ArticleGenome biology2005
Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation.
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 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it, 124 citations in OpenAlex.
- Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane.International journal of molecular sciences · 2022Pooled it
- Genome-wide comparative analysis reveals distinct evolutionary patterns of overlapping genes in prokaryotes and eukaryotes.Heredity · 2026Article
- Classification of and detection techniques for RNAi-induced effects in GM plants.Frontiers in plant science · 2025Review
- Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends.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
- Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.Molecular biology and evolution · 2020Article
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- Responsiveness and Adaptation to Salt Stress of the REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 (RRTF1) Gene are Controlled by its Promoter.Molecular biotechnology · 2019Article
- ArabidopsisPlant physiology · 2018Article
- Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase.Plant physiology · 2017Article
- Plant organ evolution revealed by phylotranscriptomics in Arabidopsis thaliana.Scientific reports · 2017Article
- Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods.International journal of molecular sciences · 2015Review
- Molecular characterization of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family from Citrus and the effect of fruit load on their expression.Frontiers in plant science · 2015Article
- NERF encodes a RING E3 ligase important for drought resistance and enhances the expression of its antisense gene NFYA5 in Arabidopsis.Nucleic acids research · 2015Article
- Development of genodynamic metrics for exploring the biophysics of DNA polymorphisms.Journal of computational biology and bioinformatics research · 2014Article
- EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.BMC genomics · 2014Article
- Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information.Plant physiology · 2014Article
- Article
- Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.Genome research · 2013Article
5 more citing papers are in PubMed but not listed here.
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4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOverlapping transcripts in antisense orientation have the potential to form double-stranded RNA (dsRNA), a substrate for a number of different RNA-modification pathways. One prominent route for dsRNA is its breakdown by Dicer enzyme complexes into small RNAs, a pathway that is widely exploited by RNA interference technology to inactivate defined genes in transgenic lines. The significance of this pathway for endogenous gene regulation remains unclear.
resultsWe have examined transcription data for overlapping gene pairs in Arabidopsis thaliana. On the basis of an analysis of transcripts with coding regions, we find the majority of overlapping gene pairs to be convergently overlapping pairs (COPs), with the potential for dsRNA formation. In all tissues, COP transcripts are present at a higher frequency compared to the overall gene pool. The probability that both the sense and antisense copy of a COP are co-transcribed matches the theoretical value for coexpression under the assumption that the expression of one partner does not affect the expression of the other. Among COPs, we observe an over-representation of spliced (intron-containing) genes (90%) and of genes with alternatively spliced transcripts. For loci where antisense transcripts overlap with sense transcript introns, we also find a significant bias in favor of alternative splicing and variation of polyadenylation.
conclusionThe results argue against a predominant RNA degradation effect induced by dsRNA formation. Instead, our data support alternative roles for dsRNAs. They suggest that at least for a subgroup of COPs, antisense expression may induce alternative splicing or polyadenylation.
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