiers in immunology · 2022Article
- Non-Coding RNAs in Response to Drought Stress.International journal of molecular sciences · 2021Review
- Tuning Beforehand: A Foresight on RNA Interference (RNAi) and In Vitro-Derived dsRNAs to Enhance Crop Resilience to Biotic and Abiotic Stresses.International journal of molecular sciences · 2021Review
- Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza.Scientific reports · 2021Article
- Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations.Non-coding RNA · 2021Review
- Modern Approaches for Transcriptome Analyses in Plants.Advances in experimental medicine and biology · 2021Article
- Identification of Small RNAs During High Light Acclimation inFrontiers in plant science · 2021Article
- Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance.Nature communications · 2020Article
81 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
backgroundNatural antisense transcripts (NAT) are a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to other transcripts. Several lines of evidence have shown that cis- and trans-NATs may participate in a broad range of gene regulatory events. Genome-wide identification of cis-NATs in human, mouse and rice has revealed their widespread occurrence in eukaryotes. However, little is known about cis-NATs in the model plant Arabidopsis thaliana.
resultsWe developed a new computational method to predict and identify cis-encoded NATs in Arabidopsis and found 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed using Arabidopsis full-length cDNAs and public massively parallel signature sequencing (MPSS) data. Three known or putative Arabidopsis imprinted genes have cis-antisense transcripts. Sequences and the genomic arrangement of two Arabidopsis NAT pairs are conserved in rice.
conclusionWe combined information from full-length cDNAs and Arabidopsis genome annotation in our NAT prediction work and reported cis-NAT pairs that could not otherwise be identified by using one of the two datasets only. Analysis of MPSS data suggested that for most Arabidopsis cis-NAT pairs, there is predominant expression of one of the two transcripts in a tissue-specific manner.
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