ArticleGenome biology2007
A genome-wide transcriptional activity survey of rice transposable element-related genes.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 57 citations in OpenAlex.
- Unraveling salt-responsive genes in Suaeda salsa through genomic and transcriptomic profiling across salinity gradients.BMC genomics · 2026Article
- How Structural Variations Influence Crop Improvement.International journal of molecular sciences · 2025Review
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning.BioData mining · 2024Article
- LTR Retroelements and Bird Adaptation to Arid Environments.International journal of molecular sciences · 2023Article
- MKKK20 works as an upstream triple-kinase of MKK3-MPK6-MYC2 module in Arabidopsis seedling development.iScience · 2023Article
- Differential nuclease sensitivity profiling uncovers a drought responsive change in maize leaf chromatin structure for two large retrotransposon derivatives,Plant direct · 2021Article
- Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice.The New phytologist · 2021Article
- Distribution and Characteristics of Transposable Elements in the Mulberry Genome.The plant genome · 2019Article
- Transcriptional activity of PIF and Pong-like Class II transposable elements in Triticeae.BMC evolutionary biology · 2017Article
- Transgenerational epimutations induced by multi-generation drought imposition mediate rice plant's adaptation to drought condition.Scientific reports · 2017Article
- DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements.Genome biology · 2016Article
- Structural Diversity of a Novel LTR Retrotransposon, RTPOSON, in the Genus Oryza.Evolutionary bioinformatics online · 2016Article
- Review
- Transcriptomic dissection of the rice-Burkholderia glumae interaction.BMC genomics · 2014Article
- Low temperature-responsive changes in the anther transcriptome's repeat sequences are indicative of stress sensitivity and pollen sterility in rice strains.Plant physiology · 2014Article
- Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data.Rice (New York, N.Y.) · 2013Article
- The SLEEPER genes: a transposase-derived angiosperm-specific gene family.BMC plant biology · 2012Article
- A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana.PLoS genetics · 2012Article
- Diversification of hAT transposase paralogues in the sugarcane genome.Molecular genetics and genomics : MGG · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTransposable element (TE)-related genes comprise a significant portion of the gene catalog of grasses, although their functions are insufficiently characterized. The recent availability of TE-related gene annotation from the complete genome sequence of rice (Oryza sativa) has created an opportunity to conduct a comprehensive evaluation of the transcriptional activities of these potentially mobile elements and their related genes.
resultsWe conducted a genome-wide survey of the transcriptional activity of TE-related genes associated with 15 developmental stages and stress conditions. This dataset was obtained using a microarray encompassing 2,191 unique TE-related rice genes, which were represented by oligonucleotide probes that were free from cross-hybridization. We found that TE-related genes exhibit much lower transcriptional activities than do non-TE-related genes, although representative transcripts were detected from all superfamilies of both type I and II TE-related genes. The strongest transcriptional activities were detected in TE-related genes from among the MULE and CACTA superfamilies. Phylogenetic analyses suggest that domesticated TE-related genes tend to form clades with active transcription. In addition, chromatin-level regulations through histone and DNA modifications, as well as enrichment of certain cis elements in the promoters, appear to contribute to the transcriptional activation of representative TE-related genes.
conclusionOur findings reveal clear, albeit low, general transcription of TE-related genes. In combination with phylogenetic analysis, transcriptional analysis has the potential to lead to the identification of domesticated TEs with adapted host functions.
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