ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Genome-wide view of natural antisense transcripts in Arabidopsis thaliana.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- The Rice Cis-Natural Antisense Transcript NAT1850 of Pri-miR1850 Negatively Regulates Cold Tolerance by Repressing NPR3.Plant biotechnology journal · 2026Article
- Comparative TSS-seq analysis among natural variations ofNAR genomics and bioinformatics · 2025Article
- Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.The Plant cell · 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
- BioGraph: Data Model for Linking and Querying Diverse Biological Metadata.International journal of molecular sciences · 2023Article
- Regulation of small RNA-mediated high temperature stress responses in crop plants.Plant cell reports · 2022Review
- Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana.Functional & integrative genomics · 2021Article
- Identification of Small RNAs During High Light Acclimation inFrontiers in plant science · 2021Article
- NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs.Nucleic acids research · 2020Article
- Identification of small RNAs during cold acclimation in Arabidopsis thaliana.BMC plant biology · 2020Article
- Article
- Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation.Plant physiology · 2020Article
- Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions.BMC genomics · 2019Article
- Identification of a novel antisense RNA that regulates growth hormone receptor expression in chickens.RNA biology · 2019Article
- Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.Plant physiology · 2019Article
- Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction.BMC plant biology · 2019Article
- Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription.RNA biology · 2017Article
- Non-coding RNAs and Their Roles in Stress Response in Plants.Genomics, proteomics & bioinformatics · 2017Review
- Plant organ evolution revealed by phylotranscriptomics in Arabidopsis thaliana.Scientific reports · 2017Article
- Natural antisense transcripts are significantly involved in regulation of drought stress in maize.Nucleic acids research · 2017Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Natural antisense transcripts (NATs) are endogenous transcripts that can form double-stranded RNA structures. Many protein-coding genes (PCs) and non-protein-coding genes (NPCs) tend to form cis-NATs and trans-NATs, respectively. In this work, we identified 4,080 cis-NATs and 2,491 trans-NATs genome-widely in Arabidopsis. Of these, 5,385 NAT-siRNAs were detected from the small RNA sequencing data. NAT-siRNAs are typically 21nt, and are processed by Dicer-like 1 (DCL1)/DCL2 and RDR6 and function in epigenetically activated situations, or 24nt, suggesting these are processed by DCL3 and RDR2 and function in environment stress. NAT-siRNAs are significantly derived from PC/PC pairs of trans-NATs and NPC/NPC pairs of cis-NATs. Furthermore, NAT pair genes typically have similar pattern of epigenetic status. Cis-NATs tend to be marked by euchromatic modifications, whereas trans-NATs tend to be marked by heterochromatic modifications.
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